Problems with logs and joint VCF file generation in latest dev build #2473
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Thanks for the report. This is definitely unexpected as we haven't made any changes to logging or anything otherwise extensive that would make everything stop working. What version were you upgrading from? Are you running this in a clean directory or in a pre-existing work directory? Is it possible it's just skipping all the work because the files already exist? |
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It's a fresh Bcbio install (one day old), upgraded to development. I've had the problem with the log files with a couple of analyses, and they were both done from scratch, in empty or newly-created directories. This is how I did the installation: I tried upgrading to the latest development version again today but it didn't make any difference. |
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Thanks for following up. I am stumped and now sure what to suggest. What version did you have previously that worked well on your system? Do you get no logging under specific run environments: does it work when running on a single machine and only fail to log on a distributed setup? I'm not exactly sure how best to diagnose this remotely but with more details can keep trying to guess. |
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The latest version that worked for me was mentioned in this post. Unfortunately, I don't have that available anymore, because I decided to do a fresh install (after a recent fix) and I deleted all the old installs I had lying around. I'll make sure to properly test any new install before deleting older (functioning) ones in the future. |
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Apologies, I'm not sure what to make of this. That looks like a pretty small update distance between two recent development packages. We haven't overhauled any of the logging in that time so I'm not sure why it disappeared on your runs. A couple of questions to help debug:
Apologies, but I don't know why you'd lose both logging and joint calling so hoping for some baseline or ideas to reproduce what you're seeing. Thanks again for helping to debug. |
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I've reinstalled, this time without upgrading to development. bcbio_conda list | grep bcbio-nextgen This time I'm getting file system errors: On this page, someone else mentioned getting a similar error and that it was caused by problems with their NFS storage. I'm installing Bcbio-nextgen on an NFS file system, so my issue might be related. No idea what could cause this, though, as I seem to be able to browse the NFS storage without issues and I doubt there was any NFS crash recently. |
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I'm installing Bcbio on an NFS storage from a VM in an OpenNebula cloud, running Debian Stretch. The working environment did, indeed, change between the working and non-working runs. I was running Ubuntu 14.04 before. I'm using the following template: |
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A small update on this issue: I've noticed that the bcbio-nextgen-commands.log created by the bcbio_prepare_samples.py script is not empty. Is there any possible reason for which that particular one would be properly created, while the one created by bcbio_nextgen.py would remain empty? |
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There is not an special reason why that should be different. I think Brad asked you : How are you running bcbio? Single machine? On a cluster? Can you tell us how you are running the different scripts? The common check we do is to run in a single machine (locally) the process to make sure the parallelization in a cluster is (or not) the cause of the issue. Cheers |
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Hi @lpantano Bcbio is installed on an NFS storage and I'm testing it on a single machine running Debian 9. I'm setting up samples like this: and then running bcbio like this: |
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@amizeranschi, were you able to resolve the issue? I seem to have a similar problem: #2520 |
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No, I never managed to solve this issue. |
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Sorry about these continued problems. We're still not sure how to best debug and fix this issue and I posted some ideas in the discussion in #2520 around running the test suite to see if that also triggers problems. If you're able to follow along and debug, any information about how to replicate on a small sample would help us try and track this down. Thanks much for all the discussion and patience with the issue. |
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I'm not able to replicate the original problem anymore, because I don't have access to the cluster where I've experienced these issues. I've installed the latest stable Bcbio version locally, on a Ubuntu machine and things are working fine, as far as I could see, with the latest stable version of Bcbio (1.1.0). The bcbio-nextgen-commands.log and bcbio-nextgen-debug.log are created just as they used to. However, after upgrading to the most recent development version, deleting the old analysis files/directories and rerunning, the joint VCF file does not get created in the final directory, although it did with the previous (stable) version. I can't tell if the problem is with the creation of the joint VCF file, or if it simply gets omitted during the stage-out process at the end. I am still using the same template as before. |
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Thanks for following up and glad to hear things are working as expected with the latest version in terms of logging. I am still perplexed as to what is going on here with logging. For the joint VCF issue, everything looks fine with your template so I'm not sure why you wouldn't see an output VCF file. It's a bit tough to debug remotely from the information we have so far but I can share what it should look like with the bcbio test data. The output directory should have individual sample gVCFs and a joint called shared VCF: and in the work directory the joint calls should be in |
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The work directory from my previous test seems to contain the joint VCF files: In the final directory, the sample-specific VCF files are present, but the main directory (2018-10-27_project) doesn't contain a joint VCF file. This only happens with Bcbio's development version. After cloning the Bcbio-nexgen repo and executing However, this doesn't appear to run joint variant calling. The main output directory ( |
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Thanks again for helping debug and providing all the additional information. It does look like things ran through joint calling successfully so I'm not sure why this would be missing from the final output directory. If you re-run If you want to confirm with the tests, |
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Would it be possible to mention the I tried re-running my test in the same work directory and nothing changed. The joint VCF file did not get copied. I also tried running new separate tests using HaplotypeCaller and, respectively, Strelka2 (as I saw this used in the automated tests) and the same thing happened. I don't see any errors in the logs. It seems like the joint VCF file is just not being copied in the end stage, for some reason. I can't figure out why this only happens during my test, while the "official" Bcbio automatic test runs fine, even with the latest development version. I am using a set of FASTQ files that I created some time ago by sampling 10000 reads from some larger files. I've been using them to test the pipeline for a while and never had any trouble until now. Finally, I ran my test again with Strelka2 using the stable version of Bcbio and, sure enough, the testingVC-strelka2-joint-annotated.vcf.gz file has been created in the final upload directory, just as it did with the HaplotypeCaller tests, when using the stable Bcbio version. Is there anything that has changed between the last stable version and the development version that could cause this? |
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The issue persists with the newly-released stable version, as well as the latest development version, as of today. Running single-threaded did not make a difference. |
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Sorry you're still having issues and thank you for continuing to test and help debug. If the tests are running cleanly for you, there must be something in your actual run configuration that's causing bcbio to go down a different path and lead to issues. I know you've posted your template above, but I don't see any substantial differences between that and the tests that run fine for you. Is it possible to share your final configuration that doesn't work? Perhaps there is something in the batching we're missing that we could spot by looking at this. Thank you for the help trying to reproduce the problem. |
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Sure. This is the full config file: |
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I've had an attempt at applying the logic from Issue #2520. I've installed Docker and bcbio_vm as per documentation and I've pulled several bcbio-vc images from quay.io. Note: I had to edit the file My tests run fine with the Docker images |
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Thanks so much for all the debugging work and help figuring out this issue. I've been struggling to reproduce and understand this for a few days but all your input finally helped me realize the issue. With the changes to do more post-variant annotation, we were implicitly assuming the output joint called VCF would have vcfanno annotations and be uploaded through that path. However, for your genome it likely doesn't get annotated so gets left out of the list of files to upload. I've added a check for this case that I hope will resolve the issue if you run the latest development version. Please let me know if not and we can investigate further. Thank you again for all your patience and working helping debug this issue. |
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Thank you, this fixed it alright. If I may, I also have a couple of last questions about this. Is bcbio_vm still being maintained and will it be in the future? I remember reading somewhere that it's going to get phased out in the future, but I'm not sure whether that was referring to bcbio_vm or something else. If it's still being maintained, would it be possible to include the following patch? bcbio/bcbio-nextgen-vm#51 This would help quite a bit with reproducibility, allowing one to use any of the old Docker images from quay.io. Alternatively, is there any other (better) way to achieve this? Thanks a lot for fixing the joint VCF generation bug and for all the great work with bcbio-nextgen and bcbio_vm! |
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Thank you for following up. I'm glad that fixed the issue for you and thanks again for all the patience as we identified the underlying problem. For running with Docker containers, we now recommend using the common workflow language (CWL) interface with the Cromwell runner, documented here: https://bcbio-nextgen.readthedocs.io/en/latest/contents/cwl.html This still uses bcbio_vm.py for setting up the run environment and launching jobs, but the actually running takes place via external runners to get improved runtime support over what we can develop as part of bcbio. To lock down to specific tags in your workflows for reproducibility, there is a CWL is still a work in progress but improving and being used more often. Hope this works for your use. |
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I gave this a try but I'm stuck at running I have previously saved the datadir ( However, running without CWL works fine: The *.loc files are in How can I get the correct paths inside the .loc files (without having to edit them manually)? And why isn't this issue affecting bcbio_vm.py when running without CWL? P.S. Should I open a separate ticket for these issues? |
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Sorry about the issues and confusion here. The bcbio_vm.py data install is going to be confusing as it works with data both inside and outside the container, which is what leads to the disconnect here. Practically, we've tried to avoid all this by no longer depending on the https://bcbio-nextgen.readthedocs.io/en/latest/contents/cwl.html#generating-cwl-for-input-to-a-tool This approach should be much cleaner and avoid the need for any custom install tweaks. You point it at the genome directory and it finds all the inputs from that. Once you have the file in place you pass it to the CWL generation command with Hope this helps get CWL generation working for you. Thanks for exploring this and all the patience. |
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Alright, thanks for following up on this. I edited the file bcbio_system.yaml and got that to work, but now I tried adding it and providing a valid BED file, but this didn't make the error go away. Here's the full output that I get: |
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Thanks for testing this and apologies about the additional problems. What we're running into here is that bcbio isn't finding transcript files for your sacCer3 genome install, so doesn't have the BED files derived from that which is uses for annotations. In CWL it will fail up front with these type of issues. Are you using the standard bcbio sacCer3 configuration: https://github.com/bcbio/bcbio-nextgen/blob/master/config/genomes/sacCer3-resources.yaml or something custom? Do you have the transcript files available in your install? I'd definitely like to get the yeast genome install fixed for you but haven't worked with it in a while so am not entirely sure what might be missing. If you can provide more details I'm happy to help dig into it. |
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Thanks. The two CWL tests are running fine now. I've also tested on yeast data. I ran into a problem with Toil where it tried to use more CPU cores (16) than what my system actually has available (8). This was due to the default setting ( I remember that the bcbio_nextgen installer automatically detected the CPU cores and available memory and set these up in the system yaml file. Is there a way to do this for bcbio_vm as well? I tried adding the option After setting the right number cores (and amount of memory) in It seems that the problem is with handling the multi-sample VCF file. Recall, I am testing joint variant calling using Strelka2 on two samples, using the YAML file posted above. I've also tested Cromwell. Interestingly, it didn't fail due to the default CPU-core and memory settings from the However, Cromwell did run into the same VCF-related problems as Toil: |
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I noticed that there's a CWL test called |
chapmanb
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Nov 26, 2018
Moves to new gvcfgenotyper approach from Illumina for handling joint calling with strelka2. Provides equivalent pipeline to GATK HaplotypeCaller joint calling with separate gVCF production and joint calling, improving over old conversion and merge approach. Fixes #2473 issues with gvcftools based approach (sequencing/gvcftools#9).
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Glad we're making progress and thank you for this detailed feedback and testing on joint calling with your workflow. I believe we're running into an issue with gvcftools during strelka2 joint calling: sequencing/gvcftools#9 Practically, strelka2 joint calling was pretty primitive and outdated and I've moved it to use the updated gvcfgenotyper (https://github.com/Illumina/gvcfgenotyper) approach the Illumina team has been developing. If you re-try the runs with the latest Docker container (1.1.2a-1ffac4b: https://quay.io/repository/bcbio/bcbio-vc?tab=tags) I hope it will work cleanly for you. Also, going forward all new Docker builds will pin to the version of bcbio-base so you'll avoid the issues you saw was pinning versions in CWL and getting bcbio-base:latest. Finally, I updated the gvcf_joint test which is working cleanly for me now with Cromwell. I'm not sure what is happening with toil in your example as the missing file it's complaining about appears to be present in the repository. I hope the updated version will work cleanly for you. Thanks again for all this work and debugging and hope this now runs cleanly for you. |
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Hi, thanks a lot for the update. I'm afraid I don't quite understand what you meant by "all new Docker builds will pin to the version of bcbio-base so you'll avoid the issues you saw was pinning versions in CWL and getting bcbio-base:latest". Will the bcbio-base:latest image still be needed from now on, or will it suffice to have e.g. bcbio_vc:1.1.2a-1ffac4b installed? I removed all the Docker images from my system (both bcbio_vc and bcbio_base) and got the latest CWL tests from Git. The Cromwell test failed due to wrong input file paths, and then proceeded to download the Docker image I then removed the This ended up downloading both the bcbio-vc (with unknown tag) and bcbio-base images: Unfortunately, my test also failed. It seems that gvcfgenotyper isn't working properly: |
chapmanb
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Nov 27, 2018
Makes managing data from bcbio_vm.py easier. Thanks to discussion in bcbio/bcbio-nextgen#2473
chapmanb
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Nov 27, 2018
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Thanks much for the updates and continued testing. I'll try to tackle all 3 of the issue from your last message:
Hope this all helps. |
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The latest joint call tests are running fine on my system now. However, regarding my failed tests with yeast data, the error I pasted above doesn't seem to be related to a specific genomic region. There are many similar error blocks, related to all of the analyzed genomic regions, as far as I could tell. I've attached the full output here: https://gist.githubusercontent.com/amizeranschi/48204a751510880b20211cc5e7f07a9d/raw/abb1d685e17a13c6302a4da7cfae3a7b3985aca4/gistfile1.txt. Unfortunately, I couldn't find any of the gVCF files in the temporary directories mentioned in the gvcfgenotyper errors. All of the temporary directories have been automatically deleted: |
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Glad the CWL tests are now passing and thanks for the work debugging. The files you'd need for reproducing would be the gVCF input files. These are present (or at least linked to) in the inputs directory of different steps: The transactional directories get removed when tasks end so you don't expect those to have files. We'd need a couple of inputs gVCFs that are failing and then could run the gvcfgenotyper command outside of bcbio to try and reproduce. Thanks again for the help. |
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Thanks for clarifying the location of the input files. I've just sent them by e-mail. I hope they will be useful. |
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Thanks for passing these along; I appreciate the help debugging. Are these the input to one of the failing steps using gvcfgenotyper? The only input VCF there is not a gVCF but rather a combined and called VCF file with two samples, so I'm confused. I wouldn't expect you to have these if the gvcfgenotyper step failed earlier. Are these the input files from the path I referenced or a different one? Also, could you share your configuration for the actual run? Maybe I'm missing something in reproducing and understanding the issue. Thanks again for all the help. |
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Yes, those are the files from the directory you mentioned in your previous post ( This is the YAML template: This is the CSV file: And this is the YAML config file: |
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I tried running the same test (Yeast data + CWL with Cromwell), but I've replaced Strelka2 with GATK's HaplotypeCaller. It's been running for almost 7 hours now and I'm not sure if it's still working or just stuck somehow. The last lines of the output so far are: Is there a way to check if this is still running or just stuck? For comparison, the same workflow (with Strelka2) took 20 minutes when running on a local Bcbio_nextgen copy, and around an hour when running with Bcbio_vm and Docker (no CWL). Strelka2 has run aprox. 2X faster than GATK's HaplotypeCaller for me, locally, in Bcbio_nextgen (tested a couple of weeks ago). Is it expected for Bcbio_vm+Docker+CWL to run significantly slower than Bcbio_nextgen or the older Bcbio_vm+Docker workflow (now CWL)? |
chapmanb
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Nov 30, 2018
When specifying jointcaller without `tools_on: [gvcf]`, intermediate files got pooled together and called. This adds it automatically to correctly run joint calling. #2473
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Thanks much for the example, this was a big help to identify the issue. If you add However, the way you specified should work and not fail, so I've also pushed fixes to make that happen. Those should be in place by tomorrow but in the short term just removing For the GATK issue, I'm not sure if this is a symptom of the same underlying problem or if something else is happening. You should be able to use top to check if there is anything running, which is the most straightforward way. In general, we don't expect the CWL approach to be significantly slower than the older approach so taking this much longer doesn't seem right. For smaller runs on a single machine CWL might be slower depending on the core allocation, but should be relatively similar. Hope this all helps and gets your analysis finally finished. Thanks again for all the work and patience. |
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I've been checking Just to check, should the I'll test this tomorrow and report back. |
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Adding the option Is there any good reason to still use HaplotypeCaller instead of Strelka2? One thing I noticed was that the upload directory seems to have changed when using CWL, compared with what I've expected from Bcbio_nextgen. This is what the directory structure looks like for my test: To run both Bcbio_nextgen and Bcbio_vm+CWL, I cd into or Bcbio_nextgen seems to set the upload directory to In addition, the name of the directory where the joint VCF file and multiqc results are copied differs between Bcbio_nextgen and Bcbio_vm+CWL. With the former, that directory was called something like I also noticed a file called WIth Bcbio_nextgen, I expected Manta VCFs to be in the What's the plan with the two workflows (Bcbio_nextgen and Bcbio_vm+CWL)? Are they going to diverge in terms of directory set-up and output file locations? Is Bcbio_vm+CWL going to replace Bcbio_nextgen in the future? |
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It's brilliant to hear this is now working for you. Thanks for all the patience getting it running and for the usage report. In terms of GATK HaplotypeCaller and strelka2, both are good choices for joint variant calling. They do have different intermediate gVCF formats so you might also make a decision based on other platforms or analyses you want to integrate with. Thanks also for the detailed investigation of the output directory. It's expected to be non-identical for the CWL case. Replicating some of what we did previously was difficult since we get the results in a different manner from the CWL runner so can't allocate to sample and project directories in the exact same way. We were also hoping to clean up some of the historical cruft and confusion in the upload directory. Please let us know if anything is problematic and we can investigate. For manta, you're right that is should be a merged VCF of the batched samples. It's not joint called, but rather called together within a group. Hope that works as expected when you're able to put together a realistic case for it. Thanks again for all the feedback and work on getting this going. |
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OK, great. Thanks for all your help! |
dpryan79
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Dec 8, 2018
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Should only run once during the first mob_typer run. Should be good now for parallel runs. * PeptideShaker updated to v1.16.35 & SearchGUI updated to 3.3.9 (#12241) * PeptideShaker updated to v1.16.32 SearchGUI updated to v3.3.6 * PeptideShaker updated to v1.16.35 * SearchGUI updated to v3.3.9 * First attempt at a recipe for ncrf (#12101) * First attempt at a recipe for ncrf * changed from copies to symlinks * including absolute path in symlinks * PacBio: Update `pbmm2` to version 0.11.0 (#12246) * Gimmemotifs version 0.13.0 (#12245) * new release to fix numpy incompatibility * GimmeMotifs 0.13.0 release test * numpy 1.15 * version 0.13.0 * Fix about:home and extra: * PacBio: Update `isoseq3` to version 3.1.0 (#12263) * add python to host section (#12264) * Update confindr to 0.4.7 (#12266) * new build of GRiD (#12269) * update grid * update build num * edit grid to use mosdepth for depth coverage * edit grid to use mosdepth for depth coverage * Update meta.yaml * new build for grid * Update meta.yaml * peptideshaker, searchgui: version bump (#12136) * peptideshaker, searchgui: version bump solving compomics/searchgui#192 * Update peptide-shaker.py * searchgui: added c compiler for building test if linking errors go away this way * searchgui: removed noarch * Update: bcbio, bcbio-vm with CWL non-human fixes (bcbio/bcbio-nextgen#2473) (#12273) * Make snakemake a noarch package. (#12274) * noarch: python in combination with version constraint * Cleanup deps and simplify version definition. * Genenotebook v0.1.9 (#12277) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * Create r-airr recipe (#12284) * Create r-airr recipe using bgruening/conda_r_skeleton_helper * Update meta.yaml * Findbin::Real added (#12291) * Added version bump to 1.3 (#12292) * ngs-bits 2018_11 (#12262) * Updated ngs-bits to version 2018_10 * Updated ngs-bits to version 2018_11 * minor edit in grid (#12287) * update grid * update build num * edit grid to use mosdepth for depth coverage * edit grid to use mosdepth for depth coverage * Update meta.yaml * new build for grid * Update meta.yaml * minor edit to grid * Fred2 update (#12259) * Update FRED2 Recipe * msstitch version 2.9 (#12296) * r-mvr (#12300) This is a non-parametric method for joint adaptive mean-variance regularization and variance sta- bilization of high-dimensional data. * Bump to Gromacs 2018.3 + re-enable OSX build (#12299) * Gromacs 2018.3 + re-enable osx build See also #7825 on OSX build Include RRID for Gromacs (see bioconda/bioconda-utils#252) * disabled ocl-icd on osx; not available (or needed?) https://anaconda.org/conda-forge/ocl-icd * pyGenomeTracks update of dependencies (#12279) * Update pyGenomeTracks recipe to enable py3 support and updating outdated dependecy list * Increase build number * Update meta.yaml * Exclude Python 3.5 * Gromacs 2018.4 (#12302) * quast 5.0.2 (#12303) * Update meta.yaml (#12275) * Update meta.yaml r-rsqlite version dependency added * Update meta.yaml Updated build number to 1 * Use the extended-base container because of wget issues when downloading databases (#12297) * Update duphold to 0.1.0 (#12257) * Update flashlfq to 0.1.109 (#12256) * Update planemo to 0.57.0 (#12251) * Update meta.yaml (#12258) * Update scalpel to 0.5.4 (#12249) * Update scalpel to 0.5.4 * Fix url * edit grid (#12298) * update grid * update build num * edit grid to use mosdepth for depth coverage * edit grid to use mosdepth for depth coverage * Update meta.yaml * new build for grid * Update meta.yaml * minor edit to grid * minor edit to recipe grid * added feather to deps (#12293) * R tigger (#12286) * Create recipe for r-tigger (#12271) * Create recipe for r-tigger using bgruening/conda_r_skeleton_helper. * Delete bld.bat * Remove windows support * update scprep to v0.8.1 (#12306) * Update nanoget to 1.7.5 (#12252) * Update nanoget to 1.7.5 * Bump to version 1.7.6 should fix the README.md problem * gffcompare: version bump (#12308) * Update: cromwell (36), bcbio (Cromwell Docker runs) (#12307) * Update: cromwell (36), bcbio (Cromwell Docker runs) * Pin java to 8 to avoid compile errors on 11 * HiCExplorer update to version 2.2-beta (#12309) * HiCExplorer update to version 2.2-beta * Remove of '-' from version number * Numpy set to 1.15 * Update meta.yaml * upgrade to version 2.8.1 (#12316) * Create Airr recipe (#12318) * Create AIRR recipe using conda skeleton pypi. * Add noarch python * Clean host requirements * Added nimnexus [v0.1] (#12133) * added nimnexus * Fix sha * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * [WIP] Add R-loom (#12320) * initial WIP skeleton * Update meta.yaml * Update meta.yaml * Update meta.yaml * try osx * Create Changeo recipe (#12321) * Create changeo recipe using conda skeleton pypi. * EDIT about section * ADD noarch generic * Update noarch to python * Clean host requirements * Add test for scripts * Change requirement to python>=3.4 * Add noarch pyton * r-corbi (#12325) * r-nam (#12327) * Update pybedtools to 0.8.0 (#12324) * Update pybedtools to 0.8.0 * rm cython requirement * MSGFplus does not work with newer Java (#12330) * Trying to not use a very new java version since the latest versions have dropped some classes * Increment build * Update atropos to 1.1.21 (#12322) * Update CONCOCT to 0.4.2 (#12317) * Update CONCOCT to 0.4.2 * Wrong shasum given * Reset build number for new version * New: gvcfgenotyper for joint calling with Illumina strelka2 (#12331) * Apparently we need openJDK to be below 9, not below 11 as in the previous PR (#12332) * Update Picard to 2.18.17. (#12333) * Unblacklist IgDiscover (#12335) * PacBio: Add missing licenses and post-link message (#12334) * Bioconductor DEqMS package (#12336) * Bioconductor DEqMS package * Limma version could be set lower (checked with the bioconductor recipe page) to include limma in bioconda * Genenotebook v0.1.10 (#12337) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * removed cloudpickle requirement for blockclust (#12242) * blockclust latest source and added cloudpickle as requirement * removed cloudpickle requirement for blockclust * added a tagged release to the source * back to source url but with release tarball and checksum * R guilds (#12341) * Strict rec (#12113) * added metawrap * fixed perl and jdk * added more strict req * fixed java and perl * removed extra boost * Update qcat to v1.0.1 (#12343) * Add better error checking (#12345) * Add mhcnames python package (#12349) * Add MHCflurry pMHC class I binding affinity prediction tool (#12346) * Bump pilon (#12354) * Update pronto to 0.11.1 (#12377) * Update perl-json-xs to 4.0 (#12373) * Update planemo to 0.57.1 (#12370) * Update snippy to 4.3.6 (#12372) * Update intarna to 2.3.1 (#12367) * Update agfusion to 1.231 (#12366) * Update bioconda-utils to 0.15.0 (#12359) * Update mapdamage2 to 2.0.9 (#12358) * Update scanpy to 1.3.4 (#12357) * Update goatools to 0.8.11 (#12361) * Update perl-math-random-mt-auto to 6.23 (#12362) * Update kipoi to 0.6.3 (#12374) * Update kipoi_veff to 0.2.1 (#12364) * Update perl-object-insideout to 4.05 (#12380) * Update sevenbridges-python to 0.17.1 (#12379) * Update nanosv to 1.2.3 (#12378) * Update starfish to 0.0.30 (#12368) * Update clust to 1.8.10 (#12356) * Update pypairs to 2.0.6 (#12381) * Update khmer to 3.0.0a2 (#12360) * Update flashlfq to 0.1.110 (#12385) * Update perl-algorithm-cluster to 1.57 (#12384) * Update arvados-python-client to 1.2.0.20181121194423 (#12382) * Update avro-cwl to 1.8.9 (#12355) * Update avro-cwl to 1.8.9 * Set noarch: python * r-breakaway (#12386) * R sads (#12388) * Update python-sortedcontainers to 2.1.0 (#12383) * r-ebimetagenomics (#12339) * pin armadilo on major version (#12389) * IgDiscover version 0.11 (#12351) * IgDiscover version 0.11 * IgDiscover requires Python 3.6 * Fix build on macOS with a small patch * Remove unneeded host dependencies * Update goatools to 0.8.12 (#12391) * Update bioconda-utils to 0.15.1 (#12390) * R ebimetagenomics (#12393) * Add dimspy recipes for reference purposes (#12387) * Add dimspy recipes for reference purposes * Remove filename * remove from blacklist * Update build-fail-blacklist * Added BioExcel_SeqQC to bioconda-recipes (#12276) * PacBio: Update pbalign to 0.3.2 (#12396) * PacBio: Update pbalign to 0.3.2 Closes: PacificBiosciences/pbbioconda#39 * add bgreat to bioconda (#12350) * bgreat addition * zlib in build should not be needed * btrim integration to conda (#12395) * Format sleuth recipe. Trigger rebuild because latest version was never uploaded for some reason. (#12399) * PacBio: Update `pbsv2` to version 2.1.0 (#12400) * Genenotebook v0.1.11 (#12398) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * v0.1.11 * prosolo: new package version 0.6.0 (#12397) * Update sevenbridges-python to 0.17.2 (#12404) * Add recipe for ICED (#12406) * Downgrade version for iced (#12409) * Update recipe for libstatgen 1.0.5 (#12348) * Add recipe for libstatgen-1.0.5 * Update iced to 0.5.0 (#12411) * Update perl-test2-suite to 0.000116 (#12412) * fix compatibility with other tools (#12415) * Restore dexseq python helper scripts (#12352) * Restore dexseq python helper scripts * Add python requirement for helper scripts * Add python noarch to build section * pin it to python2k * Add htseq requirement, support only python <3 for now * Genenotebook v0.1.12 (#12418) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * v0.1.11 * v0.1.12 * updated source * added medpy recipe (#12417) * added medpy recipe * removed osx from build * Update meta.yaml * Update meta.yaml * add boost and a compiler * Update meta.yaml * Update meta.yaml * add itk * Updated ddrage to version 1.6.1. (#12421) * Add r-mcpcounter recipe. (#12261) * Add MCPcounter recipe. * fix lint: remove 'fn' * fix license_file, version number and doi * Update DEXSeq requirements to force compatible HTSeq version (#12423) * ARB: Pin glib (#11782) * Pin glib * Update meta.yaml * Update meta.yaml * Work around CB3 issues * Work around bioconda-utils lint false positive * Disable lint check should_not_be_noarch * Can't reference other packages built in recipe from anything but run * Move perl to host section. Maybe that helps. * constraining interpreter version breaks with CB3? * disable perl version constraint :( * Update meta.yaml (#12426) * stacks: fix for fix 'fixing' @ in exe_path (#12420) * stacks: fix for fix 'fixing' @ in exe_path the previous fix #11580 tried to solve the problem with the @ in the exe_path by setting this variable empty. But the perl scripts - append a / to the empty string and (i.e. the bin path gets /binary) - check for file presence (problem: neither binary nor /binary are present) Now I quote the @ in the exe_path. * stacks: add refmap bugfix * Genenotebook v0.1.13 (#12424) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * v0.1.11 * v0.1.12 * updated source * v0.1.13 * metaQuantome (#12413) replaces metaquant, which is now deprecated. * New MMseqs2 release 7-4e23d (#12432) New mmseqs2 release 7-4e23d * update spades to 3.13.0 (#12408) * update spades to 3.13.0 * spades: removed dipspades; added 3.12.0 recipe in subdir * bumped build number for 3.11.1 due to CI failure * Update Crossmap to 0.3.1 (#12439) * Update Crossmap to 0.3.1 * Make metaquantome dependencies more specific (#12442) * less stringent deps * bump build * pin goatools * test extra pins * integration of bcool to bioconda (#12422) * Update hifive to 1.5.7 (#12433) * Update scvi to 0.2.3 (#12434) * Update Subread from 1.6.2 to 1.6.3. (#12425) * Update Subread from 1.6.2 to 1.6.3. * Subread executable coverageCount has been removed. https://groups.google.com/d/msg/subread/Au1CpKGAXaA/KndhDbrfAwAJ * UCSC Cell Browser 0.4.23 (#12347) * Starting files for ucsc-cell-browser * Customised recipe for ucsc-cell-browser * meta update for ucsc-cell-browser * Changes cbTrackHub to cbHub * Point to static release * Moves to 0.25 * Updates sha hash for ucsc-browser * Reverts to 0.1.9 * At ebi * Update meta.yaml * pins numpy to last know working version * Back to 0.25, no numpy pinning. * Remove git, pin python and numpy. Add build section. * Update meta.yaml * Update meta.yaml * Move to 0.4.20 without skeleton on provisional commit * Typo on executable name * Moves to release version and adds dependencies for converters * Update libstatgen to 1.0.14 (#12437) * Update arvados-python-client to 1.2.1 (#12438) * Update tirmite to 1.1.3 (#12435) * Bump metaquantome (#12449) * less stringent deps * bump build * pin goatools * test extra pins * bump metaquantome to 0.99.3 * Update ADAM to 0.25.0 (#12445) * Update: bcbio, bcbio-vm with viral QC, Docker fixes (#12453) * update rgi4.2.2 recipe (#12282) * update to enforce python3.6 and load card.json * remove lines from build.sh * update build number * make PR comment changes * add test to verify db is loaded * update build script * update build script * fix lint errors * fix linting errors * fix liniting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * revert test change * Add CRAN R package leapp. (#12428) * Bump DECIPHER to Bioconductor 3.7 (#12463) * Bump DECIPHER to Bioconductor 3.7 * Change r-rsqlite version dependency * Update meta.yaml * updated scVI to 0.2.3 (#12429) * Add recipe for PyAAVF 0.1.0 (#12451) * Add recipe for PyAAVF 0.1.0 * Fix linting error * seqkit 0.9.3 (#12455) * HTSeq - Pin numpy version (#12467) * update eigensoft to 7.2.1 (#12469) * Update scnic to 0.6.0 (#12436) * Update scnic to 0.6.0 * Work around fastspar insufficient armadillo pin * fix pin * GimmeMotifs 0.13.1 (#12471) * Bumped version to newest, with introspective text (#12461) * Update Segway 2.0.2 recipe to use older depedencies (#11803) * Update Segway 2.0.2 recipe to use older depedencies * Update maximum genomedata version supported * Update build number * Fix missing older dependency information * Update meta.yaml * updating dependencies for reparation_blast (#12443) * updating dependencies for reparation_blast * changed dependency of pysam * Added DropletUtils package (#12448) * Create recipe for SVIM (#12272) * add svim recipe * fix bugs in svim recipe * replace source file * remove license file * Lowercase biopython * upgrade to svim 0.4.1 * add GPL LICENSE file, allow python 3.6.* patch releases, add minimap2 dependency * fix python version * try to fix lint error * replace "skip: True" with "noarch: python" * Update bioconductor-biocgenerics (#12477) * [X] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)). * [X] This PR updates an existing recipe. * [ ] This PR does something else (explain below). * Irida sistr results 0.6.0 (#12478) * Update irida-sistr-results to 0.6.0 * Fixed dependency string * Adding recipe for clinvar-tsv v0.1.0. (#12481) * no fixed boost version (#12483) * New recipe: pysradb (#12470) * Pyseer 1.2.0 (#12444) * Update pyseer to 1.1.2 * Update pyseer to 1.2.0 * Update pyseer to 1.2.0 Update pyseer to 1.2.0 Update pyseer to 1.2.0 (fixed) * Final touches to pyseer 1.2.0 * Additional update to pyseer recipe * sentieon: minor version bump to 201808.01 (#12480) * adding java to mutations recipe (#12485) * Update ncrf to 1.00.06 (#12369) * Update ncrf to 1.00.06 * Update test string * Bump umitools (#12486) * Mob suite version 1.4.9 no arch build number 2 (#12479) * Updated to version 1.4.9 * Downgraded to python >= 3.4 to accomodate lowandrew request * new build * no arch commit for python 3.4 * no arch conda package version * Set build number to 1 * Update r-goeveg to 0.4.2 (#12375) * Update r-goeveg to 0.4.2 * Add r-hmisc as dependency * Removes r-seurat-scripts from blacklisting (#12489) * Removes r-seurat-scripts from blacklisting * Unblacklist some non bioconductor packages * For VarDict-Java, install utility scripts. (#12488) * For VarDict-Java, install utility scripts. Utility script that were previously only shipped with VarDict are not part of VarDict-Java as well, making installation of both packages unnecessary. * Bump build. * Improve variable name. * Make vardict depend on vardict-java for utility scripts. * Pin compatible numpy for older HTSEQ versions (#12490) * Pin compatible numpy for older HTSEQ versions This is required to keep older versions of HTSEQ functional * HTSeq - update old versions to build properly with new build system * HTSeq 0.6.1 - Increment build number * add recipe for r-epic (#12473) * Add new recipe - RVTESTS (#12465) * Add rvtests * Update pre-req * Update meta.yaml * Update build.sh * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Create LICENSE * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh * Create run_test.sh * Update meta.yaml * Delete run_test.sh * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Adding recipe for var-agg v0.1.0 (#12482) * Adding recipe for var-agg v0.1.0 * runtime deps do have run-exports defined * move rust into the host section * Adding dependency to clangdev * Adding var-agg v0.1.1. (#12495) * [WIP] Salmon v0.12.0 --- try to fix OSX build for real (#12441) Salmon v0.12.0 --- version bump and fix OSX build * Considerable updates in terms of features and fixes (check release notes). * Fix OSX build that would compile, but segfault in quant (but only when built on "old" OSX). * Performancean alytics (#12498) * Add bioconductor package RNASeqR * Add performanceanalytics * Performancean alytics (#12499) * Add bioconductor package RNASeqR * Add performanceanalytics * Move recipes/r-performanceanalytics and add r-rafalib * Move r-performanceanalytics/ to recipes * Update recipes/r-performanceanalytics * Update r-rafalib * Remove recipes/r-performanceanalytics/bld.bat * Remove recipes/r-performanceanalytics * Update r-performanceanalytics/ * Update r-performanceanalytics/ * Add r-performanceanalytics/ * remove r-performanceanalytics * Add performanceanalytics * Remove r-performanceanalytics * Update Picard to 2.18.20. (#12501) * Update vsearch to 2.10.0. (#12504) * Update Purge Haplotigs to v1.0.4 (#12497) * Update duphold to 0.1.1 (#12516) * Update starfish to 0.0.31 (#12515) * Update perl-term-app-roles to 0.02 (#12512) * Update perl-dbd-sqlite to 1.60 (#12511) * Update perl-json to 4.00 (#12509) * Update kipoi to 0.6.5 (#12508) * Update illumina-interop to 1.1.8 (#12507) * Update beagle-lib to 3.1.2 (#12523) * Update pysradb to 0.3.0 (#12522) * Update bioconda-utils to 0.15.2 (#12525) * Update perl-json-pp to 4.0 (#12524) * Update perl-term-table to 0.013 (#12529) * Update abyss to 2.1.5 (#12528) * Update perl-test2-suite to 0.000117 (#12527) * Update wtforms-alchemy to 0.16.8 (#12505) * Update perl-carp-clan to 6.07 (#12518) * Update perl-date-manip to 6.75 (#12519) * Update: seq2c, multiqc-bcbio (#12533) * tracy v0.3.7 (#12534) * Version bump 2.10 (#12535) * Version bump 2.10 * Copy paste error forgot the https * Missing deps for ucsc-cell-browser 0.4.23 (#12537) * Missing deps for ucsc-cell-browser * Bumps build nuber * Update vsearch to 2.10.1 (#12540) * New recipe for MicroHapDB 0.2 (#12531) * New recipe for MicroHapDB 0.2 * Troubleshoot config * Successful build locally! * Clean up recipe * Update moff to 2.0.2 (#12539) * Update PopDel to version 1.0.5 (#12502) * Update PopDel to version 1.0.5 * Remove Makefile.patch Remove Makefile.patch and adapt build.sh to set the correct version, date and CXX-path in its stead. * Automatically get version from PKG_VERSION * Update to teloclip v0.0.3 (#12542) * Update biolite to 1.2.0 (#12544) * Update kneaddata to 0.7.2 (#12543) * snakemake 5.3.1 (#12500) * snakemake 5.3.1 * fix jinja variables * only warn if git not present in tests * use explicit jinja for version again. Conda seems to have lost the ability to use PKG_VERSION in meta.yaml. * try masking env var * try defining env var before command * nextflow: pin openjdk=8 to solve java version parsing issue (#12493) * Pin openjdk=8 * Alllow openjdk 8 or 9 * Update bioconda-utils to 0.15.3 (#12546) * Test with bioconductor-roc * add a noarch test case * biocgenerics should work * CXXFLAGS * revert a4base bump * remove tab * try src/Makevars
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Dec 9, 2018
* r-classdiscovery (#12105) * r-oompabase * r-classdiscovery * Remove oompabase * Fixed Dependency Biobase * R lncpipereporter (#12102) * ADD lncPipeReporter * update * update * seqkit 0.9.2 (#12110) * Update fastq-scan to v0.3 (#12109) * Add perl-clone-choose (#12108) * Update perl-hash-merge to 0.300 (#11941) * Update perl-hash-merge to 0.300 * Update perl-hash-merge to 0.300 * Update meta.yaml * Update perl-file-slurper to 0.012 (#11910) * Update perl-file-slurper to 0.012 * Adding dependencies * Update perl-moo to 2.003004 (#11897) * Update perl-moo to 2.003004 * Update meta.yaml * Add deeptoolsintervals (#12114) * Add deeptoolsintervals * blah * No nose in the mulled container * Fix octopus binary "invalid instruction" (-march too new) (#11822) * This attempts to make the binary more portable by only requiring Sandybridge. * Fix march set to native * Update perl-bio-asn1-entrezgene to 1.73 (#11914) * Update perl-bio-asn1-entrezgene to 1.73 * Update perl-bio-asn1-entrezgene to 1.73 * Update meta.yaml * Update perl-file-slurp to 9999.25 (#12127) * Update manta to 1.5.0 (#12126) * Update nanocomp to 1.0.0 (#12124) * Update masurca to 3.2.9 (#12121) * Update beagle-lib to 3.1.1 (#12119) * Update r-spocc to 0.9.0 (#12118) * Update kallisto to 0.45.0 (#12117) * Update validators to 0.12.3 (#12116) * Update illumina-interop to 1.1.7 (#12115) * Update umi_tools to 0.5.5 (#12123) * Update tiptoft to 1.0.0 (#12122) * Update: TitanCNA with fix for hg38 plotting (#12130) * blockclust (#12111) * added eden 1.1 version used in blockclust * Update meta.yaml * eden checksum and test * added zlib requirement * add include and lib paths to build.sh * add include and lib paths to build.sh * modify makefile flags using sed * modify makefile flags using sed * use c++ * Update build.sh * Update build.sh * LDFLAGS not used in makefile * remove v1.1 * add blockclust 1.1.0 recipe * skip osx build * added tarball url and checksum; removed conda_build_config.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update chewbbaca to 2.0.16 (#12132) * Update abeona to 0.40.0 (#12131) * ping to eden 1.1 (#12134) * clean swap file (#12137) * Update corset to 1.07 (#12143) * Update peddy to 0.4.3 (#12144) * blockclust latest source and added cloudpickle as requirement (#12142) * Update nanomath to 0.22.0 (#12149) * Update pymvpa to 2.6.5 (#12152) * Updated to version 1.4.0 (#12138) * Updated to version 1.4.0 * Resetting build number to 0 and build->host * Update transdecoder to 5.5.0 (#12172) * Update gridss to 2.0.1 (#12190) * Update tracer to 1.7.1 (#12189) * Update flowcraft to 1.4.0 (#12179) * Update seqbuster to 3.2 (#12182) * Update perl-io-compress to 2.081 (#12201) * Update twobitreader to 3.1.6 (#12205) * Update twobitreader to 3.1.6 * Update meta.yaml * Update gtfparse to 1.2.0 (#12186) * Update gtfparse to 1.2.0 * remove compiler * Update htseq to 0.11.0 (#12177) * Update htseq to 0.11.0 * add compiler * Update htseq to 0.11.0 (#12239) [testing co-author] * Update htseq to 0.11.0 * add compiler Co-authored-by: Bjoern Gruening <[email protected]> * alfred v0.1.16 (#12240) * alfred v0.1.16 * makefile patch * makefile patch * Update scrm to 1.7.3 (#12150) * Update scrm to 1.7.3 * Update scrm to 1.7.3 * Mob suite update 1.4.8 --> 1.4.9 (#12244) We fixed a small bug related to repetitive elements database reconstruction on each run. Should only run once during the first mob_typer run. Should be good now for parallel runs. * PeptideShaker updated to v1.16.35 & SearchGUI updated to 3.3.9 (#12241) * PeptideShaker updated to v1.16.32 SearchGUI updated to v3.3.6 * PeptideShaker updated to v1.16.35 * SearchGUI updated to v3.3.9 * First attempt at a recipe for ncrf (#12101) * First attempt at a recipe for ncrf * changed from copies to symlinks * including absolute path in symlinks * PacBio: Update `pbmm2` to version 0.11.0 (#12246) * Gimmemotifs version 0.13.0 (#12245) * new release to fix numpy incompatibility * GimmeMotifs 0.13.0 release test * numpy 1.15 * version 0.13.0 * Fix about:home and extra: * PacBio: Update `isoseq3` to version 3.1.0 (#12263) * add python to host section (#12264) * Update confindr to 0.4.7 (#12266) * new build of GRiD (#12269) * update grid * update build num * edit grid to use mosdepth for depth coverage * edit grid to use mosdepth for depth coverage * Update meta.yaml * new build for grid * Update meta.yaml * peptideshaker, searchgui: version bump (#12136) * peptideshaker, searchgui: version bump solving compomics/searchgui#192 * Update peptide-shaker.py * searchgui: added c compiler for building test if linking errors go away this way * searchgui: removed noarch * Update: bcbio, bcbio-vm with CWL non-human fixes (bcbio/bcbio-nextgen#2473) (#12273) * Make snakemake a noarch package. (#12274) * noarch: python in combination with version constraint * Cleanup deps and simplify version definition. * Genenotebook v0.1.9 (#12277) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * Create r-airr recipe (#12284) * Create r-airr recipe using bgruening/conda_r_skeleton_helper * Update meta.yaml * Findbin::Real added (#12291) * Added version bump to 1.3 (#12292) * ngs-bits 2018_11 (#12262) * Updated ngs-bits to version 2018_10 * Updated ngs-bits to version 2018_11 * minor edit in grid (#12287) * update grid * update build num * edit grid to use mosdepth for depth coverage * edit grid to use mosdepth for depth coverage * Update meta.yaml * new build for grid * Update meta.yaml * minor edit to grid * Fred2 update (#12259) * Update FRED2 Recipe * msstitch version 2.9 (#12296) * r-mvr (#12300) This is a non-parametric method for joint adaptive mean-variance regularization and variance sta- bilization of high-dimensional data. * Bump to Gromacs 2018.3 + re-enable OSX build (#12299) * Gromacs 2018.3 + re-enable osx build See also #7825 on OSX build Include RRID for Gromacs (see bioconda/bioconda-utils#252) * disabled ocl-icd on osx; not available (or needed?) https://anaconda.org/conda-forge/ocl-icd * pyGenomeTracks update of dependencies (#12279) * Update pyGenomeTracks recipe to enable py3 support and updating outdated dependecy list * Increase build number * Update meta.yaml * Exclude Python 3.5 * Gromacs 2018.4 (#12302) * quast 5.0.2 (#12303) * Update meta.yaml (#12275) * Update meta.yaml r-rsqlite version dependency added * Update meta.yaml Updated build number to 1 * Use the extended-base container because of wget issues when downloading databases (#12297) * Update duphold to 0.1.0 (#12257) * Update flashlfq to 0.1.109 (#12256) * Update planemo to 0.57.0 (#12251) * Update meta.yaml (#12258) * Update scalpel to 0.5.4 (#12249) * Update scalpel to 0.5.4 * Fix url * edit grid (#12298) * update grid * update build num * edit grid to use mosdepth for depth coverage * edit grid to use mosdepth for depth coverage * Update meta.yaml * new build for grid * Update meta.yaml * minor edit to grid * minor edit to recipe grid * added feather to deps (#12293) * R tigger (#12286) * Create recipe for r-tigger (#12271) * Create recipe for r-tigger using bgruening/conda_r_skeleton_helper. * Delete bld.bat * Remove windows support * update scprep to v0.8.1 (#12306) * Update nanoget to 1.7.5 (#12252) * Update nanoget to 1.7.5 * Bump to version 1.7.6 should fix the README.md problem * gffcompare: version bump (#12308) * Update: cromwell (36), bcbio (Cromwell Docker runs) (#12307) * Update: cromwell (36), bcbio (Cromwell Docker runs) * Pin java to 8 to avoid compile errors on 11 * HiCExplorer update to version 2.2-beta (#12309) * HiCExplorer update to version 2.2-beta * Remove of '-' from version number * Numpy set to 1.15 * Update meta.yaml * upgrade to version 2.8.1 (#12316) * Create Airr recipe (#12318) * Create AIRR recipe using conda skeleton pypi. * Add noarch python * Clean host requirements * Added nimnexus [v0.1] (#12133) * added nimnexus * Fix sha * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * [WIP] Add R-loom (#12320) * initial WIP skeleton * Update meta.yaml * Update meta.yaml * Update meta.yaml * try osx * Create Changeo recipe (#12321) * Create changeo recipe using conda skeleton pypi. * EDIT about section * ADD noarch generic * Update noarch to python * Clean host requirements * Add test for scripts * Change requirement to python>=3.4 * Add noarch pyton * r-corbi (#12325) * r-nam (#12327) * Update pybedtools to 0.8.0 (#12324) * Update pybedtools to 0.8.0 * rm cython requirement * MSGFplus does not work with newer Java (#12330) * Trying to not use a very new java version since the latest versions have dropped some classes * Increment build * Update atropos to 1.1.21 (#12322) * Update CONCOCT to 0.4.2 (#12317) * Update CONCOCT to 0.4.2 * Wrong shasum given * Reset build number for new version * New: gvcfgenotyper for joint calling with Illumina strelka2 (#12331) * Apparently we need openJDK to be below 9, not below 11 as in the previous PR (#12332) * Update Picard to 2.18.17. (#12333) * Unblacklist IgDiscover (#12335) * PacBio: Add missing licenses and post-link message (#12334) * Bioconductor DEqMS package (#12336) * Bioconductor DEqMS package * Limma version could be set lower (checked with the bioconductor recipe page) to include limma in bioconda * Genenotebook v0.1.10 (#12337) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * removed cloudpickle requirement for blockclust (#12242) * blockclust latest source and added cloudpickle as requirement * removed cloudpickle requirement for blockclust * added a tagged release to the source * back to source url but with release tarball and checksum * R guilds (#12341) * Strict rec (#12113) * added metawrap * fixed perl and jdk * added more strict req * fixed java and perl * removed extra boost * Update qcat to v1.0.1 (#12343) * Add better error checking (#12345) * Add mhcnames python package (#12349) * Add MHCflurry pMHC class I binding affinity prediction tool (#12346) * Bump pilon (#12354) * Update pronto to 0.11.1 (#12377) * Update perl-json-xs to 4.0 (#12373) * Update planemo to 0.57.1 (#12370) * Update snippy to 4.3.6 (#12372) * Update intarna to 2.3.1 (#12367) * Update agfusion to 1.231 (#12366) * Update bioconda-utils to 0.15.0 (#12359) * Update mapdamage2 to 2.0.9 (#12358) * Update scanpy to 1.3.4 (#12357) * Update goatools to 0.8.11 (#12361) * Update perl-math-random-mt-auto to 6.23 (#12362) * Update kipoi to 0.6.3 (#12374) * Update kipoi_veff to 0.2.1 (#12364) * Update perl-object-insideout to 4.05 (#12380) * Update sevenbridges-python to 0.17.1 (#12379) * Update nanosv to 1.2.3 (#12378) * Update starfish to 0.0.30 (#12368) * Update clust to 1.8.10 (#12356) * Update pypairs to 2.0.6 (#12381) * Update khmer to 3.0.0a2 (#12360) * Update flashlfq to 0.1.110 (#12385) * Update perl-algorithm-cluster to 1.57 (#12384) * Update arvados-python-client to 1.2.0.20181121194423 (#12382) * Update avro-cwl to 1.8.9 (#12355) * Update avro-cwl to 1.8.9 * Set noarch: python * r-breakaway (#12386) * R sads (#12388) * Update python-sortedcontainers to 2.1.0 (#12383) * r-ebimetagenomics (#12339) * pin armadilo on major version (#12389) * IgDiscover version 0.11 (#12351) * IgDiscover version 0.11 * IgDiscover requires Python 3.6 * Fix build on macOS with a small patch * Remove unneeded host dependencies * Update goatools to 0.8.12 (#12391) * Update bioconda-utils to 0.15.1 (#12390) * R ebimetagenomics (#12393) * Add dimspy recipes for reference purposes (#12387) * Add dimspy recipes for reference purposes * Remove filename * remove from blacklist * Update build-fail-blacklist * Added BioExcel_SeqQC to bioconda-recipes (#12276) * PacBio: Update pbalign to 0.3.2 (#12396) * PacBio: Update pbalign to 0.3.2 Closes: PacificBiosciences/pbbioconda#39 * add bgreat to bioconda (#12350) * bgreat addition * zlib in build should not be needed * btrim integration to conda (#12395) * Format sleuth recipe. Trigger rebuild because latest version was never uploaded for some reason. (#12399) * PacBio: Update `pbsv2` to version 2.1.0 (#12400) * Genenotebook v0.1.11 (#12398) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * v0.1.11 * prosolo: new package version 0.6.0 (#12397) * Update sevenbridges-python to 0.17.2 (#12404) * Add recipe for ICED (#12406) * Downgrade version for iced (#12409) * Update recipe for libstatgen 1.0.5 (#12348) * Add recipe for libstatgen-1.0.5 * Update iced to 0.5.0 (#12411) * Update perl-test2-suite to 0.000116 (#12412) * fix compatibility with other tools (#12415) * Restore dexseq python helper scripts (#12352) * Restore dexseq python helper scripts * Add python requirement for helper scripts * Add python noarch to build section * pin it to python2k * Add htseq requirement, support only python <3 for now * Genenotebook v0.1.12 (#12418) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * v0.1.11 * v0.1.12 * updated source * added medpy recipe (#12417) * added medpy recipe * removed osx from build * Update meta.yaml * Update meta.yaml * add boost and a compiler * Update meta.yaml * Update meta.yaml * add itk * Updated ddrage to version 1.6.1. (#12421) * Add r-mcpcounter recipe. (#12261) * Add MCPcounter recipe. * fix lint: remove 'fn' * fix license_file, version number and doi * Update DEXSeq requirements to force compatible HTSeq version (#12423) * ARB: Pin glib (#11782) * Pin glib * Update meta.yaml * Update meta.yaml * Work around CB3 issues * Work around bioconda-utils lint false positive * Disable lint check should_not_be_noarch * Can't reference other packages built in recipe from anything but run * Move perl to host section. Maybe that helps. * constraining interpreter version breaks with CB3? * disable perl version constraint :( * Update meta.yaml (#12426) * stacks: fix for fix 'fixing' @ in exe_path (#12420) * stacks: fix for fix 'fixing' @ in exe_path the previous fix #11580 tried to solve the problem with the @ in the exe_path by setting this variable empty. But the perl scripts - append a / to the empty string and (i.e. the bin path gets /binary) - check for file presence (problem: neither binary nor /binary are present) Now I quote the @ in the exe_path. * stacks: add refmap bugfix * Genenotebook v0.1.13 (#12424) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * v0.1.11 * v0.1.12 * updated source * v0.1.13 * metaQuantome (#12413) replaces metaquant, which is now deprecated. * New MMseqs2 release 7-4e23d (#12432) New mmseqs2 release 7-4e23d * update spades to 3.13.0 (#12408) * update spades to 3.13.0 * spades: removed dipspades; added 3.12.0 recipe in subdir * bumped build number for 3.11.1 due to CI failure * Update Crossmap to 0.3.1 (#12439) * Update Crossmap to 0.3.1 * Make metaquantome dependencies more specific (#12442) * less stringent deps * bump build * pin goatools * test extra pins * integration of bcool to bioconda (#12422) * Update hifive to 1.5.7 (#12433) * Update scvi to 0.2.3 (#12434) * Update Subread from 1.6.2 to 1.6.3. (#12425) * Update Subread from 1.6.2 to 1.6.3. * Subread executable coverageCount has been removed. https://groups.google.com/d/msg/subread/Au1CpKGAXaA/KndhDbrfAwAJ * UCSC Cell Browser 0.4.23 (#12347) * Starting files for ucsc-cell-browser * Customised recipe for ucsc-cell-browser * meta update for ucsc-cell-browser * Changes cbTrackHub to cbHub * Point to static release * Moves to 0.25 * Updates sha hash for ucsc-browser * Reverts to 0.1.9 * At ebi * Update meta.yaml * pins numpy to last know working version * Back to 0.25, no numpy pinning. * Remove git, pin python and numpy. Add build section. * Update meta.yaml * Update meta.yaml * Move to 0.4.20 without skeleton on provisional commit * Typo on executable name * Moves to release version and adds dependencies for converters * Update libstatgen to 1.0.14 (#12437) * Update arvados-python-client to 1.2.1 (#12438) * Update tirmite to 1.1.3 (#12435) * Bump metaquantome (#12449) * less stringent deps * bump build * pin goatools * test extra pins * bump metaquantome to 0.99.3 * Update ADAM to 0.25.0 (#12445) * Update: bcbio, bcbio-vm with viral QC, Docker fixes (#12453) * update rgi4.2.2 recipe (#12282) * update to enforce python3.6 and load card.json * remove lines from build.sh * update build number * make PR comment changes * add test to verify db is loaded * update build script * update build script * fix lint errors * fix linting errors * fix liniting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * revert test change * Add CRAN R package leapp. (#12428) * Bump DECIPHER to Bioconductor 3.7 (#12463) * Bump DECIPHER to Bioconductor 3.7 * Change r-rsqlite version dependency * Update meta.yaml * updated scVI to 0.2.3 (#12429) * Add recipe for PyAAVF 0.1.0 (#12451) * Add recipe for PyAAVF 0.1.0 * Fix linting error * seqkit 0.9.3 (#12455) * HTSeq - Pin numpy version (#12467) * update eigensoft to 7.2.1 (#12469) * Update scnic to 0.6.0 (#12436) * Update scnic to 0.6.0 * Work around fastspar insufficient armadillo pin * fix pin * GimmeMotifs 0.13.1 (#12471) * Bumped version to newest, with introspective text (#12461) * Update Segway 2.0.2 recipe to use older depedencies (#11803) * Update Segway 2.0.2 recipe to use older depedencies * Update maximum genomedata version supported * Update build number * Fix missing older dependency information * Update meta.yaml * updating dependencies for reparation_blast (#12443) * updating dependencies for reparation_blast * changed dependency of pysam * Added DropletUtils package (#12448) * Create recipe for SVIM (#12272) * add svim recipe * fix bugs in svim recipe * replace source file * remove license file * Lowercase biopython * upgrade to svim 0.4.1 * add GPL LICENSE file, allow python 3.6.* patch releases, add minimap2 dependency * fix python version * try to fix lint error * replace "skip: True" with "noarch: python" * Update bioconductor-biocgenerics (#12477) * [X] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)). * [X] This PR updates an existing recipe. * [ ] This PR does something else (explain below). * Irida sistr results 0.6.0 (#12478) * Update irida-sistr-results to 0.6.0 * Fixed dependency string * Adding recipe for clinvar-tsv v0.1.0. (#12481) * no fixed boost version (#12483) * New recipe: pysradb (#12470) * Pyseer 1.2.0 (#12444) * Update pyseer to 1.1.2 * Update pyseer to 1.2.0 * Update pyseer to 1.2.0 Update pyseer to 1.2.0 Update pyseer to 1.2.0 (fixed) * Final touches to pyseer 1.2.0 * Additional update to pyseer recipe * sentieon: minor version bump to 201808.01 (#12480) * adding java to mutations recipe (#12485) * Update ncrf to 1.00.06 (#12369) * Update ncrf to 1.00.06 * Update test string * Bump umitools (#12486) * Mob suite version 1.4.9 no arch build number 2 (#12479) * Updated to version 1.4.9 * Downgraded to python >= 3.4 to accomodate lowandrew request * new build * no arch commit for python 3.4 * no arch conda package version * Set build number to 1 * Update r-goeveg to 0.4.2 (#12375) * Update r-goeveg to 0.4.2 * Add r-hmisc as dependency * Removes r-seurat-scripts from blacklisting (#12489) * Removes r-seurat-scripts from blacklisting * Unblacklist some non bioconductor packages * For VarDict-Java, install utility scripts. (#12488) * For VarDict-Java, install utility scripts. Utility script that were previously only shipped with VarDict are not part of VarDict-Java as well, making installation of both packages unnecessary. * Bump build. * Improve variable name. * Make vardict depend on vardict-java for utility scripts. * Pin compatible numpy for older HTSEQ versions (#12490) * Pin compatible numpy for older HTSEQ versions This is required to keep older versions of HTSEQ functional * HTSeq - update old versions to build properly with new build system * HTSeq 0.6.1 - Increment build number * add recipe for r-epic (#12473) * Add new recipe - RVTESTS (#12465) * Add rvtests * Update pre-req * Update meta.yaml * Update build.sh * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Create LICENSE * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh * Create run_test.sh * Update meta.yaml * Delete run_test.sh * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Adding recipe for var-agg v0.1.0 (#12482) * Adding recipe for var-agg v0.1.0 * runtime deps do have run-exports defined * move rust into the host section * Adding dependency to clangdev * Adding var-agg v0.1.1. (#12495) * [WIP] Salmon v0.12.0 --- try to fix OSX build for real (#12441) Salmon v0.12.0 --- version bump and fix OSX build * Considerable updates in terms of features and fixes (check release notes). * Fix OSX build that would compile, but segfault in quant (but only when built on "old" OSX). * Performancean alytics (#12498) * Add bioconductor package RNASeqR * Add performanceanalytics * Performancean alytics (#12499) * Add bioconductor package RNASeqR * Add performanceanalytics * Move recipes/r-performanceanalytics and add r-rafalib * Move r-performanceanalytics/ to recipes * Update recipes/r-performanceanalytics * Update r-rafalib * Remove recipes/r-performanceanalytics/bld.bat * Remove recipes/r-performanceanalytics * Update r-performanceanalytics/ * Update r-performanceanalytics/ * Add r-performanceanalytics/ * remove r-performanceanalytics * Add performanceanalytics * Remove r-performanceanalytics * Update Picard to 2.18.20. (#12501) * Update vsearch to 2.10.0. (#12504) * Update Purge Haplotigs to v1.0.4 (#12497) * Update duphold to 0.1.1 (#12516) * Update starfish to 0.0.31 (#12515) * Update perl-term-app-roles to 0.02 (#12512) * Update perl-dbd-sqlite to 1.60 (#12511) * Update perl-json to 4.00 (#12509) * Update kipoi to 0.6.5 (#12508) * Update illumina-interop to 1.1.8 (#12507) * Update beagle-lib to 3.1.2 (#12523) * Update pysradb to 0.3.0 (#12522) * Update bioconda-utils to 0.15.2 (#12525) * Update perl-json-pp to 4.0 (#12524) * Update perl-term-table to 0.013 (#12529) * Update abyss to 2.1.5 (#12528) * Update perl-test2-suite to 0.000117 (#12527) * Update wtforms-alchemy to 0.16.8 (#12505) * Update perl-carp-clan to 6.07 (#12518) * Update perl-date-manip to 6.75 (#12519) * Update to bioconductor 3.8, use gcc7 in bulk * Should have double checked the circleci yaml * fix a few shell files * copy over bulk change
dpryan79
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Feb 23, 2019
* update mzr as a test
* Begin building for R 3.5.1 (#11252)
* Bump everything for R 3.5.1
* Fix most of the linting issues
* Update blacklist
* Revert "Fix most of the linting issues"
This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5.
* should_not_use_fn
* More fixes
* Fix incorrect yaml
* Should really fix the linting blacklist stuff
* Fix many recipes
* Fix some linting
* Fix r-wicket
* Update derfinder
* Pin to a given bioconductor release.
* Add missing packages
* Restore identifiers to bioconductor packages
* Restore extra information to R packages
* Update R bulk (#11283)
* fixed incorrect doi of publication (#11175)
* Added recipe for kinSimRiboswitch (#10838)
Added recipe for kinSimRiboswitch, a pipeline for simulating the folding
kinetics of RNA switches.
* update multiqc-bcbio (#11187)
* Add recipe for PopDel (#11181)
* Add recipe for PopDel
* Add clang and clangxx to build config
* update seqbuster (#11190)
* update seqbuster
* fix build
* fix test
* Update pyseer to 1.1.2 (#11172)
* bump sourmash (#11197)
* Update BASIC to v1.4.1 (#11195)
* Update BASIC to v1.4.1
* Trigger circleci
* Fix build number
* Update nf-core-1.2 (#11191)
* Update nf-core-1.2
* Update build script
* Update to InterMine 1.11.0 (#11182)
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Add tinyfasta-0.1.0 (#11177)
* Add tinyfasta
* Update build script
* Fix structure of build section
* Bumping snippy (#11198)
* Remove older version
* Bump snippy
* VEP: bump major version (#11201)
* VEP: bump major version
* VEP: bumped plugin major version
* VEP: update plugin install
Download and install all plugin modules, instead of just a selection
* Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200)
* Update: PureCN to latest devel (1.11.13); wrapper scripts
PureCN development (https://github.com/lima1/PureCN) has several
improvements over the BioC 3.6 release for handling multiple VCF input
types, and is back compatible with R 3.4.1 so still builds cleanly
with two new dependencies.
Also exposes PureCN wrapper scripts for running from the command line.
Prefixes ambiguous scripts with PureCN_.
* Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet
* add cassiopee release 1.0.9 (#11168)
* add cassiopee release 1.0.9
* update to conda build 3
* remove old version backup and use sha256 for source
* Bump abeona version to 0.26.0 (#11202)
* Bump abeona version to 0.24.0
* Bump abeona version to 0.26.0
* Update LexMapr to v0.1.2 (#11192)
* Update LexMapr to v0.1.2
* Add rdflib dep
* Update svtyper to 0.7.0 (#11196)
* Update svtyper to 0.7.0
* Add recipe for perl-gtdbtk (#11194)
* Add recipe for perl-gtdbtk
* New recipe for RFMix (#11205)
* New recipe for RFMix
* updated version number information
* updated version number information
* updated version number information
* initial purge_haplotigs commit (#11049)
* initial purge_haplotigs commit
* bioconda revisions, updating test commands to run the pipeline on the test dataset
* rolling back test commands
* Add recipe for fsm-lite (#11209)
* Add recipe for fsm-lite
* Add prefix to make
* Remove v from version string
* Updated reparation_blast to version v.1.0.7 (#11210)
* Update sambamba to 0.6.8 (#11212)
* Bump sambamba to 0.6.8
* It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified.
* Set some environment variables
* The compiled binary is in a different place now
* ldc provides some libraries that are linked against.
* mtbseq: update recipe (#11110)
* changed download location/add test
* remove test
* Confindr (#11217)
* Update confindr to 0.4.2
* Fix typo in specifying version of pysam
* Update Genenotebook to v0.1.4 (#11218)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* updating to 0.1.3 (#11221)
* sartools1.6.6 (#11222)
* Perl bio automatedannotation (#11216)
* Initial recipe for Bio-AutomatedAnnotation
* Change URL
* Run cpanm tests
* Temporarily set HOME
* Use cpan version instead
* Add more depencencies
* Set bioperl version
* unset bioperl version, add bioperl-run
* New release including version in modules
* Remove comments
* build -> host
* Upgrade r-biodb to v1.1.2. (#11213)
* Upgrade r-biodb to v1.1.2.
* Remove old versions of r-biodb.
* Comment out libgfortran.
* PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215)
* PeptideShaker: updated to version 1.16.30
- Bugfix: HOME was still being used when folder with customised reports was specified.
- Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line.
* SearchGUI: updated to version 3.3.5.
- BUG FIX: Cleanup of the temp path options when used as options for the other command lines.
- FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2.
- LIBRARY UPDATE: Updated utilities to version 4.12.8.
* Update meta.yaml (#11227)
* Svtools 0.4.0 (#11208)
* Remove directories for old svtools versions
* Update svtools to v0.4.0
* Move build number back to 0
* Anvio 52 (#11230)
* Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software.
* Remove cgat-scripts from blacklist. (#11228)
* Add new formula: bazam 1.0.1 (#11229)
* Update gatk4 to 4.0.10.0 (#11224)
* Add recipe for gtdbtk 0.1.3 (#11211)
* Add recipe for gtdbtk
* Added initial htstream recipe (#11113)
* HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data.
* DeepTools 3.1.3 (#11226)
* PacBio: Update `pbmm2` to version 0.10.0 (#11225)
* fastqc: update to version 0.11.8 (#11214)
* fastqc: update to version 0.11.8
* Update meta.yaml
* Phame (#11223)
* mac recipe and added bioperl
* changing bill number
* added no osx
* adding new version
* removed separate recipe for mac, dont need it
* now running same recipe for mac and linux
* fixed the way fasttrees version was being parsed
* minor change test
* adding detailed description
* restaging the build number
* new version
* Make sure to use bioperl and perl 5.26
* Updated ngs-bits to version 2018_10 (#11235)
* PacBio: Update `pbsv2` to version 2.0.2 (#11236)
* Update VSEARCH to 2.8.5 (#11239)
* Fix shorah recipe and remove from blacklist. (#11241)
* Fix shorah recipe and remove from blacklist.
* Fix blas variant.
* Remove imports from tests.
* unicycler 0.4.7 (#11240)
* unicycler 0.4.7
* unicycler: Work around ValueError: invalid
Unicycler thinks the terminal has 0 columns and produces this error:
File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks
raise ValueError("invalid width %r (must be > 0)" % self.width)
ValueError: invalid width -5 (must be > 0)
* Octopus: update to 0.5.1-beta (#11244)
* New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247)
- PURPLE SV and heterogeneity caller for somatic tumor/normal samples.
- VarDictJava -- 1.5.6 release with fixes for SV calling
- PureCN -- add signature dependency and update with fixes for test
samples.
* Dinucleotide patterns analysis tools v1.0 (#11245)
* Dinucleotide patterns analysis tools v1.0
* Lets try it, it seems to work locally for me.
* Enable SpoTyping_plot.r (#11248)
* rerun again (#11233)
* rerun again
* Update meta.yaml
* Delete build.sh
* Update segway dependency optbuild to 0.2 (#10459)
* Update segway dependency optbuild to 0.2
* Update build and architecture requirements for optbuild 0.2
* Add six as a dependency to the optbuild recipe
* Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249)
* Add prefix dnp- to the package names
* Update build.sh
* Update build.sh
* Bump beast version to 1.10.2 (#11250)
* add maxquant (#11253)
* add mayquant
* relax tests
* PacBio: Update `pbmm2` to version 0.10.1 (#11256)
* PacBio: Update `pbmm2` to version 0.10.1-1 (#11257)
* remove xsv recipe (#11259)
* add blast dependency (#11258)
* Added riborex recipe (#11251)
* Added riborex recipe
* Relaxed version constraints
* Pinned r-core for fdr tools
* fixed the r-base stuff upstream
* Update meta.yaml
* fix graphprot (#11234)
* increase build number
* remove from blacklist
* use cxx instead of c
* move coreutoils to build section
* set additional paths
* patch makefile
* blind try
* update patch
* explicitely copy from src_dir
* update deprecated prefix variable
* Revert "update deprecated prefix variable"
This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d.
* update deprecated prefix variable
* try moving to host section
* Bump mash (#11264)
* Add fmlrc (#11265)
* Add fmlrc
* add doi
* PacBio: Update pb-falcon to 0.2.4. (#11266)
* Add kopt recipe (#11269)
* Genomepy 0.5.2 (#11267)
* release 0.5.2 of genomepy
* trigger new build
* remove genomepy from blacklist
* locale for osx
* updated locale test
* PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275)
* Update mmseqs2 recipe to new release 6-f5a1c (#11272)
* Update yacrd to version 0.4.1 (#11273)
* Add scprep (#11270)
* Add scprep
* All of these should not be needed as host dep
* Metawrap preqs2 (#11242)
* fixed issues
* fixed issues
* added tests
* fixed tab
* gemma 0.98 (#11254)
* gemma 0.98
* gemma 0.98
Leave gsl and zlib out of runtime dependencies
* Add DCA recipe (#11274)
* Add DCA recipe
* add noarch and doi
* remove skip
* Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib
* Various fixes for bulk and trigger a rebuild (#11313)
* Various fixes, at least 4 packages (and their dependencies) should still fail (#11320)
* A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336)
* Fix various recipes (#11354)
* Fix various recipes
* Fix more recipes
* Various CRAN package fixes, since they all lack license files (#11372)
* Various CRAN package fixes, since they all lack license files
* Fix the r-dartr recipe
* There is a light at the end of the tunnel (#11381)
* There is a light at the end of the tunnel
* Licenses no longer exist
* [BULK] Fixes for R/Bioconductor packages (#11406)
* Require `r-base >=3.5` for some packages
* Fix various CRAN packages lacking license file
* Add missing libnetcdf requirement to bioconductor-mzr
* Remove r-alakazam (moved to conda-forge)
Fix linting issue:
```
recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating
```
* [BULK] Many R 3.5 only packages (#11410)
* [BULK] Bulk update 191018b (#11419)
* update mzr as a test
* Begin building for R 3.5.1 (#11252)
* Bump everything for R 3.5.1
* Fix most of the linting issues
* Update blacklist
* Revert "Fix most of the linting issues"
This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5.
* should_not_use_fn
* More fixes
* Fix incorrect yaml
* Should really fix the linting blacklist stuff
* Fix many recipes
* Fix some linting
* Fix r-wicket
* Update derfinder
* Pin to a given bioconductor release.
* Add missing packages
* Restore identifiers to bioconductor packages
* Restore extra information to R packages
* Update R bulk (#11283)
* fixed incorrect doi of publication (#11175)
* Added recipe for kinSimRiboswitch (#10838)
Added recipe for kinSimRiboswitch, a pipeline for simulating the folding
kinetics of RNA switches.
* update multiqc-bcbio (#11187)
* Add recipe for PopDel (#11181)
* Add recipe for PopDel
* Add clang and clangxx to build config
* update seqbuster (#11190)
* update seqbuster
* fix build
* fix test
* Update pyseer to 1.1.2 (#11172)
* bump sourmash (#11197)
* Update BASIC to v1.4.1 (#11195)
* Update BASIC to v1.4.1
* Trigger circleci
* Fix build number
* Update nf-core-1.2 (#11191)
* Update nf-core-1.2
* Update build script
* Update to InterMine 1.11.0 (#11182)
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Add tinyfasta-0.1.0 (#11177)
* Add tinyfasta
* Update build script
* Fix structure of build section
* Bumping snippy (#11198)
* Remove older version
* Bump snippy
* VEP: bump major version (#11201)
* VEP: bump major version
* VEP: bumped plugin major version
* VEP: update plugin install
Download and install all plugin modules, instead of just a selection
* Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200)
* Update: PureCN to latest devel (1.11.13); wrapper scripts
PureCN development (https://github.com/lima1/PureCN) has several
improvements over the BioC 3.6 release for handling multiple VCF input
types, and is back compatible with R 3.4.1 so still builds cleanly
with two new dependencies.
Also exposes PureCN wrapper scripts for running from the command line.
Prefixes ambiguous scripts with PureCN_.
* Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet
* add cassiopee release 1.0.9 (#11168)
* add cassiopee release 1.0.9
* update to conda build 3
* remove old version backup and use sha256 for source
* Bump abeona version to 0.26.0 (#11202)
* Bump abeona version to 0.24.0
* Bump abeona version to 0.26.0
* Update LexMapr to v0.1.2 (#11192)
* Update LexMapr to v0.1.2
* Add rdflib dep
* Update svtyper to 0.7.0 (#11196)
* Update svtyper to 0.7.0
* Add recipe for perl-gtdbtk (#11194)
* Add recipe for perl-gtdbtk
* New recipe for RFMix (#11205)
* New recipe for RFMix
* updated version number information
* updated version number information
* updated version number information
* initial purge_haplotigs commit (#11049)
* initial purge_haplotigs commit
* bioconda revisions, updating test commands to run the pipeline on the test dataset
* rolling back test commands
* Add recipe for fsm-lite (#11209)
* Add recipe for fsm-lite
* Add prefix to make
* Remove v from version string
* Updated reparation_blast to version v.1.0.7 (#11210)
* Update sambamba to 0.6.8 (#11212)
* Bump sambamba to 0.6.8
* It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified.
* Set some environment variables
* The compiled binary is in a different place now
* ldc provides some libraries that are linked against.
* mtbseq: update recipe (#11110)
* changed download location/add test
* remove test
* Confindr (#11217)
* Update confindr to 0.4.2
* Fix typo in specifying version of pysam
* Update Genenotebook to v0.1.4 (#11218)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* updating to 0.1.3 (#11221)
* sartools1.6.6 (#11222)
* Perl bio automatedannotation (#11216)
* Initial recipe for Bio-AutomatedAnnotation
* Change URL
* Run cpanm tests
* Temporarily set HOME
* Use cpan version instead
* Add more depencencies
* Set bioperl version
* unset bioperl version, add bioperl-run
* New release including version in modules
* Remove comments
* build -> host
* Upgrade r-biodb to v1.1.2. (#11213)
* Upgrade r-biodb to v1.1.2.
* Remove old versions of r-biodb.
* Comment out libgfortran.
* PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215)
* PeptideShaker: updated to version 1.16.30
- Bugfix: HOME was still being used when folder with customised reports was specified.
- Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line.
* SearchGUI: updated to version 3.3.5.
- BUG FIX: Cleanup of the temp path options when used as options for the other command lines.
- FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2.
- LIBRARY UPDATE: Updated utilities to version 4.12.8.
* Update meta.yaml (#11227)
* Svtools 0.4.0 (#11208)
* Remove directories for old svtools versions
* Update svtools to v0.4.0
* Move build number back to 0
* Anvio 52 (#11230)
* Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software.
* Remove cgat-scripts from blacklist. (#11228)
* Add new formula: bazam 1.0.1 (#11229)
* Update gatk4 to 4.0.10.0 (#11224)
* Add recipe for gtdbtk 0.1.3 (#11211)
* Add recipe for gtdbtk
* Added initial htstream recipe (#11113)
* HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data.
* DeepTools 3.1.3 (#11226)
* PacBio: Update `pbmm2` to version 0.10.0 (#11225)
* fastqc: update to version 0.11.8 (#11214)
* fastqc: update to version 0.11.8
* Update meta.yaml
* Phame (#11223)
* mac recipe and added bioperl
* changing bill number
* added no osx
* adding new version
* removed separate recipe for mac, dont need it
* now running same recipe for mac and linux
* fixed the way fasttrees version was being parsed
* minor change test
* adding detailed description
* restaging the build number
* new version
* Make sure to use bioperl and perl 5.26
* Updated ngs-bits to version 2018_10 (#11235)
* PacBio: Update `pbsv2` to version 2.0.2 (#11236)
* Update VSEARCH to 2.8.5 (#11239)
* Fix shorah recipe and remove from blacklist. (#11241)
* Fix shorah recipe and remove from blacklist.
* Fix blas variant.
* Remove imports from tests.
* unicycler 0.4.7 (#11240)
* unicycler 0.4.7
* unicycler: Work around ValueError: invalid
Unicycler thinks the terminal has 0 columns and produces this error:
File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks
raise ValueError("invalid width %r (must be > 0)" % self.width)
ValueError: invalid width -5 (must be > 0)
* Octopus: update to 0.5.1-beta (#11244)
* New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247)
- PURPLE SV and heterogeneity caller for somatic tumor/normal samples.
- VarDictJava -- 1.5.6 release with fixes for SV calling
- PureCN -- add signature dependency and update with fixes for test
samples.
* Dinucleotide patterns analysis tools v1.0 (#11245)
* Dinucleotide patterns analysis tools v1.0
* Lets try it, it seems to work locally for me.
* Enable SpoTyping_plot.r (#11248)
* rerun again (#11233)
* rerun again
* Update meta.yaml
* Delete build.sh
* Update segway dependency optbuild to 0.2 (#10459)
* Update segway dependency optbuild to 0.2
* Update build and architecture requirements for optbuild 0.2
* Add six as a dependency to the optbuild recipe
* Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249)
* Add prefix dnp- to the package names
* Update build.sh
* Update build.sh
* Bump beast version to 1.10.2 (#11250)
* add maxquant (#11253)
* add mayquant
* relax tests
* PacBio: Update `pbmm2` to version 0.10.1 (#11256)
* PacBio: Update `pbmm2` to version 0.10.1-1 (#11257)
* remove xsv recipe (#11259)
* add blast dependency (#11258)
* Added riborex recipe (#11251)
* Added riborex recipe
* Relaxed version constraints
* Pinned r-core for fdr tools
* fixed the r-base stuff upstream
* Update meta.yaml
* fix graphprot (#11234)
* increase build number
* remove from blacklist
* use cxx instead of c
* move coreutoils to build section
* set additional paths
* patch makefile
* blind try
* update patch
* explicitely copy from src_dir
* update deprecated prefix variable
* Revert "update deprecated prefix variable"
This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d.
* update deprecated prefix variable
* try moving to host section
* Bump mash (#11264)
* Add fmlrc (#11265)
* Add fmlrc
* add doi
* PacBio: Update pb-falcon to 0.2.4. (#11266)
* Add kopt recipe (#11269)
* Genomepy 0.5.2 (#11267)
* release 0.5.2 of genomepy
* trigger new build
* remove genomepy from blacklist
* locale for osx
* updated locale test
* PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275)
* Update mmseqs2 recipe to new release 6-f5a1c (#11272)
* Update yacrd to version 0.4.1 (#11273)
* Add scprep (#11270)
* Add scprep
* All of these should not be needed as host dep
* Metawrap preqs2 (#11242)
* fixed issues
* fixed issues
* added tests
* fixed tab
* gemma 0.98 (#11254)
* gemma 0.98
* gemma 0.98
Leave gsl and zlib out of runtime dependencies
* Add DCA recipe (#11274)
* Add DCA recipe
* add noarch and doi
* remove skip
* Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib
* Various fixes for bulk and trigger a rebuild (#11313)
* Various fixes, at least 4 packages (and their dependencies) should still fail (#11320)
* A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336)
* Fix various recipes (#11354)
* Fix various recipes
* Fix more recipes
* Various CRAN package fixes, since they all lack license files (#11372)
* Various CRAN package fixes, since they all lack license files
* Fix the r-dartr recipe
* There is a light at the end of the tunnel (#11381)
* There is a light at the end of the tunnel
* Licenses no longer exist
* [BULK] Fixes for R/Bioconductor packages (#11406)
* Require `r-base >=3.5` for some packages
* Fix various CRAN packages lacking license file
* Add missing libnetcdf requirement to bioconductor-mzr
* Remove r-alakazam (moved to conda-forge)
Fix linting issue:
```
recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating
```
* [BULK] Many R 3.5 only packages (#11410)
* Update pinning to R>=3.5 and a few runtime dependencies.
* CSAW is R 3.5 only
* Packages using beachmat are 3.5 only
* Packages using bioconductor-singlecellexperiment are R 3.5 only
* [BULK] Don't use r-base >=3.5, use a conda_build_config.yaml instead (#11452)
* Don't use r-base >=3.5, use a conda_build_config.yaml instead
* blacklist r-phangorn
* Update variancepartition
* R 3.5 for packages requiring singlecellexperiment
* Update a few packages
* Update a number of recipes (#11482)
* Update ensemblVEP and derfinder (#11504)
* Bulk update 251018 (#11577)
* [BULK] various package updates
* blacklist bioconductor-mzr
* A couple tweaks
* [BULK] Update 261018 (#11611)
* Apparently the r-rgeos bit works properly now.
* Add tissueenrich and try to fix scpipe on Linux
* A meaningless change just to trigger an update in bulk. (#11618)
* [BULK] update 271018 (#11628)
* Bump bioconductor-esetvis
* Fix yaqcaffy
* Fix more
* Another R 3.5 recipe
* [BULK] update 281018 (#11689)
* Add some files
* Fix arrayexpress
* Fix another 2
* Blacklist a bunch of bioconductor recipes that aren't likely to get built for a variety of reasons (mostly due to mzR). (#11697)
* Update blacklist (#11706)
* [BULK] fix bioconductor-tissueenrich (#11720)
* taxonkit 0.2.5 (#11318)
* Update csvtk (#11319)
* taxonkit 0.2.5
* csvtk 0.15.0
* bumping GROOT to 0.8.1 (#11323)
* HiCMatrix version 3 (#11322)
* Correcting dependencies
* Version 3 of HiCMatrix, the October release
* Update confindr to 0.4.3 (#11330)
* Drop-seq_tools: Version 2.0.0 (#11326)
* Update meta.yaml
* Update build.sh
some tool names changed to fit Camel case
* Update motus to build only for python3 (#11331)
* Update fpa to 0.2 version (#11333)
* update taxonkit to 0.3.0 (#11339)
* ntcard 1.1.0 (#11338)
* Update rgi (#11335)
* first commit
* update dependencies list
* change source to github
* change build number
* testing circleci
* update meta and build
* fix build
* move build script into meta
* remove older recipes
* line fix in bootstrap.py
* change python & matplotlib versions; add build.sh file
* add preprocessing selector to skip python 2.7
* move build script into meta.yaml
* Revert "line fix in bootstrap.py"
This reverts commit 5ac1ecd0142a5cfdfc8499c5b6ef4e1f629cd046.
* Update gmap to version 2018-07-04. (#11332)
MAX_READLENGTH environment variable has been disused since 2016-08-16.
* Upgrade r-biodb to 1.2.0a. (#11341)
* Upgrade r-biodb to 1.2.0a.
* Update meta.yaml
* Updated ont-tombo to version 1.5. (#11329)
* Updated ont-tombo to version 1.5.
* Updated with actual github release version hash.
* remove graphicsmagick (#11342)
* Build kraken2 for osx (#11343)
* First try for a bcalm recipes (#11344)
* New: cgpbigwig (BigWig manipulation); Update: bcbio (#11347)
- cgpbigwig (https://github.com/cancerit/cgpBigWig) provides bigwig
generation and manipulation command line tools including bam to bigwig
conversion.
- bcbio: fixes for QC on variants and peddy for CWL runs
* Try avoid some dependancy (#11349)
* Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8 (#11348)
* Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8
Also add about:home .
* Workaround https://github.com/conda-forge/bison-feedstock/issues/7
* Better bcalm recipes (#11350)
* Try avoid some dependancy
* Correct mess in build number, sorry
* R biodb (#11351)
* rebuild r-biodb
* trigger build
* Add recipe for pypairs (#11356)
* Update smoove to 0.2.1. (#11360)
* Update duphold to 0.0.9. (#11359)
* Update goleft to 0.2.0 (#11361)
* Bump slicedimage to 1.0.0 (#11362)
* Bump slicedimage to 1.0.1 (#11365)
* Added new versions for biopet-sampleconfig (#11268)
* perl-velvetoptimiser: update to 2.2.6 (#11369)
* update to 2.2.6
* remove unneeded patch
* Scanpy upgrade (#11371)
* Bump version
* Upgrade Scanpy
* Bump starfish to 0.0.25 (#11370)
* bumping groot to 0.8.2 (#11374)
* vep: bump subversion (#11367)
* Updated Krocus 1.0.1 (#11355)
* Add tiptoft
* Fix meta.yaml for tiptoft
* Add build script
* Updated krocus 1.0.1
* Add tiptoft 0.1.4 (#11352)
* Add tiptoft
* Fix meta.yaml for tiptoft
* Add build script
* Kodoja v0.0.9 (#11373)
* Add recipe for seer (#11263)
* Add recipe for seer
* lets try this
* Add newer compiler
* Using boost-cpp
* messed up version string
* Attempt building boost
* Use c++11 in boost
* Use python for boost install
* Correct python version spec
* try with different python version
* Fix b2 command
* Fix popd command
* build and link boost program options statically
* Fix tests
* Match dependency order
* Link openblas instead of blas
* Forcing rebuild with openblas
* Don't use armadillo wrapper
* Making review changes. Also trying original tests
* Previous tests were correct
* Add recipe for the translate-gard npm package version 1.0.3 (#11364)
* Fix umi tools (#11376)
umi_tools: clean up dependencies
* add support tools to PATH (#11379)
* Bump to v2.2.1 (#11380)
* Bump starfish to 0.0.26 (#11378)
* Update fpa to 0.3 (#11375)
* Update fpa to 0.3
* Correct error in sha256
* Reset build number
* Update trial to 2.5.5 (#11386)
* Update: bioconductor-titancna; 1.19.1 with hg38 support (#11388)
* Update: bioconductor-titancna; 1.19.1 with hg38 support
* Pin to R 3.4 to avoid pulling in 3.3 and 3.5 during mulled
* Add r-polysat version 1.7-3 (#11384)
* Update biomart version so that compatible with r351 (#11366)
* Update biomart version so that compatible with r351
* Update meta.yaml
reset build number as per https://bioconda.github.io/guidelines.html#buildnum
* Update entrez-direct to 10.0.20180927. (#11387)
* Added recipe for SonicParanoid 1.0.13 (#11271)
* Added recipe for SonicParanoid 1.0.13
* removed 'x.x' for numpy, added basic test
* fixed linter related errors
* compiler set to cxx and added host section (same build error!)
* removed host section
* moved numpy and cython to host section; restored build: noarch: python; added LICENSE.md
* removed build: noarch
* added build and extra sections
* set build number to 0; removed skip build; added python3 minimum version; added test for all executables.
* restored sh python module as requirement
* added Make to run; updated release to latest commit
* remove c compiler from meta.yaml
* modified build.sh to compile source codel added make in build section
* updated to latest commit
* updated to latest version with make included in setup.py
* reverted build.sh to the simplest version (python setup.py install)
* Add perl-json to build requirements to allow meme-chip to run to completion. Change meme-chip to use dreme-py3 instead of dreme if building with python 3. (#11389)
* Bump IgBLAST to 1.9.0 (#11393)
Bump IgBLAST to 1.9.0
Re-package the binary version this time. There are problems building the
source version when the configure script reaches this step:
"trying to build the NCBI SRA/VDB Toolkit from GitHub"
The previous problem about the binaries linking against libbz2.so, for
which we had no conda package, is now solved.
Also, this saves about 45 minutes compilation time.
* Add consan (#11395)
* Add consan
* Skip osx
* Update: vardict, vardict-java 1.5.7 (#11394)
* Update: vardict, vardict-java 1.5.7
Latest vardict-java release and corresponding vardict with bug fixes
after testing with 1.5.6
* Reduce test output to try and fix build problems
* Experiment 2 for build problems: remove r-base from run
* Experiment 3 for build problems: add r-base in host
* update recipe for 3.9.1 (#11397)
* evofold2 (#11396)
* evofold2
* wrapper
* Update meta.yaml
* minor
* Update rnastructure to 6.1. (#11400)
* Ctat mut (#11401)
* updating version number
* correct URL
* proper hash
* Revert "Ctat mut (#11401)" (#11402)
This reverts commit 6db10ac7ffd7abaf8fbf1762b7ea6c63b2585fe0.
* update version (#11403)
* any2fasta 0.4.2 (new formula) (#11407)
* W4mclassfilter v0.98.9 (#11385)
* Added files to build version 0.98.9
* Update meta.yaml
* Update meta.yaml
* updated SonicParanoid recipe to version 1.0.14 (#11409)
* updated SonicParanoid recipe to version 1.0.14
* Update to version 1.0.2 of PopDel (#11398)
* Update to version 1.0.2 of PopDel
Update to version 1.0.2.
* Reset build number to 0
* PacBio: require Meson 0.48.1 for all recipes (#11090)
* Meson 0.47 inserted duplicate RPATHs in
macOS binaries, causing `install_name_tool`
failures when installing the package.
Requiring 0.48.1 ensures we do not run into
these issues anymore in the future.
* rebuild with latest openmpi (#11411)
* Remove kfoots from the blacklist (#11416)
* Update gseapy to 0.9.7 (#11417)
* Update gseapy to 0.9.7
* remove noarch
* Add SC3 as dependency (#11427)
* Add recipe for r-poppr (#11418)
* Update knitr version because of Issue: https://github.com/rstudio/rmarkdown/pull/1271 (#11412)
* Update IQ-TREE to 1.6.7.1 (#11429)
* Update IQ-TREE to 1.6.7.1
* Change build number
* Update: r-deconstructsigs with fixes for hg38 (#11431)
The 1.8.0 release, from 2016, has some issues with hg38 and other
custom genomes that are fixed in development (raerose01/deconstructSigs#27).
There hasn't been a new release pushed so this rolls these into a new
sub-version and makes them available.
* Update entrez-direct to 10.2.20181018. (#11432)
* Add assembly-scan recipe (#11425)
* remove python 2.7 skip (#11424)
Preparation for rnaQUAST
* Add fastq-scan recipe (#11415)
* Add patch to fix racon/rampler path in racon_wrapper. (#11434)
Fixes #11405.
* meme rebuild (#11433)
* Update nanocomp to 0.23.1 (#11436)
* Update nanocomp to 0.23.1
* remove noarch
* Update abricate to 0.8.10 (#11446)
* Update angsd to 0.923 (#11445)
* Update alfred to 0.1.13 (#11444)
* Update alfred to 0.1.13
* Try w/o patch
* Update antarna to 2.0.6 (#11442)
* Update admixtools to 5.1 (#11443)
* Update admixtools to 5.1
* Let makefile choose which bins to install
* Update alignstats to 0.5 (#11441)
* Update xatlas to 0.2.1 (#11437)
* r-gpca (#11428)
* r-gpca
* r-gpca recipe
* Update meta.yaml
* Removed All Comments
* gseapy bump version 0.9.8 (#11440)
* gseapy bump version 0.9.8
* version
* titancna: fix for hg38, remove conda build hacks (#11447)
* titancna: fix for hg38, remove conda build hacks
* Re-add r-base 3.4 pin to avoid 3.5 errors
* Hmmlearn older version (#11450)
* Adding pygtftk
* removed pygtftk from master
* add older version of hmmlearn
* Add card_trick (#11451)
* Add card_trick
* Restrict to py3
* Update checkm-genome to 1.0.12 (#11455)
* Bump drep (#11457)
* Update squid to 1.5 (#11466)
* Update ncbi-ngs-sdk to 2.9.3 (#11467)
* elprep: bumped major version (#11414)
* elprep: bumped major version
* fixed hash
* fix download link, fixed licence
* fixed tests
* skip osx build
* FRED2 as a conda package (#11469)
* Attempt to get FRED2 as a conda package
* SHA update
* 99 little bugs in the code
* Fix things Björn mentioned
* add rnaQUAST recipe (#11470)
* Update bioconda-utils to 0.14.9 (#11454)
* Rapidup (#11474)
* Update to v0.7
* Update Buildnumber
* rapid: update to v0.6
* rapid: update to v0.6
* update grid (#11478)
* Adding biobb_model recipe (#11472)
* Updated wtdbg to v2.1 (#11486)
* update stream to 0.2.6 (#11483)
* update stream to 0.2.2
* update stream to 0.2.3
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.5
* update stream to 0.2.6
* Update meta.yaml (#11487)
* Update connectome-workbench to 1.3.2 (#11468)
Now needs QT 5.7
* Update deblur to 1.1.0 (#11500)
* Update domclust to 1.2.8 (#11498)
* WisecondorX: bump version (#11501)
* Bump as GitHub wasn't working yesterday (#11502)
* Added recipe for Sequenza (#10367)
* Added recipe for Sequenza
* Removed fn entry in source section
* Trying with only one URL
* copynumber is a bioconductor package
* Added missing requirements section
* Removed mailing list address
* Added doi
* Added license_file
* Trying with different license_file path
* Fred2 bump (#11503)
* Bump as GitHub wasn't working yesterday
* Fix licence etc
* Scanpy scripts (#11413)
Doing squash and merge as requested by @nh3
* Bump version
* First implementation of scanpy-scripts bioconda recipe.
* fix path in build.sh
* Remove "noarch" flag as requested by bioconda recipe checklist
* Add a post install notice that post install test needs bats-core.
* Add more dependencies
* Skip building for python versions other than 3.6
* Target v0.0.2 which has non-ascii characters removed
* Lower version requirement for pandas and matplotlib to be the same as scanpy
* Requirement matplotlib>=3.0.0, declare noarch
* New: hmftools-cobalt; Update: hmftools-purple (#11507)
- hmftools-cobalt: Add latest version of PURPLE associated read counter,
COBALT, with support for hg38.
- hmftools-purple: PURPLE release with hg38 support.
* Update Picard to 2.18.15. (#11505)
* Genenotebook (#11476)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* Update pinning (#11514)
* Bump build number for updated dependency (#11510)
* Bump build number for updated dependency
* Try adding r-base to host requirements
* Try adding other requirements to host
* Pin to R version
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Tweak dependency version syntax
* Pin R and package versions correctly
* PacBio: Update pbcore to 1.6.5 (#11513)
* Bump r seurat scripts version (#11292)
* Bump version
* Remove noarch
* Could wrongly quoted version be causing an issue?
* Tweak pinning to try and fix CI error
* seqcluster:fix UMI detection. (#11511)
* seqcluster:fix UMI detection.
* Fix dependency
* quast 5.0.1 (#11479)
* quast 5.0.1
* quast 5.0.1: remove third-party site packages from the distibution pack
* quast 5.0.1: skip Glimmer in test
* quast 5.0.1: joblib and simplejson dependencies added to meta.yaml (Setuptools downloading is disabled in conda build)
* quast 5.0.1: explicit joblib and simplejson dependencies removed (Setuptools downloading is disabled in conda build)
* quast 5.0.1: Python 2 and 3 compatible code in build.sh
* wcX bugfixes (#11508)
* wcX bugfixes
* fixed shasum
* Update fastspar to 0.0.7 (#11515)
* Update iqtree to 1.6.7.2 (#11525)
* Update illumina-interop to 1.1.6 (#11523)
* Update hapbin to 1.3.0 (#11522)
* Update hlama to 3.0.1 (#11520)
* Update gb_taxonomy_tools to 1.0.1 (#11519)
* Update gffcompare to 0.10.5 (#11517)
* Update fast5seek to 0.1.1 (#11516)
* Update deepbinner to 0.2.0 (#11499)
* Update deepbinner to 0.2.0
* Update meta.yaml
Try same fix as in #11240
* Update ncbi-vdb to 2.9.3 (#11550)
* Update mikado to 1.2.4 (#11549)
* Update perl-pcap to 3.5.2 (#11543)
* Update python-hyphy-python to 0.1.9 (#11545)
* Update mlst to 2.15.2 (#11547)
* Update perl-sanger-cgp-vcf to 2.2.1 (#11542)
* Update merfishtools to 1.5.0 (#11537)
* Update perl-sanger-cgp-vagrent to 3.3.3 (#11536)
* Update nonpareil to 3.3.3 (#11535)
* Update prophex to 0.1.1 (#11532)
* Update krakenuniq to 0.5.3 (#11527)
* Update novoplasty to 2.7.2 (#11530)
* Update minced to 0.3.2 (#11529)
* Update mapdamage2 to 2.0.8 (#11528)
* Update perl-sanger-cgp-allelecount to 4.0.0 (#11538)
* Update pyvolve to 0.9.0 (#11531)
* Genenotebook (#11512)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* add plek (#11554)
* Update pyimzml to 1.2.4 (#11534)
* Bump shovill (#11555)
* PacBio: Update minimum pbcore version (#11556)
* We want all users of PacBio tools to be able to
use our utilities with pbmm2 alignments.
* Add recipe for translate-gard v1.0.4 (#11557)
* bioconductor-rnaseqsamplesizedata (#11475)
* Adding Recipe for bioconductor-rnaseqsamplesizedata
* Updated metadata for RnaSeqSampleSizeData
* nextflow 18.10.1 (#11558)
* Update raxml to 8.2.12 (#11567)
* Update r-fgwas to 0.3.6 (#11566)
* Update rapid to 0.7 (#11565)
* Update r-spieceasi to 1.0.2 (#11564)
* Update rcorrector to 1.0.3.1 (#11562)
* Update quicktree to 2.4 (#11560)
* Update paladin to 1.4.4 (#11541)
* Update paladin to 1.4.4
* delete md5
* Update build.sh
* Update build.sh
* Fix and unblacklist Tadarida-D (#11568)
* Add recipe for rgt
* Fix and un-blacklist tadarida-d
* Remove RGT
* bumping groot (#11575)
* update pymzml (#11573)
* Add bioconductor-rnaseqsamplesize (#11559)
* Add bioconductor-rnaseqsamplesize
* Update recipe
* Fixing some URLs
* Update dependencies missing
* Update trumicount to 0.9.11 (#11576)
* Update ConFindr to 0.4.4 (#11578)
* Added new versions for biopet-scatterregions (#11572)
* Added new versions for biopet-bamstats (#11571)
* R ggbiplot (#11584)
* add R -e 'httr::set_config(httr::config(ssl_verifypeer = 0L)); install.packages(devtools, repos=http://mirrors.ebi.ac.uk/CRAN/); library(devtools); install_github(vqv/ggbiplot); library(ggbiplot)'
* add r-ggbiplot
* update meta.yaml
* update meta.yaml
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix errors
* fix errors number 1
* Update rebaler to 0.1.2 (#11563)
* Update rebaler to 0.1.2
* Remove fn
* bump graphclust (#11585)
* Update seqyclean to 1.10.09 (#11589)
* Update stringmlst to 0.5.1 (#11590)
* Update snp-dists to 0.6.2 (#11592)
* Update snippy to 4.3.3 (#11596)
* Update canu to 1.8 (#11600)
* Update starfish to 0.0.27 (#11599)
* Update womtool to 36 (#11594)
* Update telseq to 0.0.2 (#11598)
* Update snp-sites to 2.4.1 (#11588)
* Added recipe for pydemult: Streamed and parallel demultiplexing of fastq files (#11471)
* Added recipe for pydemult
* Bumped version in favor of py3.5
* bump vcf2db to latest commit (#11601)
* bump vcf2db to latest commit
* fix shasum
* Fixing source url
* Update: TitanCNA; hg38 cytoband support and fix for normalization (#11604)
* megan (#11046)
* megan6: initial commit
* megan6: intermediate commit
* megan: made tests work
* megan: doc improvement
* megan: added osx dmg file
* megan: add java to build requirements
* megan: removed new line
* megan: removed osx sources
* Update meta.yaml
* bumping hulk (#11607)
* Update hotspot3d to 1.8.2 (#11521)
* Update hotspot3d to 1.8.2
* Add perl-json as dependency
* Add perl-archive-extract as dependency
* Fqzcomp (#11606)
* Added recipe for fqzcomp
* There is no configure script
* Maybe this works
* Added gcc as build requirement
* Removed gcc again (lint issue)
* Maybe these exports will do the trick
* Nope!
* Added cxx as host requirement
* Compilers are only allowed in build section
* There is no need for make install
* Copy-paste error...
* Add vcf-annotator recipe (#11481)
* Add vcf-annotator recipe
* added pyvcf dependency
* Update meta.yaml
* stacks: fix for @ in exe_path (#11580)
* stacks: fix for @ in exe_path
* stacks: fixed path
* New version with bugfix and different progressiveMauve version. (#11613)
* Sspupdate (#11614)
* New version with bugfix and different progressiveMauve version.
* Keeping old version as folder.
* Push build number.
* Update SVDB to version 1.3.0 (#11506)
* new file: recipes/svdb/1.1.2/meta.yaml
renamed: reipes/svdb/svdb.patch -> recipes/svdb/1.1.2/svdb.patch
modified: recipes/svdb/meta.yaml
* deleted: 1.1.2/meta.yaml
deleted: 1.1.2/svdb.patch
* Bump nanosim (#11608)
* Bump nanosim
* Add scipy as dep
* Add recipe for perl-number-range (#11621)
* New build for grid (#11620)
* update grid
* update build num
* Recipe for das_tool 1.1.1 (#10528)
* recipe for das_tool 1.1.1
* Add recipe for sompy (#11624)
* cmake modified to build with NDEBUG (#11328)
* cmake modified to build with NDEBUG
* Update meta.yaml
* new build with fasta test
* new build with fasta test
* Fix and unblacklist TwoPaCo (#11622)
* Add recipe for TwoPaCo
* Unblacklist twopaco
* Modify and unblacklist recipe for ESTmapper (#11623)
* Modify and unblacklist recipe for ESTmapper
* Add patch
* Modify and unblacklist recipe for Metaseq (#11625)
* Fix recipe for metaseq and remove from blacklist
* Remove build.sh
* nextflow 18.10.1 build 2 (#11630)
* Add Clust (#11619)
* Add clust
* Clean recipe
* Add "noarch"
* Add DOI
* Add build file
* Python 2.7
* Fix scikit-learn dependency
* Trigger new build
* Update: PureCN (multicore) and PURPLE (plotting X libraries) (#11631)
- PureCN: adds support for specifying cores on command line
- PURPLE: adds X library dependencies required for creating
plots
* scripts/travis-run.sh: added a cleaner method to check for env vars (#11612)
* Increase the number of k value usable in bcalm (request by @Malfoy) (#11610)
* Increase the number of k value usable in bcalm (request by @Malfoy)
* Change compilation parameter to reduce memory impact of compilation
* Update anndata to 0.6.11 (#11637)
* Update nglview to 1.1.7 (#11643)
* Update binsanity to 0.2.7.1 (#11644)
* Update cgat-core to 0.5.4 (#11645)
* Update nanosv to 1.2.2 (#11673)
* Update abeona to 0.36.0 (#11670)
* Update pyfaidx to 0.5.5.2 (#11659)
* Update agfusion to 1.23 (#11668)
* Update iqtree to 1.6.8 (#11686)
* update iqtree to 1.6.8
* Trigger rebuild
* Update validators to 0.12.2 (#11672)
* Update python-edlib to 1.2.3.post1 (#11664)
* update for Purge Haplotigs (#11690)
* Update loompy to 2.0.16 (#11667)
* Update loompy to 2.0.16
* Update meta.yaml
* IgBLAST 1.10.0 (#11693)
* Update wtforms-alchemy to 0.16.7 (#11679)
* Update sickle to 0.6.4 (#11663)
* Update sickle to 0.6.4
* Remove fn and libgcc runtime dep
* Update confindr to 0.4.5 (#11696)
* Batvi (#11695)
* batvi initial
* Guideline compatibility..
* Dummy test section..
* Missing java dependency..
* use openjdk instead of java-jdk ..
* source specified in github ..
* trigger build (package did not have batindel directory) ..
* update SHA256 ..
* update SHA256 ..
* Update pythonpy to 0.4.11 (#11661)
* Update cortexpy to 0.45.6 (#11660)
* Update sevenbridges-python to 0.16.0 (#11674)
* Update solvebio to 2.7.0 (#11657)
* Update mathstats to 0.2.6.5 (#11656)
* Update goatools to 0.8.9 (#11641)
* Add gnies (#11627)
* Add gnies
* noarch python
* Update meta.yaml
* Add recipe for SKA v1.0 (#11581)
* Add recipe for SKA v1.0
* Add lib path for zlib
* Older gcc
* Correct install dir
* Try static linking
* Dynamic linking on OS X
* ldd command test
* correct program
* Remove ldd command
* Add recipe for transit version 2.3.1 (#11701)
* Add recipe for transit version 2.3.1
* Use skip, add spaces.
* Update meta.yaml (#11699)
* remove pyqi (#11704)
* Update python-chado to 2.2.0 (#11714)
* update python-chado
* 2.2.1
* Update vcfanno to 0.3.1 (#11710)
* FGMP-1.0.1 (#11278)
* FGMP-1.0.1 recipe
* remove unncessary build info
* add r-nabor (#11716)
* update stream to 0.2.2
* update stream to 0.2.3
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.5
* update stream to 0.2.6
* add r-nabor recipe
* update r-nabor recipe
* update r-nabor recipe
* r-pctgcdata (#11715)
* r-pctgcdata
* r-pctgcdata - fix
* r-pctgcdata - fix
* Update meta.yaml
* Fix plek by a new branch (#11605)
* Modify the PLEK recipe
* Start fixing PLEK, though it requires compilation
* update build.sh
* update yaml
* fix build.sh
* update build.sh
* Update recipe for plek
* add bioconductor-chromvar recipe (#11718)
* add bioconductor-chromvar recipe
* fix bioconductor-tissueenrich
* Apparently the popdel recipe didn't get correctly merged
* Final merge conflicts
* Bioc quick test (#12547)
* Update kallisto to 0.45.0 (#12117)
* Update validators to 0.12.3 (#12116)
* Update illumina-interop to 1.1.7 (#12115)
* Update umi_tools to 0.5.5 (#12123)
* Update tiptoft to 1.0.0 (#12122)
* Update: TitanCNA with fix for hg38 plotting (#12130)
* blockclust (#12111)
* added eden 1.1 version used in blockclust
* Update meta.yaml
* eden checksum and test
* added zlib requirement
* add include and lib paths to build.sh
* add include and lib paths to build.sh
* modify makefile flags using sed
* modify makefile flags using sed
* use c++
* Update build.sh
* Update build.sh
* LDFLAGS not used in makefile
* remove v1.1
* add blockclust 1.1.0 recipe
* skip osx build
* added tarball url and checksum; removed conda_build_config.yaml
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Update chewbbaca to 2.0.16 (#12132)
* Update abeona to 0.40.0 (#12131)
* ping to eden 1.1 (#12134)
* clean swap file (#12137)
* Update corset to 1.07 (#12143)
* Update peddy to 0.4.3 (#12144)
* blockclust latest source and added cloudpickle as requirement (#12142)
* Update nanomath to 0.22.0 (#12149)
* Update pymvpa to 2.6.5 (#12152)
* Updated to version 1.4.0 (#12138)
* Updated to version 1.4.0
* Resetting build number to 0 and build->host
* Update transdecoder to 5.5.0 (#12172)
* Update gridss to 2.0.1 (#12190)
* Update tracer to 1.7.1 (#12189)
* Update flowcraft to 1.4.0 (#12179)
* Update seqbuster to 3.2 (#12182)
* Update perl-io-compress to 2.081 (#12201)
* Update twobitreader to 3.1.6 (#12205)
* Update twobitreader to 3.1.6
* Update meta.yaml
* Update gtfparse to 1.2.0 (#12186)
* Update gtfparse to 1.2.0
* remove compiler
* Update htseq to 0.11.0 (#12177)
* Update htseq to 0.11.0
* add compiler
* Update htseq to 0.11.0 (#12239) [testing co-author]
* Update htseq to 0.11.0
* add compiler
Co-authored-by: Bjoern Gruening <[email protected]>
* alfred v0.1.16 (#12240)
* alfred v0.1.16
* makefile patch
* makefile patch
* Update scrm to 1.7.3 (#12150)
* Update scrm to 1.7.3
* Update scrm to 1.7.3
* Mob suite update 1.4.8 --> 1.4.9 (#12244)
We fixed a small bug related to repetitive elements database reconstruction on each run. Should only run once during the first mob_typer run. Should be good now for parallel runs.
* PeptideShaker updated to v1.16.35 & SearchGUI updated to 3.3.9 (#12241)
* PeptideShaker updated to v1.16.32
SearchGUI updated to v3.3.6
* PeptideShaker updated to v1.16.35
* SearchGUI updated to v3.3.9
* First attempt at a recipe for ncrf (#12101)
* First attempt at a recipe for ncrf
* changed from copies to symlinks
* including absolute path in symlinks
* PacBio: Update `pbmm2` to version 0.11.0 (#12246)
* Gimmemotifs version 0.13.0 (#12245)
* new release to fix numpy incompatibility
* GimmeMotifs 0.13.0 release test
* numpy 1.15
* version 0.13.0
* Fix about:home and extra:
* PacBio: Update `isoseq3` to version 3.1.0 (#12263)
* add python to host section (#12264)
* Update confindr to 0.4.7 (#12266)
* new build of GRiD (#12269)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* peptideshaker, searchgui: version bump (#12136)
* peptideshaker, searchgui: version bump
solving https://github.com/compomics/searchgui/issues/192
* Update peptide-shaker.py
* searchgui: added c compiler for building
test if linking errors go away this way
* searchgui: removed noarch
* Update: bcbio, bcbio-vm with CWL non-human fixes (bcbio/bcbio-nextgen#2473) (#12273)
* Make snakemake a noarch package. (#12274)
* noarch: python in combination with version constraint
* Cleanup deps and simplify version definition.
* Genenotebook v0.1.9 (#12277)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* Create r-airr recipe (#12284)
* Create r-airr recipe using bgruening/conda_r_skeleton_helper
* Update meta.yaml
* Findbin::Real added (#12291)
* Added version bump to 1.3 (#12292)
* ngs-bits 2018_11 (#12262)
* Updated ngs-bits to version 2018_10
* Updated ngs-bits to version 2018_11
* minor edit in grid (#12287)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* minor edit to grid
* Fred2 update (#12259)
* Update FRED2 Recipe
* msstitch version 2.9 (#12296)
* r-mvr (#12300)
This is a non-parametric method for joint adaptive mean-variance regularization and variance sta-
bilization of high-dimensional data.
* Bump to Gromacs 2018.3 + re-enable OSX build (#12299)
* Gromacs 2018.3 + re-enable osx build
See also #7825 on OSX build
Include RRID for Gromacs (see bioconda/bioconda-utils#252)
* disabled ocl-icd on osx; not available (or needed?)
https://anaconda.org/conda-forge/ocl-icd
* pyGenomeTracks update of dependencies (#12279)
* Update pyGenomeTracks recipe to enable py3 support and updating outdated dependecy list
* Increase build number
* Update meta.yaml
* Exclude Python 3.5
* Gromacs 2018.4 (#12302)
* quast 5.0.2 (#12303)
* Update meta.yaml (#12275)
* Update meta.yaml
r-rsqlite version dependency added
* Update meta.yaml
Updated build number to 1
* Use the extended-base container because of wget issues when downloading databases (#12297)
* Update duphold to 0.1.0 (#12257)
* Update flashlfq to 0.1.109 (#12256)
* Update planemo to 0.57.0 (#12251)
* Update meta.yaml (#12258)
* Update scalpel to 0.5.4 (#12249)
* Update scalpel to 0.5.4
* Fix url
* edit grid (#12298)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* minor edit to grid
* minor edit to recipe grid
* added feather to deps (#12293)
* R tigger (#12286)
* Create recipe for r-tigger (#12271)
* Create recipe for r-tigger using bgruening/conda_r_skeleton_helper.
* Delete bld.bat
* Remove windows support
* update scprep to v0.8.1 (#12306)
* Update nanoget to 1.7.5 (#12252)
* Update nanoget to 1.7.5
* Bump to version 1.7.6
should fix the README.md problem
* gffcompare: version bump (#12308)
* Update: cromwell (36), bcbio (Cromwell Docker runs) (#12307)
* Update: cromwell (36), bcbio (Cromwell Docker runs)
* Pin java to 8 to avoid compile errors on 11
* HiCExplorer update to version 2.2-beta (#12309)
* HiCExplorer update to version 2.2-beta
* Remove of '-' from version number
* Numpy set to 1.15
* Update meta.yaml
* upgrade to version 2.8.1 (#12316)
* Create Airr recipe (#12318)
* Create AIRR recipe using conda skeleton pypi.
* Add noarch python
* Clean host requirements
* Added nimnexus [v0.1] (#12133)
* added nimnexus
* Fix sha
* Update build.sh
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* [WIP] Add R-loom (#12320)
* initial WIP skeleton
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* try osx
* Create Changeo recipe (#12321)
* Create changeo recipe using conda skeleton pypi.
* EDIT about section
* ADD noarch generic
* Update noarch to python
* Clean host requirements
* Add test for scripts
* Change requirement to python>=3.4
* Add noarch pyton
* r-corbi (#12325)
* r-nam (#12327)
* Update pybedtools to 0.8.0 (#12324)
* Update pybedtools to 0.8.0
* rm cython requirement
* MSGFplus does not work with newer Java (#12330)
* Trying to not use a very new java version since the latest versions have dropped some classes
* Increment build
* Update atropos to 1.1.21 (#12322)
* Update CONCOCT to 0.4.2 (#12317)
* Update CONCOCT to 0.4.2
* Wrong shasum given
* Reset build number for new version
* New: gvcfgenotyper for joint calling with Illumina strelka2 (#12331)
* Apparently we need openJDK to be below 9, not below 11 as in the previous PR (#12332)
* Update Picard to 2.18.17. (#12333)
* Unblacklist IgDiscover (#12335)
* PacBio: Add missing licenses and post-link message (#12334)
* Bioconductor DEqMS package (#12336)
* Bioconductor DEqMS package
* Limma version could be set lower (checked with the bioconductor recipe page) to include limma in bioconda
* Genenotebook v0.1.10 (#12337)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* v0.1.10
* removed cloudpickle requirement for blockclust (#12242)
* blockclust latest source and added cloudpickle as requirement
* removed cloudpickle requirement for blockclust
* added a tagged release to the source
* back to source url but with release tarball and checksum
* R guilds (#12341)
* Strict rec (#12113)
* added metawrap
* fixed perl and jdk
* added more strict req
* fixed java and perl
* removed extra boost
* Update qcat to v1.0.1 (#12343)
* Add better error checking (#12345)
* Add mhcnames python package (#12349)
* Add MHCflurry pMHC class I binding affinity prediction tool (#12346)
* Bump pilon (#12354)
* Update pronto to 0.11.1 (#12377)
* Update perl-json-xs to 4.0 (#12373)
* Update planemo to 0.57.1 (#12370)
* Update snippy to 4.3.6 (#12372)
* Update intarna to 2.3.1 (#12367)
* Update agfusion to 1.231 (#12366)
* Update bioconda-utils to 0.15.0 (#12359)
* Update mapdamage2 to 2.0.9 (#12358)
* Update scanpy to 1.3.4 (#12357)
* Update goatools to 0.8.11 (#12361)
* Update perl-math-random-mt-auto to 6.23 (#12362)
* Update kipoi to 0.6.3 (#12374)
* Update kipoi_veff to 0.2.1 (#12364)
* Update perl-object-insideout to 4.05 (#12380)
* Update sevenbridges-python to 0.17.1 (#12379)
* Update nanosv to 1.2.3 (#12378)
* Update starfish to 0.0.30 (#12368)
* Update clust to 1.8.10 (#12356)
* Update pypairs to 2.0.6 (#12381)
* Update khmer to 3.0.0a2 (#12360)
* Update flashlfq to 0.1.110 (#12385)
* Update perl-algorithm-cluster to 1.57 (#12384)
* Update arvados-python-client to 1.2.0.20181121194423 (#12382)
* Update avro-cwl to 1.8.9 (#12355)
* Update avro-cwl to 1.8.9
* Set noarch: python
* r-breakaway (#12386)
* R sads (#12388)
* Update python-sortedcontainers to 2.1.0 (#12383)
* r-ebimetagenomics (#12339)
* pin armadilo on major version (#12389)
* IgDiscover version 0.11 (#12351)
* IgDiscover version 0.11
* IgDiscover requires Python 3.6
* Fix build on macOS with a small patch
* Remove unneeded host dependencies
* Update goatools to 0.8.12 (#12391)
* Update bioconda-utils to 0.15.1 (#12390)
* R ebimetagenomics (#12393)
* Add dimspy recipes for reference purposes (#12387)
* Add dimspy recipes for reference purposes
* Remove filename
* remove from blacklist
* Update build-fail-blacklist
* Added BioExcel_SeqQC to bioconda-recipes (#12276)
* PacBio: Update pbalign to 0.3.2 (#12396)
* PacBio: Update pbalign to 0.3.2
Closes: PacificBiosciences/pbbioconda#39
* add bgreat to bioconda (#12350)
* bgreat addition
* zlib in build should not be needed
* btrim integration to conda (#12395)
* Format sleuth recipe. Trigger rebuild because latest version was never uploaded for some reason. (#12399)
* PacBio: Update `pbsv2` to version 2.1.0 (#12400)
* Genenotebook v0.1.11 (#12398)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* v0.1.10
* v0.1.11
* prosolo: new package version 0.6.0 (#12397)
* Update sevenbridges-python to 0.17.2 (#12404)
* Add recipe for ICED (#12406)
* Downgrade version for iced (#12409)
* Update recipe for libstatgen 1.0.5 (#12348)
* Add recipe for libstatgen-1.0.5
* Update iced to 0.5.0 (#12411)
* Update perl-test2-suite to 0.000116 (#12412)
* fix compatibility with other tools (#12415)
* Restore dexseq python helper scripts (#12352)
* Restore dexseq python helper scripts
* Add python requirement for helper scripts
* Add python noarch to build section
* pin it to python2k
* Add htseq requirement, support only python <3 for now
* Genenotebook v0.1.12 (#12418)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* v0.1.10
* v0.1.11
* v0.1.12
* updated source
* added medpy recipe (#12417)
* added medpy recipe
* removed osx from build
* Update meta.yaml
* Update meta.yaml
* add boost and a compiler
* Update meta.yaml
* Update meta.yaml
* add itk
* Updated ddrage to version 1.6.1. (#12421)
* Add r-mcpcounter recipe. (#12261)
* Add MCPcounter recipe.
* fix lint: remove 'fn'
* fix license_file, version number and doi
* Update DEXSeq requirements to force compatible HTSeq version (#12423)
* ARB: Pin glib (#11782)
* Pin glib
* Update meta.yaml
* Update meta.yaml
* Work around CB3 issues
* Work around bioconda-utils lint false positive
* Disable lint check should_not_be_noarch
* Can't reference other packages built in recipe from anything but run
* Move perl to host section. Maybe that helps.
* constraining interpreter version breaks with CB3?
* disable perl version constraint :(
* Update meta.yaml (#12426)
* stacks: fix for fix 'fixing' @ in exe_path (#12420)
* stacks: fix for fix 'fixing' @ in exe_path
the previous fix https://github.com/bioconda/bioconda-recipes/pull/11580
tried to solve the problem with the @ in the exe_path by setting this
variable empty. But the perl scripts
- append a / to the empty…
dpryan79
added a commit
to bioconda/bioconda-recipes
that referenced
this issue
Mar 8, 2019
* Upgrade cyvcf2 to v0.10.8 (#13726)
Patch setup.py to use conda managed htslib
* Update bcftools plot_vcfstats (#13721)
* Python-tripal 3.2 and python-apollo (#13727)
* update python-tripal
* add python-apollo recipe
* noarch
* v0.1.4 February 2019 Release (#13720)
* python3 and igv-reports (#13623)
* python3 and igv-reports
* changing test
* adding ls
* adding bin ls
* print install path contents
* run on python3
* proper test
* Update meta.yaml (#13729)
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* It looks like rJava has now been rebuilt. (#13728)
* It looks like rJava has now been rebuilt.
* r-rcdk is in conda-forge now
* Remove the first batch from the blacklist
* Update esATAC
* Update CPAT to 1.2.4 (#13732)
* Re-do an update undone by 3761102478f21107957c166e85ca843f9c3410b1 (#13733)
* Gff3sort (#13731)
* add gff3sort recipe
* add new dep to sort gff3 files properly
* lint
* add perl-data-match (for Sort::Topological)
* add dep
* oh perl, I hate you so much
* ...so much....
* take this perl-data-match
* wrong path
* rebuild with perl 5.26.2 for mac
* Update PopPUNK to v1.1.4 (#13723)
* Update PopPUNK to v1.1.4
* Add noarch
Seems to be a py36 to py37 problem
* Cannot have noarch as no python2 support
* bump build numbers on dependencies needing rebuild
* Update sharedmem recipe
* Putting sharedmem build into meta.yaml
* Correcting host/build in sharedmem meta for noarch
* Make noarch and python>=3
* Remove redundancy in sharedmem meta.yaml
* Update comet-ms to 2018014 (#13645)
* Remove more rJava packages from the blacklist (#13734)
* Remove more rJava packages from the blacklist
* update
* Sc3 scripts update (#13735)
* Bump bioconductor-sc3-scripts package to 0.0.3
* Reset build counter
* Add pychopper (#13738)
* Add pychopper
* build command
* pb-falcon: 0.2.6 (#13740)
* pbfalcon-0.2.6
* pb-falcon: Try openssl<1.1
* pb-assembly: update pb-falcon/openssl (#13575)
* Remove the remainder of the rJava bioc packages from the blacklist (#13737)
* Remove the remainder of the rJava bioc packages from the blacklist
* Update
* blacklist msgfgui
* Add slivar 0.0.5. (#13741)
* Add slivar 0.0.5.
* Fix test.
* Increment build number (#13743)
* Update sevenbridges-python to 0.18.2 (#13746)
* Bump to latest scanpy-scripts (#13747)
* r-ldrtools (#13749)
* Try to remove a few bioconductor packages from the blacklist (#13744)
* Try to remove a few bioconductor packages from the blacklist
* More updates
* Yacrd add version 0.5.1 break compatibility with previous version (#13750)
* Add version 0.5.0 break compatibility
* up to version 0.5.1
* yacrd 0.5.1 correct error in sha256sum
* r-mixkernel (#13745)
* r-mixkernel
* Spydrpick v1.1.1 (#13725)
* Update SpydrPick to v1.1.0
* Update spydrpick v1.1.1; aprgrunt 0f34bdd80315e10b2234b5aae50b53102f04fbdd
* Use SSE3 rather than AVX2
* With AVX guard around popcnt
* PacBio: Update `ccs` to version 3.4.1 (#13755)
* Remove a few more packages from the blacklist (#13753)
* Remove a few more packages from the blacklist
* a few updates
* r-parallel is part of r-base
* odd
* Ready for OSX
* needs gfortran it seems
* Update PureCLIP to v1.3.0 (#13756)
* updating the recipe for the cromwell workflow manager to version 36.1, which should be used in preference to 37.0 until problems with that version are worked out, according to cromwell developers (#13757)
updating the recipe for the cromwell workflow manager to version 36.1, which should be used in preference to 37.0 until problems with that version are worked out, according to cromwell developers
* try again (#13758)
* Barcode splitter multi (#13663)
* New directory for the barcode splitter recipe.
* created using `conda skeleton pypi barcode_splitter_multi`.
* created using `conda skeleton pypi barcode_splitter_multi`.
* Added source files and tox.
Files checked in: recipes/barcode_splitter_multi/meta.yaml
* Re-wrote meta.yaml. The existing file was mostly wrong.
Files checked in: recipes/barcode_splitter/meta.yaml
* Change dirname.
* Working out tests.
Files checked in:
* Addresses issues with conda build.
Created a run_test.sh script to work around an issue with the exit code for --help and --version being 2 instead of 0.
Added noarch: python to meta.yaml.
Added "--single-version-externally-managed --record=record.txt" to the setup.py call in build.sh.
Files checked in: recipes/barcode_splitter/build.sh recipes/barcode_splitter/meta.yaml recipes/barcode_splitter/run_test.sh
* Updated sandbox zenodo doi to real zenodo doi now that testing is done.
Files checked in: recipes/barcode_splitter/meta.yaml
* Removing pass of shell variable to echo.
This is an attempt to address a warning from the remote circleci build that passing a variable as an argument generated from the output of the tool is a security risk. It might still complain due to the if conditional checking the variable too. I'll just have to see.
Files checked in: recipes/barcode_splitter/run_test.sh
* Removed eval of shell variable in if conditional.
I suspect that this eval is still related to the security warning and subsequent failure of the test in the remote circleci build.
Files checked in: recipes/barcode_splitter/run_test.sh
* Updated to a release of barcode_splitter that exits with a status of 0 for --version.
I could not get run_test.sh to pass mulled-build tests, so instead of work through that, I just worked around it by releasing the new version with the exit code fix.
Files checked in: recipes/barcode_splitter/meta.yaml recipes/barcode_splitter/run_test.sh
* Reverted unintended changes.
Files checked in: miniconda.sh .circleci/common.sh
* Reverted another unintended change.
Didn't realize the file was created instead of changed.
Files checked in: .circleci/common.sh
* Update meta.yaml
* Delete build.sh
* CPAT: Stricter python version requirement (#13742)
* Stricter python version requirement
In CPAT's code the version check for a python version that starts with 2.7 is hardcoded.
* Correct license version
It is incorrectly reported on PYPI. In the documentation of CPAT and in the project's license file it is mentioned that any later version of GPL is also allowed.
* rdkit: remove blacklisted package - now at conda forge (#13759)
* platypus update (#13494)
* platypus update
* added back buildPlatypus.sh
* added new path to source
* reset build number to 0
* this one needs a compiler isn't it?
* Update: arvados-python-client, arvados-cwl-runner, bcbio-variation-recall (#13754)
* Update: arvados-python-client, arvados-cwl-runner, bcbio-variation-recall
- arvados: fix py3k support by avoiding subprocess32 on py3k
- bcbio-variation-recall: fix platypus contig header generation.
Fixes bcbio/bcbio-nextgen#2688
* Avoid py37 selectors, trying to fix py27 build
* Try to avoid py37 errors with noarch
* Fix python selectors
* Avoid noarch linter errors, not sure why triggered
* Avoid noarch linter errors, not sure why triggered
* Pin arvados-python-client with py37 subprocess fix
* Wasabi 1.0.0 (#13760)
* UCSC blacklist (#13763)
* update mzr as a test
* Begin building for R 3.5.1 (#11252)
* Bump everything for R 3.5.1
* Fix most of the linting issues
* Update blacklist
* Revert "Fix most of the linting issues"
This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5.
* should_not_use_fn
* More fixes
* Fix incorrect yaml
* Should really fix the linting blacklist stuff
* Fix many recipes
* Fix some linting
* Fix r-wicket
* Update derfinder
* Pin to a given bioconductor release.
* Add missing packages
* Restore identifiers to bioconductor packages
* Restore extra information to R packages
* Update R bulk (#11283)
* fixed incorrect doi of publication (#11175)
* Added recipe for kinSimRiboswitch (#10838)
Added recipe for kinSimRiboswitch, a pipeline for simulating the folding
kinetics of RNA switches.
* update multiqc-bcbio (#11187)
* Add recipe for PopDel (#11181)
* Add recipe for PopDel
* Add clang and clangxx to build config
* update seqbuster (#11190)
* update seqbuster
* fix build
* fix test
* Update pyseer to 1.1.2 (#11172)
* bump sourmash (#11197)
* Update BASIC to v1.4.1 (#11195)
* Update BASIC to v1.4.1
* Trigger circleci
* Fix build number
* Update nf-core-1.2 (#11191)
* Update nf-core-1.2
* Update build script
* Update to InterMine 1.11.0 (#11182)
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Add tinyfasta-0.1.0 (#11177)
* Add tinyfasta
* Update build script
* Fix structure of build section
* Bumping snippy (#11198)
* Remove older version
* Bump snippy
* VEP: bump major version (#11201)
* VEP: bump major version
* VEP: bumped plugin major version
* VEP: update plugin install
Download and install all plugin modules, instead of just a selection
* Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200)
* Update: PureCN to latest devel (1.11.13); wrapper scripts
PureCN development (https://github.com/lima1/PureCN) has several
improvements over the BioC 3.6 release for handling multiple VCF input
types, and is back compatible with R 3.4.1 so still builds cleanly
with two new dependencies.
Also exposes PureCN wrapper scripts for running from the command line.
Prefixes ambiguous scripts with PureCN_.
* Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet
* add cassiopee release 1.0.9 (#11168)
* add cassiopee release 1.0.9
* update to conda build 3
* remove old version backup and use sha256 for source
* Bump abeona version to 0.26.0 (#11202)
* Bump abeona version to 0.24.0
* Bump abeona version to 0.26.0
* Update LexMapr to v0.1.2 (#11192)
* Update LexMapr to v0.1.2
* Add rdflib dep
* Update svtyper to 0.7.0 (#11196)
* Update svtyper to 0.7.0
* Add recipe for perl-gtdbtk (#11194)
* Add recipe for perl-gtdbtk
* New recipe for RFMix (#11205)
* New recipe for RFMix
* updated version number information
* updated version number information
* updated version number information
* initial purge_haplotigs commit (#11049)
* initial purge_haplotigs commit
* bioconda revisions, updating test commands to run the pipeline on the test dataset
* rolling back test commands
* Add recipe for fsm-lite (#11209)
* Add recipe for fsm-lite
* Add prefix to make
* Remove v from version string
* Updated reparation_blast to version v.1.0.7 (#11210)
* Update sambamba to 0.6.8 (#11212)
* Bump sambamba to 0.6.8
* It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified.
* Set some environment variables
* The compiled binary is in a different place now
* ldc provides some libraries that are linked against.
* mtbseq: update recipe (#11110)
* changed download location/add test
* remove test
* Confindr (#11217)
* Update confindr to 0.4.2
* Fix typo in specifying version of pysam
* Update Genenotebook to v0.1.4 (#11218)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* updating to 0.1.3 (#11221)
* sartools1.6.6 (#11222)
* Perl bio automatedannotation (#11216)
* Initial recipe for Bio-AutomatedAnnotation
* Change URL
* Run cpanm tests
* Temporarily set HOME
* Use cpan version instead
* Add more depencencies
* Set bioperl version
* unset bioperl version, add bioperl-run
* New release including version in modules
* Remove comments
* build -> host
* Upgrade r-biodb to v1.1.2. (#11213)
* Upgrade r-biodb to v1.1.2.
* Remove old versions of r-biodb.
* Comment out libgfortran.
* PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215)
* PeptideShaker: updated to version 1.16.30
- Bugfix: HOME was still being used when folder with customised reports was specified.
- Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line.
* SearchGUI: updated to version 3.3.5.
- BUG FIX: Cleanup of the temp path options when used as options for the other command lines.
- FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2.
- LIBRARY UPDATE: Updated utilities to version 4.12.8.
* Update meta.yaml (#11227)
* Svtools 0.4.0 (#11208)
* Remove directories for old svtools versions
* Update svtools to v0.4.0
* Move build number back to 0
* Anvio 52 (#11230)
* Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software.
* Remove cgat-scripts from blacklist. (#11228)
* Add new formula: bazam 1.0.1 (#11229)
* Update gatk4 to 4.0.10.0 (#11224)
* Add recipe for gtdbtk 0.1.3 (#11211)
* Add recipe for gtdbtk
* Added initial htstream recipe (#11113)
* HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data.
* DeepTools 3.1.3 (#11226)
* PacBio: Update `pbmm2` to version 0.10.0 (#11225)
* fastqc: update to version 0.11.8 (#11214)
* fastqc: update to version 0.11.8
* Update meta.yaml
* Phame (#11223)
* mac recipe and added bioperl
* changing bill number
* added no osx
* adding new version
* removed separate recipe for mac, dont need it
* now running same recipe for mac and linux
* fixed the way fasttrees version was being parsed
* minor change test
* adding detailed description
* restaging the build number
* new version
* Make sure to use bioperl and perl 5.26
* Updated ngs-bits to version 2018_10 (#11235)
* PacBio: Update `pbsv2` to version 2.0.2 (#11236)
* Update VSEARCH to 2.8.5 (#11239)
* Fix shorah recipe and remove from blacklist. (#11241)
* Fix shorah recipe and remove from blacklist.
* Fix blas variant.
* Remove imports from tests.
* unicycler 0.4.7 (#11240)
* unicycler 0.4.7
* unicycler: Work around ValueError: invalid
Unicycler thinks the terminal has 0 columns and produces this error:
File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks
raise ValueError("invalid width %r (must be > 0)" % self.width)
ValueError: invalid width -5 (must be > 0)
* Octopus: update to 0.5.1-beta (#11244)
* New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247)
- PURPLE SV and heterogeneity caller for somatic tumor/normal samples.
- VarDictJava -- 1.5.6 release with fixes for SV calling
- PureCN -- add signature dependency and update with fixes for test
samples.
* Dinucleotide patterns analysis tools v1.0 (#11245)
* Dinucleotide patterns analysis tools v1.0
* Lets try it, it seems to work locally for me.
* Enable SpoTyping_plot.r (#11248)
* rerun again (#11233)
* rerun again
* Update meta.yaml
* Delete build.sh
* Update segway dependency optbuild to 0.2 (#10459)
* Update segway dependency optbuild to 0.2
* Update build and architecture requirements for optbuild 0.2
* Add six as a dependency to the optbuild recipe
* Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249)
* Add prefix dnp- to the package names
* Update build.sh
* Update build.sh
* Bump beast version to 1.10.2 (#11250)
* add maxquant (#11253)
* add mayquant
* relax tests
* PacBio: Update `pbmm2` to version 0.10.1 (#11256)
* PacBio: Update `pbmm2` to version 0.10.1-1 (#11257)
* remove xsv recipe (#11259)
* add blast dependency (#11258)
* Added riborex recipe (#11251)
* Added riborex recipe
* Relaxed version constraints
* Pinned r-core for fdr tools
* fixed the r-base stuff upstream
* Update meta.yaml
* fix graphprot (#11234)
* increase build number
* remove from blacklist
* use cxx instead of c
* move coreutoils to build section
* set additional paths
* patch makefile
* blind try
* update patch
* explicitely copy from src_dir
* update deprecated prefix variable
* Revert "update deprecated prefix variable"
This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d.
* update deprecated prefix variable
* try moving to host section
* Bump mash (#11264)
* Add fmlrc (#11265)
* Add fmlrc
* add doi
* PacBio: Update pb-falcon to 0.2.4. (#11266)
* Add kopt recipe (#11269)
* Genomepy 0.5.2 (#11267)
* release 0.5.2 of genomepy
* trigger new build
* remove genomepy from blacklist
* locale for osx
* updated locale test
* PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275)
* Update mmseqs2 recipe to new release 6-f5a1c (#11272)
* Update yacrd to version 0.4.1 (#11273)
* Add scprep (#11270)
* Add scprep
* All of these should not be needed as host dep
* Metawrap preqs2 (#11242)
* fixed issues
* fixed issues
* added tests
* fixed tab
* gemma 0.98 (#11254)
* gemma 0.98
* gemma 0.98
Leave gsl and zlib out of runtime dependencies
* Add DCA recipe (#11274)
* Add DCA recipe
* add noarch and doi
* remove skip
* Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib
* Various fixes for bulk and trigger a rebuild (#11313)
* Various fixes, at least 4 packages (and their dependencies) should still fail (#11320)
* A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336)
* Fix various recipes (#11354)
* Fix various recipes
* Fix more recipes
* Various CRAN package fixes, since they all lack license files (#11372)
* Various CRAN package fixes, since they all lack license files
* Fix the r-dartr recipe
* There is a light at the end of the tunnel (#11381)
* There is a light at the end of the tunnel
* Licenses no longer exist
* [BULK] Fixes for R/Bioconductor packages (#11406)
* Require `r-base >=3.5` for some packages
* Fix various CRAN packages lacking license file
* Add missing libnetcdf requirement to bioconductor-mzr
* Remove r-alakazam (moved to conda-forge)
Fix linting issue:
```
recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating
```
* [BULK] Many R 3.5 only packages (#11410)
* [BULK] Bulk update 191018b (#11419)
* update mzr as a test
* Begin building for R 3.5.1 (#11252)
* Bump everything for R 3.5.1
* Fix most of the linting issues
* Update blacklist
* Revert "Fix most of the linting issues"
This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5.
* should_not_use_fn
* More fixes
* Fix incorrect yaml
* Should really fix the linting blacklist stuff
* Fix many recipes
* Fix some linting
* Fix r-wicket
* Update derfinder
* Pin to a given bioconductor release.
* Add missing packages
* Restore identifiers to bioconductor packages
* Restore extra information to R packages
* Update R bulk (#11283)
* fixed incorrect doi of publication (#11175)
* Added recipe for kinSimRiboswitch (#10838)
Added recipe for kinSimRiboswitch, a pipeline for simulating the folding
kinetics of RNA switches.
* update multiqc-bcbio (#11187)
* Add recipe for PopDel (#11181)
* Add recipe for PopDel
* Add clang and clangxx to build config
* update seqbuster (#11190)
* update seqbuster
* fix build
* fix test
* Update pyseer to 1.1.2 (#11172)
* bump sourmash (#11197)
* Update BASIC to v1.4.1 (#11195)
* Update BASIC to v1.4.1
* Trigger circleci
* Fix build number
* Update nf-core-1.2 (#11191)
* Update nf-core-1.2
* Update build script
* Update to InterMine 1.11.0 (#11182)
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Add tinyfasta-0.1.0 (#11177)
* Add tinyfasta
* Update build script
* Fix structure of build section
* Bumping snippy (#11198)
* Remove older version
* Bump snippy
* VEP: bump major version (#11201)
* VEP: bump major version
* VEP: bumped plugin major version
* VEP: update plugin install
Download and install all plugin modules, instead of just a selection
* Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200)
* Update: PureCN to latest devel (1.11.13); wrapper scripts
PureCN development (https://github.com/lima1/PureCN) has several
improvements over the BioC 3.6 release for handling multiple VCF input
types, and is back compatible with R 3.4.1 so still builds cleanly
with two new dependencies.
Also exposes PureCN wrapper scripts for running from the command line.
Prefixes ambiguous scripts with PureCN_.
* Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet
* add cassiopee release 1.0.9 (#11168)
* add cassiopee release 1.0.9
* update to conda build 3
* remove old version backup and use sha256 for source
* Bump abeona version to 0.26.0 (#11202)
* Bump abeona version to 0.24.0
* Bump abeona version to 0.26.0
* Update LexMapr to v0.1.2 (#11192)
* Update LexMapr to v0.1.2
* Add rdflib dep
* Update svtyper to 0.7.0 (#11196)
* Update svtyper to 0.7.0
* Add recipe for perl-gtdbtk (#11194)
* Add recipe for perl-gtdbtk
* New recipe for RFMix (#11205)
* New recipe for RFMix
* updated version number information
* updated version number information
* updated version number information
* initial purge_haplotigs commit (#11049)
* initial purge_haplotigs commit
* bioconda revisions, updating test commands to run the pipeline on the test dataset
* rolling back test commands
* Add recipe for fsm-lite (#11209)
* Add recipe for fsm-lite
* Add prefix to make
* Remove v from version string
* Updated reparation_blast to version v.1.0.7 (#11210)
* Update sambamba to 0.6.8 (#11212)
* Bump sambamba to 0.6.8
* It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified.
* Set some environment variables
* The compiled binary is in a different place now
* ldc provides some libraries that are linked against.
* mtbseq: update recipe (#11110)
* changed download location/add test
* remove test
* Confindr (#11217)
* Update confindr to 0.4.2
* Fix typo in specifying version of pysam
* Update Genenotebook to v0.1.4 (#11218)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* updating to 0.1.3 (#11221)
* sartools1.6.6 (#11222)
* Perl bio automatedannotation (#11216)
* Initial recipe for Bio-AutomatedAnnotation
* Change URL
* Run cpanm tests
* Temporarily set HOME
* Use cpan version instead
* Add more depencencies
* Set bioperl version
* unset bioperl version, add bioperl-run
* New release including version in modules
* Remove comments
* build -> host
* Upgrade r-biodb to v1.1.2. (#11213)
* Upgrade r-biodb to v1.1.2.
* Remove old versions of r-biodb.
* Comment out libgfortran.
* PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215)
* PeptideShaker: updated to version 1.16.30
- Bugfix: HOME was still being used when folder with customised reports was specified.
- Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line.
* SearchGUI: updated to version 3.3.5.
- BUG FIX: Cleanup of the temp path options when used as options for the other command lines.
- FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2.
- LIBRARY UPDATE: Updated utilities to version 4.12.8.
* Update meta.yaml (#11227)
* Svtools 0.4.0 (#11208)
* Remove directories for old svtools versions
* Update svtools to v0.4.0
* Move build number back to 0
* Anvio 52 (#11230)
* Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software.
* Remove cgat-scripts from blacklist. (#11228)
* Add new formula: bazam 1.0.1 (#11229)
* Update gatk4 to 4.0.10.0 (#11224)
* Add recipe for gtdbtk 0.1.3 (#11211)
* Add recipe for gtdbtk
* Added initial htstream recipe (#11113)
* HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data.
* DeepTools 3.1.3 (#11226)
* PacBio: Update `pbmm2` to version 0.10.0 (#11225)
* fastqc: update to version 0.11.8 (#11214)
* fastqc: update to version 0.11.8
* Update meta.yaml
* Phame (#11223)
* mac recipe and added bioperl
* changing bill number
* added no osx
* adding new version
* removed separate recipe for mac, dont need it
* now running same recipe for mac and linux
* fixed the way fasttrees version was being parsed
* minor change test
* adding detailed description
* restaging the build number
* new version
* Make sure to use bioperl and perl 5.26
* Updated ngs-bits to version 2018_10 (#11235)
* PacBio: Update `pbsv2` to version 2.0.2 (#11236)
* Update VSEARCH to 2.8.5 (#11239)
* Fix shorah recipe and remove from blacklist. (#11241)
* Fix shorah recipe and remove from blacklist.
* Fix blas variant.
* Remove imports from tests.
* unicycler 0.4.7 (#11240)
* unicycler 0.4.7
* unicycler: Work around ValueError: invalid
Unicycler thinks the terminal has 0 columns and produces this error:
File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks
raise ValueError("invalid width %r (must be > 0)" % self.width)
ValueError: invalid width -5 (must be > 0)
* Octopus: update to 0.5.1-beta (#11244)
* New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247)
- PURPLE SV and heterogeneity caller for somatic tumor/normal samples.
- VarDictJava -- 1.5.6 release with fixes for SV calling
- PureCN -- add signature dependency and update with fixes for test
samples.
* Dinucleotide patterns analysis tools v1.0 (#11245)
* Dinucleotide patterns analysis tools v1.0
* Lets try it, it seems to work locally for me.
* Enable SpoTyping_plot.r (#11248)
* rerun again (#11233)
* rerun again
* Update meta.yaml
* Delete build.sh
* Update segway dependency optbuild to 0.2 (#10459)
* Update segway dependency optbuild to 0.2
* Update build and architecture requirements for optbuild 0.2
* Add six as a dependency to the optbuild recipe
* Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249)
* Add prefix dnp- to the package names
* Update build.sh
* Update build.sh
* Bump beast version to 1.10.2 (#11250)
* add maxquant (#11253)
* add mayquant
* relax tests
* PacBio: Update `pbmm2` to version 0.10.1 (#11256)
* PacBio: Update `pbmm2` to version 0.10.1-1 (#11257)
* remove xsv recipe (#11259)
* add blast dependency (#11258)
* Added riborex recipe (#11251)
* Added riborex recipe
* Relaxed version constraints
* Pinned r-core for fdr tools
* fixed the r-base stuff upstream
* Update meta.yaml
* fix graphprot (#11234)
* increase build number
* remove from blacklist
* use cxx instead of c
* move coreutoils to build section
* set additional paths
* patch makefile
* blind try
* update patch
* explicitely copy from src_dir
* update deprecated prefix variable
* Revert "update deprecated prefix variable"
This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d.
* update deprecated prefix variable
* try moving to host section
* Bump mash (#11264)
* Add fmlrc (#11265)
* Add fmlrc
* add doi
* PacBio: Update pb-falcon to 0.2.4. (#11266)
* Add kopt recipe (#11269)
* Genomepy 0.5.2 (#11267)
* release 0.5.2 of genomepy
* trigger new build
* remove genomepy from blacklist
* locale for osx
* updated locale test
* PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275)
* Update mmseqs2 recipe to new release 6-f5a1c (#11272)
* Update yacrd to version 0.4.1 (#11273)
* Add scprep (#11270)
* Add scprep
* All of these should not be needed as host dep
* Metawrap preqs2 (#11242)
* fixed issues
* fixed issues
* added tests
* fixed tab
* gemma 0.98 (#11254)
* gemma 0.98
* gemma 0.98
Leave gsl and zlib out of runtime dependencies
* Add DCA recipe (#11274)
* Add DCA recipe
* add noarch and doi
* remove skip
* Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib
* Various fixes for bulk and trigger a rebuild (#11313)
* Various fixes, at least 4 packages (and their dependencies) should still fail (#11320)
* A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336)
* Fix various recipes (#11354)
* Fix various recipes
* Fix more recipes
* Various CRAN package fixes, since they all lack license files (#11372)
* Various CRAN package fixes, since they all lack license files
* Fix the r-dartr recipe
* There is a light at the end of the tunnel (#11381)
* There is a light at the end of the tunnel
* Licenses no longer exist
* [BULK] Fixes for R/Bioconductor packages (#11406)
* Require `r-base >=3.5` for some packages
* Fix various CRAN packages lacking license file
* Add missing libnetcdf requirement to bioconductor-mzr
* Remove r-alakazam (moved to conda-forge)
Fix linting issue:
```
recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating
```
* [BULK] Many R 3.5 only packages (#11410)
* Update pinning to R>=3.5 and a few runtime dependencies.
* CSAW is R 3.5 only
* Packages using beachmat are 3.5 only
* Packages using bioconductor-singlecellexperiment are R 3.5 only
* [BULK] Don't use r-base >=3.5, use a conda_build_config.yaml instead (#11452)
* Don't use r-base >=3.5, use a conda_build_config.yaml instead
* blacklist r-phangorn
* Update variancepartition
* R 3.5 for packages requiring singlecellexperiment
* Update a few packages
* Update a number of recipes (#11482)
* Update ensemblVEP and derfinder (#11504)
* Bulk update 251018 (#11577)
* [BULK] various package updates
* blacklist bioconductor-mzr
* A couple tweaks
* [BULK] Update 261018 (#11611)
* Apparently the r-rgeos bit works properly now.
* Add tissueenrich and try to fix scpipe on Linux
* A meaningless change just to trigger an update in bulk. (#11618)
* [BULK] update 271018 (#11628)
* Bump bioconductor-esetvis
* Fix yaqcaffy
* Fix more
* Another R 3.5 recipe
* [BULK] update 281018 (#11689)
* Add some files
* Fix arrayexpress
* Fix another 2
* Blacklist a bunch of bioconductor recipes that aren't likely to get built for a variety of reasons (mostly due to mzR). (#11697)
* Update blacklist (#11706)
* [BULK] fix bioconductor-tissueenrich (#11720)
* taxonkit 0.2.5 (#11318)
* Update csvtk (#11319)
* taxonkit 0.2.5
* csvtk 0.15.0
* bumping GROOT to 0.8.1 (#11323)
* HiCMatrix version 3 (#11322)
* Correcting dependencies
* Version 3 of HiCMatrix, the October release
* Update confindr to 0.4.3 (#11330)
* Drop-seq_tools: Version 2.0.0 (#11326)
* Update meta.yaml
* Update build.sh
some tool names changed to fit Camel case
* Update motus to build only for python3 (#11331)
* Update fpa to 0.2 version (#11333)
* update taxonkit to 0.3.0 (#11339)
* ntcard 1.1.0 (#11338)
* Update rgi (#11335)
* first commit
* update dependencies list
* change source to github
* change build number
* testing circleci
* update meta and build
* fix build
* move build script into meta
* remove older recipes
* line fix in bootstrap.py
* change python & matplotlib versions; add build.sh file
* add preprocessing selector to skip python 2.7
* move build script into meta.yaml
* Revert "line fix in bootstrap.py"
This reverts commit 5ac1ecd0142a5cfdfc8499c5b6ef4e1f629cd046.
* Update gmap to version 2018-07-04. (#11332)
MAX_READLENGTH environment variable has been disused since 2016-08-16.
* Upgrade r-biodb to 1.2.0a. (#11341)
* Upgrade r-biodb to 1.2.0a.
* Update meta.yaml
* Updated ont-tombo to version 1.5. (#11329)
* Updated ont-tombo to version 1.5.
* Updated with actual github release version hash.
* remove graphicsmagick (#11342)
* Build kraken2 for osx (#11343)
* First try for a bcalm recipes (#11344)
* New: cgpbigwig (BigWig manipulation); Update: bcbio (#11347)
- cgpbigwig (https://github.com/cancerit/cgpBigWig) provides bigwig
generation and manipulation command line tools including bam to bigwig
conversion.
- bcbio: fixes for QC on variants and peddy for CWL runs
* Try avoid some dependancy (#11349)
* Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8 (#11348)
* Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8
Also add about:home .
* Workaround https://github.com/conda-forge/bison-feedstock/issues/7
* Better bcalm recipes (#11350)
* Try avoid some dependancy
* Correct mess in build number, sorry
* R biodb (#11351)
* rebuild r-biodb
* trigger build
* Add recipe for pypairs (#11356)
* Update smoove to 0.2.1. (#11360)
* Update duphold to 0.0.9. (#11359)
* Update goleft to 0.2.0 (#11361)
* Bump slicedimage to 1.0.0 (#11362)
* Bump slicedimage to 1.0.1 (#11365)
* Added new versions for biopet-sampleconfig (#11268)
* perl-velvetoptimiser: update to 2.2.6 (#11369)
* update to 2.2.6
* remove unneeded patch
* Scanpy upgrade (#11371)
* Bump version
* Upgrade Scanpy
* Bump starfish to 0.0.25 (#11370)
* bumping groot to 0.8.2 (#11374)
* vep: bump subversion (#11367)
* Updated Krocus 1.0.1 (#11355)
* Add tiptoft
* Fix meta.yaml for tiptoft
* Add build script
* Updated krocus 1.0.1
* Add tiptoft 0.1.4 (#11352)
* Add tiptoft
* Fix meta.yaml for tiptoft
* Add build script
* Kodoja v0.0.9 (#11373)
* Add recipe for seer (#11263)
* Add recipe for seer
* lets try this
* Add newer compiler
* Using boost-cpp
* messed up version string
* Attempt building boost
* Use c++11 in boost
* Use python for boost install
* Correct python version spec
* try with different python version
* Fix b2 command
* Fix popd command
* build and link boost program options statically
* Fix tests
* Match dependency order
* Link openblas instead of blas
* Forcing rebuild with openblas
* Don't use armadillo wrapper
* Making review changes. Also trying original tests
* Previous tests were correct
* Add recipe for the translate-gard npm package version 1.0.3 (#11364)
* Fix umi tools (#11376)
umi_tools: clean up dependencies
* add support tools to PATH (#11379)
* Bump to v2.2.1 (#11380)
* Bump starfish to 0.0.26 (#11378)
* Update fpa to 0.3 (#11375)
* Update fpa to 0.3
* Correct error in sha256
* Reset build number
* Update trial to 2.5.5 (#11386)
* Update: bioconductor-titancna; 1.19.1 with hg38 support (#11388)
* Update: bioconductor-titancna; 1.19.1 with hg38 support
* Pin to R 3.4 to avoid pulling in 3.3 and 3.5 during mulled
* Add r-polysat version 1.7-3 (#11384)
* Update biomart version so that compatible with r351 (#11366)
* Update biomart version so that compatible with r351
* Update meta.yaml
reset build number as per https://bioconda.github.io/guidelines.html#buildnum
* Update entrez-direct to 10.0.20180927. (#11387)
* Added recipe for SonicParanoid 1.0.13 (#11271)
* Added recipe for SonicParanoid 1.0.13
* removed 'x.x' for numpy, added basic test
* fixed linter related errors
* compiler set to cxx and added host section (same build error!)
* removed host section
* moved numpy and cython to host section; restored build: noarch: python; added LICENSE.md
* removed build: noarch
* added build and extra sections
* set build number to 0; removed skip build; added python3 minimum version; added test for all executables.
* restored sh python module as requirement
* added Make to run; updated release to latest commit
* remove c compiler from meta.yaml
* modified build.sh to compile source codel added make in build section
* updated to latest commit
* updated to latest version with make included in setup.py
* reverted build.sh to the simplest version (python setup.py install)
* Add perl-json to build requirements to allow meme-chip to run to completion. Change meme-chip to use dreme-py3 instead of dreme if building with python 3. (#11389)
* Bump IgBLAST to 1.9.0 (#11393)
Bump IgBLAST to 1.9.0
Re-package the binary version this time. There are problems building the
source version when the configure script reaches this step:
"trying to build the NCBI SRA/VDB Toolkit from GitHub"
The previous problem about the binaries linking against libbz2.so, for
which we had no conda package, is now solved.
Also, this saves about 45 minutes compilation time.
* Add consan (#11395)
* Add consan
* Skip osx
* Update: vardict, vardict-java 1.5.7 (#11394)
* Update: vardict, vardict-java 1.5.7
Latest vardict-java release and corresponding vardict with bug fixes
after testing with 1.5.6
* Reduce test output to try and fix build problems
* Experiment 2 for build problems: remove r-base from run
* Experiment 3 for build problems: add r-base in host
* update recipe for 3.9.1 (#11397)
* evofold2 (#11396)
* evofold2
* wrapper
* Update meta.yaml
* minor
* Update rnastructure to 6.1. (#11400)
* Ctat mut (#11401)
* updating version number
* correct URL
* proper hash
* Revert "Ctat mut (#11401)" (#11402)
This reverts commit 6db10ac7ffd7abaf8fbf1762b7ea6c63b2585fe0.
* update version (#11403)
* any2fasta 0.4.2 (new formula) (#11407)
* W4mclassfilter v0.98.9 (#11385)
* Added files to build version 0.98.9
* Update meta.yaml
* Update meta.yaml
* updated SonicParanoid recipe to version 1.0.14 (#11409)
* updated SonicParanoid recipe to version 1.0.14
* Update to version 1.0.2 of PopDel (#11398)
* Update to version 1.0.2 of PopDel
Update to version 1.0.2.
* Reset build number to 0
* PacBio: require Meson 0.48.1 for all recipes (#11090)
* Meson 0.47 inserted duplicate RPATHs in
macOS binaries, causing `install_name_tool`
failures when installing the package.
Requiring 0.48.1 ensures we do not run into
these issues anymore in the future.
* rebuild with latest openmpi (#11411)
* Remove kfoots from the blacklist (#11416)
* Update gseapy to 0.9.7 (#11417)
* Update gseapy to 0.9.7
* remove noarch
* Add SC3 as dependency (#11427)
* Add recipe for r-poppr (#11418)
* Update knitr version because of Issue: https://github.com/rstudio/rmarkdown/pull/1271 (#11412)
* Update IQ-TREE to 1.6.7.1 (#11429)
* Update IQ-TREE to 1.6.7.1
* Change build number
* Update: r-deconstructsigs with fixes for hg38 (#11431)
The 1.8.0 release, from 2016, has some issues with hg38 and other
custom genomes that are fixed in development (raerose01/deconstructSigs#27).
There hasn't been a new release pushed so this rolls these into a new
sub-version and makes them available.
* Update entrez-direct to 10.2.20181018. (#11432)
* Add assembly-scan recipe (#11425)
* remove python 2.7 skip (#11424)
Preparation for rnaQUAST
* Add fastq-scan recipe (#11415)
* Add patch to fix racon/rampler path in racon_wrapper. (#11434)
Fixes #11405.
* meme rebuild (#11433)
* Update nanocomp to 0.23.1 (#11436)
* Update nanocomp to 0.23.1
* remove noarch
* Update abricate to 0.8.10 (#11446)
* Update angsd to 0.923 (#11445)
* Update alfred to 0.1.13 (#11444)
* Update alfred to 0.1.13
* Try w/o patch
* Update antarna to 2.0.6 (#11442)
* Update admixtools to 5.1 (#11443)
* Update admixtools to 5.1
* Let makefile choose which bins to install
* Update alignstats to 0.5 (#11441)
* Update xatlas to 0.2.1 (#11437)
* r-gpca (#11428)
* r-gpca
* r-gpca recipe
* Update meta.yaml
* Removed All Comments
* gseapy bump version 0.9.8 (#11440)
* gseapy bump version 0.9.8
* version
* titancna: fix for hg38, remove conda build hacks (#11447)
* titancna: fix for hg38, remove conda build hacks
* Re-add r-base 3.4 pin to avoid 3.5 errors
* Hmmlearn older version (#11450)
* Adding pygtftk
* removed pygtftk from master
* add older version of hmmlearn
* Add card_trick (#11451)
* Add card_trick
* Restrict to py3
* Update checkm-genome to 1.0.12 (#11455)
* Bump drep (#11457)
* Update squid to 1.5 (#11466)
* Update ncbi-ngs-sdk to 2.9.3 (#11467)
* elprep: bumped major version (#11414)
* elprep: bumped major version
* fixed hash
* fix download link, fixed licence
* fixed tests
* skip osx build
* FRED2 as a conda package (#11469)
* Attempt to get FRED2 as a conda package
* SHA update
* 99 little bugs in the code
* Fix things Björn mentioned
* add rnaQUAST recipe (#11470)
* Update bioconda-utils to 0.14.9 (#11454)
* Rapidup (#11474)
* Update to v0.7
* Update Buildnumber
* rapid: update to v0.6
* rapid: update to v0.6
* update grid (#11478)
* Adding biobb_model recipe (#11472)
* Updated wtdbg to v2.1 (#11486)
* update stream to 0.2.6 (#11483)
* update stream to 0.2.2
* update stream to 0.2.3
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.5
* update stream to 0.2.6
* Update meta.yaml (#11487)
* Update connectome-workbench to 1.3.2 (#11468)
Now needs QT 5.7
* Update deblur to 1.1.0 (#11500)
* Update domclust to 1.2.8 (#11498)
* WisecondorX: bump version (#11501)
* Bump as GitHub wasn't working yesterday (#11502)
* Added recipe for Sequenza (#10367)
* Added recipe for Sequenza
* Removed fn entry in source section
* Trying with only one URL
* copynumber is a bioconductor package
* Added missing requirements section
* Removed mailing list address
* Added doi
* Added license_file
* Trying with different license_file path
* Fred2 bump (#11503)
* Bump as GitHub wasn't working yesterday
* Fix licence etc
* Scanpy scripts (#11413)
Doing squash and merge as requested by @nh3
* Bump version
* First implementation of scanpy-scripts bioconda recipe.
* fix path in build.sh
* Remove "noarch" flag as requested by bioconda recipe checklist
* Add a post install notice that post install test needs bats-core.
* Add more dependencies
* Skip building for python versions other than 3.6
* Target v0.0.2 which has non-ascii characters removed
* Lower version requirement for pandas and matplotlib to be the same as scanpy
* Requirement matplotlib>=3.0.0, declare noarch
* New: hmftools-cobalt; Update: hmftools-purple (#11507)
- hmftools-cobalt: Add latest version of PURPLE associated read counter,
COBALT, with support for hg38.
- hmftools-purple: PURPLE release with hg38 support.
* Update Picard to 2.18.15. (#11505)
* Genenotebook (#11476)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* Update pinning (#11514)
* Bump build number for updated dependency (#11510)
* Bump build number for updated dependency
* Try adding r-base to host requirements
* Try adding other requirements to host
* Pin to R version
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Tweak dependency version syntax
* Pin R and package versions correctly
* PacBio: Update pbcore to 1.6.5 (#11513)
* Bump r seurat scripts version (#11292)
* Bump version
* Remove noarch
* Could wrongly quoted version be causing an issue?
* Tweak pinning to try and fix CI error
* seqcluster:fix UMI detection. (#11511)
* seqcluster:fix UMI detection.
* Fix dependency
* quast 5.0.1 (#11479)
* quast 5.0.1
* quast 5.0.1: remove third-party site packages from the distibution pack
* quast 5.0.1: skip Glimmer in test
* quast 5.0.1: joblib and simplejson dependencies added to meta.yaml (Setuptools downloading is disabled in conda build)
* quast 5.0.1: explicit joblib and simplejson dependencies removed (Setuptools downloading is disabled in conda build)
* quast 5.0.1: Python 2 and 3 compatible code in build.sh
* wcX bugfixes (#11508)
* wcX bugfixes
* fixed shasum
* Update fastspar to 0.0.7 (#11515)
* Update iqtree to 1.6.7.2 (#11525)
* Update illumina-interop to 1.1.6 (#11523)
* Update hapbin to 1.3.0 (#11522)
* Update hlama to 3.0.1 (#11520)
* Update gb_taxonomy_tools to 1.0.1 (#11519)
* Update gffcompare to 0.10.5 (#11517)
* Update fast5seek to 0.1.1 (#11516)
* Update deepbinner to 0.2.0 (#11499)
* Update deepbinner to 0.2.0
* Update meta.yaml
Try same fix as in #11240
* Update ncbi-vdb to 2.9.3 (#11550)
* Update mikado to 1.2.4 (#11549)
* Update perl-pcap to 3.5.2 (#11543)
* Update python-hyphy-python to 0.1.9 (#11545)
* Update mlst to 2.15.2 (#11547)
* Update perl-sanger-cgp-vcf to 2.2.1 (#11542)
* Update merfishtools to 1.5.0 (#11537)
* Update perl-sanger-cgp-vagrent to 3.3.3 (#11536)
* Update nonpareil to 3.3.3 (#11535)
* Update prophex to 0.1.1 (#11532)
* Update krakenuniq to 0.5.3 (#11527)
* Update novoplasty to 2.7.2 (#11530)
* Update minced to 0.3.2 (#11529)
* Update mapdamage2 to 2.0.8 (#11528)
* Update perl-sanger-cgp-allelecount to 4.0.0 (#11538)
* Update pyvolve to 0.9.0 (#11531)
* Genenotebook (#11512)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* add plek (#11554)
* Update pyimzml to 1.2.4 (#11534)
* Bump shovill (#11555)
* PacBio: Update minimum pbcore version (#11556)
* We want all users of PacBio tools to be able to
use our utilities with pbmm2 alignments.
* Add recipe for translate-gard v1.0.4 (#11557)
* bioconductor-rnaseqsamplesizedata (#11475)
* Adding Recipe for bioconductor-rnaseqsamplesizedata
* Updated metadata for RnaSeqSampleSizeData
* nextflow 18.10.1 (#11558)
* Update raxml to 8.2.12 (#11567)
* Update r-fgwas to 0.3.6 (#11566)
* Update rapid to 0.7 (#11565)
* Update r-spieceasi to 1.0.2 (#11564)
* Update rcorrector to 1.0.3.1 (#11562)
* Update quicktree to 2.4 (#11560)
* Update paladin to 1.4.4 (#11541)
* Update paladin to 1.4.4
* delete md5
* Update build.sh
* Update build.sh
* Fix and unblacklist Tadarida-D (#11568)
* Add recipe for rgt
* Fix and un-blacklist tadarida-d
* Remove RGT
* bumping groot (#11575)
* update pymzml (#11573)
* Add bioconductor-rnaseqsamplesize (#11559)
* Add bioconductor-rnaseqsamplesize
* Update recipe
* Fixing some URLs
* Update dependencies missing
* Update trumicount to 0.9.11 (#11576)
* Update ConFindr to 0.4.4 (#11578)
* Added new versions for biopet-scatterregions (#11572)
* Added new versions for biopet-bamstats (#11571)
* R ggbiplot (#11584)
* add R -e 'httr::set_config(httr::config(ssl_verifypeer = 0L)); install.packages(devtools, repos=http://mirrors.ebi.ac.uk/CRAN/); library(devtools); install_github(vqv/ggbiplot); library(ggbiplot)'
* add r-ggbiplot
* update meta.yaml
* update meta.yaml
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix errors
* fix errors number 1
* Update rebaler to 0.1.2 (#11563)
* Update rebaler to 0.1.2
* Remove fn
* bump graphclust (#11585)
* Update seqyclean to 1.10.09 (#11589)
* Update stringmlst to 0.5.1 (#11590)
* Update snp-dists to 0.6.2 (#11592)
* Update snippy to 4.3.3 (#11596)
* Update canu to 1.8 (#11600)
* Update starfish to 0.0.27 (#11599)
* Update womtool to 36 (#11594)
* Update telseq to 0.0.2 (#11598)
* Update snp-sites to 2.4.1 (#11588)
* Added recipe for pydemult: Streamed and parallel demultiplexing of fastq files (#11471)
* Added recipe for pydemult
* Bumped version in favor of py3.5
* bump vcf2db to latest commit (#11601)
* bump vcf2db to latest commit
* fix shasum
* Fixing source url
* Update: TitanCNA; hg38 cytoband support and fix for normalization (#11604)
* megan (#11046)
* megan6: initial commit
* megan6: intermediate commit
* megan: made tests work
* megan: doc improvement
* megan: added osx dmg file
* megan: add java to build requirements
* megan: removed new line
* megan: removed osx sources
* Update meta.yaml
* bumping hulk (#11607)
* Update hotspot3d to 1.8.2 (#11521)
* Update hotspot3d to 1.8.2
* Add perl-json as dependency
* Add perl-archive-extract as dependency
* Fqzcomp (#11606)
* Added recipe for fqzcomp
* There is no configure script
* Maybe this works
* Added gcc as build requirement
* Removed gcc again (lint issue)
* Maybe these exports will do the trick
* Nope!
* Added cxx as host requirement
* Compilers are only allowed in build section
* There is no need for make install
* Copy-paste error...
* Add vcf-annotator recipe (#11481)
* Add vcf-annotator recipe
* added pyvcf dependency
* Update meta.yaml
* stacks: fix for @ in exe_path (#11580)
* stacks: fix for @ in exe_path
* stacks: fixed path
* New version with bugfix and different progressiveMauve version. (#11613)
* Sspupdate (#11614)
* New version with bugfix and different progressiveMauve version.
* Keeping old version as folder.
* Push build number.
* Update SVDB to version 1.3.0 (#11506)
* new file: recipes/svdb/1.1.2/meta.yaml
renamed: reipes/svdb/svdb.patch -> recipes/svdb/1.1.2/svdb.patch
modified: recipes/svdb/meta.yaml
* deleted: 1.1.2/meta.yaml
deleted: 1.1.2/svdb.patch
* Bump nanosim (#11608)
* Bump nanosim
* Add scipy as dep
* Add recipe for perl-number-range (#11621)
* New build for grid (#11620)
* update grid
* update build num
* Recipe for das_tool 1.1.1 (#10528)
* recipe for das_tool 1.1.1
* Add recipe for sompy (#11624)
* cmake modified to build with NDEBUG (#11328)
* cmake modified to build with NDEBUG
* Update meta.yaml
* new build with fasta test
* new build with fasta test
* Fix and unblacklist TwoPaCo (#11622)
* Add recipe for TwoPaCo
* Unblacklist twopaco
* Modify and unblacklist recipe for ESTmapper (#11623)
* Modify and unblacklist recipe for ESTmapper
* Add patch
* Modify and unblacklist recipe for Metaseq (#11625)
* Fix recipe for metaseq and remove from blacklist
* Remove build.sh
* nextflow 18.10.1 build 2 (#11630)
* Add Clust (#11619)
* Add clust
* Clean recipe
* Add "noarch"
* Add DOI
* Add build file
* Python 2.7
* Fix scikit-learn dependency
* Trigger new build
* Update: PureCN (multicore) and PURPLE (plotting X libraries) (#11631)
- PureCN: adds support for specifying cores on command line
- PURPLE: adds X library dependencies required for creating
plots
* scripts/travis-run.sh: added a cleaner method to check for env vars (#11612)
* Increase the number of k value usable in bcalm (request by @Malfoy) (#11610)
* Increase the number of k value usable in bcalm (request by @Malfoy)
* Change compilation parameter to reduce memory impact of compilation
* Update anndata to 0.6.11 (#11637)
* Update nglview to 1.1.7 (#11643)
* Update binsanity to 0.2.7.1 (#11644)
* Update cgat-core to 0.5.4 (#11645)
* Update nanosv to 1.2.2 (#11673)
* Update abeona to 0.36.0 (#11670)
* Update pyfaidx to 0.5.5.2 (#11659)
* Update agfusion to 1.23 (#11668)
* Update iqtree to 1.6.8 (#11686)
* update iqtree to 1.6.8
* Trigger rebuild
* Update validators to 0.12.2 (#11672)
* Update python-edlib to 1.2.3.post1 (#11664)
* update for Purge Haplotigs (#11690)
* Update loompy to 2.0.16 (#11667)
* Update loompy to 2.0.16
* Update meta.yaml
* IgBLAST 1.10.0 (#11693)
* Update wtforms-alchemy to 0.16.7 (#11679)
* Update sickle to 0.6.4 (#11663)
* Update sickle to 0.6.4
* Remove fn and libgcc runtime dep
* Update confindr to 0.4.5 (#11696)
* Batvi (#11695)
* batvi initial
* Guideline compatibility..
* Dummy test section..
* Missing java dependency..
* use openjdk instead of java-jdk ..
* source specified in github ..
* trigger build (package did not have batindel directory) ..
* update SHA256 ..
* update SHA256 ..
* Update pythonpy to 0.4.11 (#11661)
* Update cortexpy to 0.45.6 (#11660)
* Update sevenbridges-python to 0.16.0 (#11674)
* Update solvebio to 2.7.0 (#11657)
* Update mathstats to 0.2.6.5 (#11656)
* Update goatools to 0.8.9 (#11641)
* Add gnies (#11627)
* Add gnies
* noarch python
* Update meta.yaml
* Add recipe for SKA v1.0 (#11581)
* Add recipe for SKA v1.0
* Add lib path for zlib
* Older gcc
* Correct install dir
* Try static linking
* Dynamic linking on OS X
* ldd command test
* correct program
* Remove ldd command
* Add recipe for transit version 2.3.1 (#11701)
* Add recipe for transit version 2.3.1
* Use skip, add spaces.
* Update meta.yaml (#11699)
* remove pyqi (#11704)
* Update python-chado to 2.2.0 (#11714)
* update python-chado
* 2.2.1
* Update vcfanno to 0.3.1 (#11710)
* FGMP-1.0.1 (#11278)
* FGMP-1.0.1 recipe
* remove unncessary build info
* add r-nabor (#11716)
* update stream to 0.2.2
* update stream to 0.2.3
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.5
* update stream to 0.2.6
* add r-nabor recipe
* update r-nabor recipe
* update r-nabor recipe
* r-pctgcdata (#11715)
* r-pctgcdata
* r-pctgcdata - fix
* r-pctgcdata - fix
* Update meta.yaml
* Fix plek by a new branch (#11605)
* Modify the PLEK recipe
* Start fixing PLEK, though it requires compilation
* update build.sh
* update yaml
* fix build.sh
* update build.sh
* Update recipe for plek
* add bioconductor-chromvar recipe (#11718)
* add bioconductor-chromvar recipe
* fix bioconductor-tissueenrich
* Apparently the popdel recipe didn't get correctly merged
* Final merge conflicts
* Bioc quick test (#12547)
* Update kallisto to 0.45.0 (#12117)
* Update validators to 0.12.3 (#12116)
* Update illumina-interop to 1.1.7 (#12115)
* Update umi_tools to 0.5.5 (#12123)
* Update tiptoft to 1.0.0 (#12122)
* Update: TitanCNA with fix for hg38 plotting (#12130)
* blockclust (#12111)
* added eden 1.1 version used in blockclust
* Update meta.yaml
* eden checksum and test
* added zlib requirement
* add include and lib paths to build.sh
* add include and lib paths to build.sh
* modify makefile flags using sed
* modify makefile flags using sed
* use c++
* Update build.sh
* Update build.sh
* LDFLAGS not used in makefile
* remove v1.1
* add blockclust 1.1.0 recipe
* skip osx build
* added tarball url and checksum; removed conda_build_config.yaml
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Update chewbbaca to 2.0.16 (#12132)
* Update abeona to 0.40.0 (#12131)
* ping to eden 1.1 (#12134)
* clean swap file (#12137)
* Update corset to 1.07 (#12143)
* Update peddy to 0.4.3 (#12144)
* blockclust latest source and added cloudpickle as requirement (#12142)
* Update nanomath to 0.22.0 (#12149)
* Update pymvpa to 2.6.5 (#12152)
* Updated to version 1.4.0 (#12138)
* Updated to version 1.4.0
* Resetting build number to 0 and build->host
* Update transdecoder to 5.5.0 (#12172)
* Update gridss to 2.0.1 (#12190)
* Update tracer to 1.7.1 (#12189)
* Update flowcraft to 1.4.0 (#12179)
* Update seqbuster to 3.2 (#12182)
* Update perl-io-compress to 2.081 (#12201)
* Update twobitreader to 3.1.6 (#12205)
* Update twobitreader to 3.1.6
* Update meta.yaml
* Update gtfparse to 1.2.0 (#12186)
* Update gtfparse to 1.2.0
* remove compiler
* Update htseq to 0.11.0 (#12177)
* Update htseq to 0.11.0
* add compiler
* Update htseq to 0.11.0 (#12239) [testing co-author]
* Update htseq to 0.11.0
* add compiler
Co-authored-by: Bjoern Gruening <[email protected]>
* alfred v0.1.16 (#12240)
* alfred v0.1.16
* makefile patch
* makefile patch
* Update scrm to 1.7.3 (#12150)
* Update scrm to 1.7.3
* Update scrm to 1.7.3
* Mob suite update 1.4.8 --> 1.4.9 (#12244)
We fixed a small bug related to repetitive elements database reconstruction on each run. Should only run once during the first mob_typer run. Should be good now for parallel runs.
* PeptideShaker updated to v1.16.35 & SearchGUI updated to 3.3.9 (#12241)
* PeptideShaker updated to v1.16.32
SearchGUI updated to v3.3.6
* PeptideShaker updated to v1.16.35
* SearchGUI updated to v3.3.9
* First attempt at a recipe for ncrf (#12101)
* First attempt at a recipe for ncrf
* changed from copies to symlinks
* including absolute path in symlinks
* PacBio: Update `pbmm2` to version 0.11.0 (#12246)
* Gimmemotifs version 0.13.0 (#12245)
* new release to fix numpy incompatibility
* GimmeMotifs 0.13.0 release test
* numpy 1.15
* version 0.13.0
* Fix about:home and extra:
* PacBio: Update `isoseq3` to version 3.1.0 (#12263)
* add python to host section (#12264)
* Update confindr to 0.4.7 (#12266)
* new build of GRiD (#12269)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* peptideshaker, searchgui: version bump (#12136)
* peptideshaker, searchgui: version bump
solving https://github.com/compomics/searchgui/issues/192
* Update peptide-shaker.py
* searchgui: added c compiler for building
test if linking errors go away this way
* searchgui: removed noarch
* Update: bcbio, bcbio-vm with CWL non-human fixes (bcbio/bcbio-nextgen#2473) (#12273)
* Make snakemake a noarch package. (#12274)
* noarch: python in combination with version constraint
* Cleanup deps and simplify version definition.
* Genenotebook v0.1.9 (#12277)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* Create r-airr recipe (#12284)
* Create r-airr recipe using bgruening/conda_r_skeleton_helper
* Update meta.yaml
* Findbin::Real added (#12291)
* Added version bump to 1.3 (#12292)
* ngs-bits 2018_11 (#12262)
* Updated ngs-bits to version 2018_10
* Updated ngs-bits to version 2018_11
* minor edit in grid (#12287)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* minor edit to grid
* Fred2 update (#12259)
* Update FRED2 Recipe
* msstitch version 2.9 (#12296)
* r-mvr (#12300)
This is a non-parametric method for joint adaptive mean-variance regularization and variance sta-
bilization of high-dimensional data.
* Bump to Gromacs 2018.3 + re-enable OSX build (#12299)
* Gromacs 2018.3 + re-enable osx build
See also #7825 on OSX build
Include RRID for Gromacs (see bioconda/bioconda-utils#252)
* disabled ocl-icd on osx; not available (or needed?)
https://anaconda.org/conda-forge/ocl-icd
* pyGenomeTracks update of dependencies (#12279)
* Update pyGenomeTracks recipe to enable py3 support and updating outdated dependecy list
* Increase build number
* Update meta.yaml
* Exclude Python 3.5
* Gromacs 2018.4 (#12302)
* quast 5.0.2 (#12303)
* Update meta.yaml (#12275)
* Update meta.yaml
r-rsqlite version dependency added
* Update meta.yaml
Updated build number to 1
* Use the extended-base container because of wget issues when downloading databases (#12297)
* Update duphold to 0.1.0 (#12257)
* Update flashlfq to 0.1.109 (#12256)
* Update planemo to 0.57.0 (#12251)
* Update meta.yaml (#12258)
* Update scalpel to 0.5.4 (#12249)
* Update scalpel to 0.5.4
* Fix url
* edit grid (#12298)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* minor edit to grid
* minor edit to recipe grid
* added feather to deps (#12293)
* R tigger (#12286)
* Create recipe for r-tigger (#12271)
* Create recipe for r-tigger using bgruening/conda_r_skeleton_helper.
* Delete bld.bat
* Remove windows support
* update scprep to v0.8.1 (#12306)
* Update nanoget to 1.7.5 (#12252)
* Update nanoget to 1.7.5
* Bump to version 1.7.6
should fix the README.md problem
* gffcompare: version bump (#12308)
* Update: cromwell (36), bcbio (Cromwell Docker runs) (#12307)
* Update: cromwell (36), bcbio (Cromwell Docker runs)
* Pin java to 8 to avoid compile errors on 11
* HiCExplorer update to version 2.2-beta (#12309)
* HiCExplorer update to version 2.2-beta
* Remove of '-' from version number
* Numpy set to 1.15
* Update meta.yaml
* upgrade to version 2.8.1 (#12316)
* Create Airr recipe (#12318)
* Create AIRR recipe using conda skeleton pypi.
* Add noarch python
* Clean host requirements
* Added nimnexus [v0.1] (#12133)
* added nimnexus
* Fix sha
* Update build.sh
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* [WIP] Add R-loom (#12320)
* initial WIP skeleton
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* try osx
* Create Changeo recipe (#12321)
* Create changeo recipe using conda skeleton pypi.
* EDIT about section
* ADD noarch generic
* Update noarch to python
* Clean host requirements
* Add test for scripts
* Change requirement to python>=3.4
* Add noarch pyton
* r-corbi (#12325)
* r-nam (#12327)
* Update pybedtools to 0.8.0 (#12324)
* Update pybedtools to 0.8.0
* rm cython requirement
* MSGFplus does not work with newer Java (#12330)
* Trying to not use a very new java version since the latest ver…
dpryan79
added a commit
to bioconda/bioconda-recipes
that referenced
this issue
Mar 13, 2019
* update mzr as a test
* Begin building for R 3.5.1 (#11252)
* Bump everything for R 3.5.1
* Fix most of the linting issues
* Update blacklist
* Revert "Fix most of the linting issues"
This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5.
* should_not_use_fn
* More fixes
* Fix incorrect yaml
* Should really fix the linting blacklist stuff
* Fix many recipes
* Fix some linting
* Fix r-wicket
* Update derfinder
* Pin to a given bioconductor release.
* Add missing packages
* Restore identifiers to bioconductor packages
* Restore extra information to R packages
* Update R bulk (#11283)
* fixed incorrect doi of publication (#11175)
* Added recipe for kinSimRiboswitch (#10838)
Added recipe for kinSimRiboswitch, a pipeline for simulating the folding
kinetics of RNA switches.
* update multiqc-bcbio (#11187)
* Add recipe for PopDel (#11181)
* Add recipe for PopDel
* Add clang and clangxx to build config
* update seqbuster (#11190)
* update seqbuster
* fix build
* fix test
* Update pyseer to 1.1.2 (#11172)
* bump sourmash (#11197)
* Update BASIC to v1.4.1 (#11195)
* Update BASIC to v1.4.1
* Trigger circleci
* Fix build number
* Update nf-core-1.2 (#11191)
* Update nf-core-1.2
* Update build script
* Update to InterMine 1.11.0 (#11182)
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Add tinyfasta-0.1.0 (#11177)
* Add tinyfasta
* Update build script
* Fix structure of build section
* Bumping snippy (#11198)
* Remove older version
* Bump snippy
* VEP: bump major version (#11201)
* VEP: bump major version
* VEP: bumped plugin major version
* VEP: update plugin install
Download and install all plugin modules, instead of just a selection
* Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200)
* Update: PureCN to latest devel (1.11.13); wrapper scripts
PureCN development (https://github.com/lima1/PureCN) has several
improvements over the BioC 3.6 release for handling multiple VCF input
types, and is back compatible with R 3.4.1 so still builds cleanly
with two new dependencies.
Also exposes PureCN wrapper scripts for running from the command line.
Prefixes ambiguous scripts with PureCN_.
* Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet
* add cassiopee release 1.0.9 (#11168)
* add cassiopee release 1.0.9
* update to conda build 3
* remove old version backup and use sha256 for source
* Bump abeona version to 0.26.0 (#11202)
* Bump abeona version to 0.24.0
* Bump abeona version to 0.26.0
* Update LexMapr to v0.1.2 (#11192)
* Update LexMapr to v0.1.2
* Add rdflib dep
* Update svtyper to 0.7.0 (#11196)
* Update svtyper to 0.7.0
* Add recipe for perl-gtdbtk (#11194)
* Add recipe for perl-gtdbtk
* New recipe for RFMix (#11205)
* New recipe for RFMix
* updated version number information
* updated version number information
* updated version number information
* initial purge_haplotigs commit (#11049)
* initial purge_haplotigs commit
* bioconda revisions, updating test commands to run the pipeline on the test dataset
* rolling back test commands
* Add recipe for fsm-lite (#11209)
* Add recipe for fsm-lite
* Add prefix to make
* Remove v from version string
* Updated reparation_blast to version v.1.0.7 (#11210)
* Update sambamba to 0.6.8 (#11212)
* Bump sambamba to 0.6.8
* It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified.
* Set some environment variables
* The compiled binary is in a different place now
* ldc provides some libraries that are linked against.
* mtbseq: update recipe (#11110)
* changed download location/add test
* remove test
* Confindr (#11217)
* Update confindr to 0.4.2
* Fix typo in specifying version of pysam
* Update Genenotebook to v0.1.4 (#11218)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* updating to 0.1.3 (#11221)
* sartools1.6.6 (#11222)
* Perl bio automatedannotation (#11216)
* Initial recipe for Bio-AutomatedAnnotation
* Change URL
* Run cpanm tests
* Temporarily set HOME
* Use cpan version instead
* Add more depencencies
* Set bioperl version
* unset bioperl version, add bioperl-run
* New release including version in modules
* Remove comments
* build -> host
* Upgrade r-biodb to v1.1.2. (#11213)
* Upgrade r-biodb to v1.1.2.
* Remove old versions of r-biodb.
* Comment out libgfortran.
* PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215)
* PeptideShaker: updated to version 1.16.30
- Bugfix: HOME was still being used when folder with customised reports was specified.
- Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line.
* SearchGUI: updated to version 3.3.5.
- BUG FIX: Cleanup of the temp path options when used as options for the other command lines.
- FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2.
- LIBRARY UPDATE: Updated utilities to version 4.12.8.
* Update meta.yaml (#11227)
* Svtools 0.4.0 (#11208)
* Remove directories for old svtools versions
* Update svtools to v0.4.0
* Move build number back to 0
* Anvio 52 (#11230)
* Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software.
* Remove cgat-scripts from blacklist. (#11228)
* Add new formula: bazam 1.0.1 (#11229)
* Update gatk4 to 4.0.10.0 (#11224)
* Add recipe for gtdbtk 0.1.3 (#11211)
* Add recipe for gtdbtk
* Added initial htstream recipe (#11113)
* HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data.
* DeepTools 3.1.3 (#11226)
* PacBio: Update `pbmm2` to version 0.10.0 (#11225)
* fastqc: update to version 0.11.8 (#11214)
* fastqc: update to version 0.11.8
* Update meta.yaml
* Phame (#11223)
* mac recipe and added bioperl
* changing bill number
* added no osx
* adding new version
* removed separate recipe for mac, dont need it
* now running same recipe for mac and linux
* fixed the way fasttrees version was being parsed
* minor change test
* adding detailed description
* restaging the build number
* new version
* Make sure to use bioperl and perl 5.26
* Updated ngs-bits to version 2018_10 (#11235)
* PacBio: Update `pbsv2` to version 2.0.2 (#11236)
* Update VSEARCH to 2.8.5 (#11239)
* Fix shorah recipe and remove from blacklist. (#11241)
* Fix shorah recipe and remove from blacklist.
* Fix blas variant.
* Remove imports from tests.
* unicycler 0.4.7 (#11240)
* unicycler 0.4.7
* unicycler: Work around ValueError: invalid
Unicycler thinks the terminal has 0 columns and produces this error:
File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks
raise ValueError("invalid width %r (must be > 0)" % self.width)
ValueError: invalid width -5 (must be > 0)
* Octopus: update to 0.5.1-beta (#11244)
* New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247)
- PURPLE SV and heterogeneity caller for somatic tumor/normal samples.
- VarDictJava -- 1.5.6 release with fixes for SV calling
- PureCN -- add signature dependency and update with fixes for test
samples.
* Dinucleotide patterns analysis tools v1.0 (#11245)
* Dinucleotide patterns analysis tools v1.0
* Lets try it, it seems to work locally for me.
* Enable SpoTyping_plot.r (#11248)
* rerun again (#11233)
* rerun again
* Update meta.yaml
* Delete build.sh
* Update segway dependency optbuild to 0.2 (#10459)
* Update segway dependency optbuild to 0.2
* Update build and architecture requirements for optbuild 0.2
* Add six as a dependency to the optbuild recipe
* Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249)
* Add prefix dnp- to the package names
* Update build.sh
* Update build.sh
* Bump beast version to 1.10.2 (#11250)
* add maxquant (#11253)
* add mayquant
* relax tests
* PacBio: Update `pbmm2` to version 0.10.1 (#11256)
* PacBio: Update `pbmm2` to version 0.10.1-1 (#11257)
* remove xsv recipe (#11259)
* add blast dependency (#11258)
* Added riborex recipe (#11251)
* Added riborex recipe
* Relaxed version constraints
* Pinned r-core for fdr tools
* fixed the r-base stuff upstream
* Update meta.yaml
* fix graphprot (#11234)
* increase build number
* remove from blacklist
* use cxx instead of c
* move coreutoils to build section
* set additional paths
* patch makefile
* blind try
* update patch
* explicitely copy from src_dir
* update deprecated prefix variable
* Revert "update deprecated prefix variable"
This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d.
* update deprecated prefix variable
* try moving to host section
* Bump mash (#11264)
* Add fmlrc (#11265)
* Add fmlrc
* add doi
* PacBio: Update pb-falcon to 0.2.4. (#11266)
* Add kopt recipe (#11269)
* Genomepy 0.5.2 (#11267)
* release 0.5.2 of genomepy
* trigger new build
* remove genomepy from blacklist
* locale for osx
* updated locale test
* PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275)
* Update mmseqs2 recipe to new release 6-f5a1c (#11272)
* Update yacrd to version 0.4.1 (#11273)
* Add scprep (#11270)
* Add scprep
* All of these should not be needed as host dep
* Metawrap preqs2 (#11242)
* fixed issues
* fixed issues
* added tests
* fixed tab
* gemma 0.98 (#11254)
* gemma 0.98
* gemma 0.98
Leave gsl and zlib out of runtime dependencies
* Add DCA recipe (#11274)
* Add DCA recipe
* add noarch and doi
* remove skip
* Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib
* Various fixes for bulk and trigger a rebuild (#11313)
* Various fixes, at least 4 packages (and their dependencies) should still fail (#11320)
* A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336)
* Fix various recipes (#11354)
* Fix various recipes
* Fix more recipes
* Various CRAN package fixes, since they all lack license files (#11372)
* Various CRAN package fixes, since they all lack license files
* Fix the r-dartr recipe
* There is a light at the end of the tunnel (#11381)
* There is a light at the end of the tunnel
* Licenses no longer exist
* [BULK] Fixes for R/Bioconductor packages (#11406)
* Require `r-base >=3.5` for some packages
* Fix various CRAN packages lacking license file
* Add missing libnetcdf requirement to bioconductor-mzr
* Remove r-alakazam (moved to conda-forge)
Fix linting issue:
```
recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating
```
* [BULK] Many R 3.5 only packages (#11410)
* [BULK] Bulk update 191018b (#11419)
* update mzr as a test
* Begin building for R 3.5.1 (#11252)
* Bump everything for R 3.5.1
* Fix most of the linting issues
* Update blacklist
* Revert "Fix most of the linting issues"
This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5.
* should_not_use_fn
* More fixes
* Fix incorrect yaml
* Should really fix the linting blacklist stuff
* Fix many recipes
* Fix some linting
* Fix r-wicket
* Update derfinder
* Pin to a given bioconductor release.
* Add missing packages
* Restore identifiers to bioconductor packages
* Restore extra information to R packages
* Update R bulk (#11283)
* fixed incorrect doi of publication (#11175)
* Added recipe for kinSimRiboswitch (#10838)
Added recipe for kinSimRiboswitch, a pipeline for simulating the folding
kinetics of RNA switches.
* update multiqc-bcbio (#11187)
* Add recipe for PopDel (#11181)
* Add recipe for PopDel
* Add clang and clangxx to build config
* update seqbuster (#11190)
* update seqbuster
* fix build
* fix test
* Update pyseer to 1.1.2 (#11172)
* bump sourmash (#11197)
* Update BASIC to v1.4.1 (#11195)
* Update BASIC to v1.4.1
* Trigger circleci
* Fix build number
* Update nf-core-1.2 (#11191)
* Update nf-core-1.2
* Update build script
* Update to InterMine 1.11.0 (#11182)
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Add tinyfasta-0.1.0 (#11177)
* Add tinyfasta
* Update build script
* Fix structure of build section
* Bumping snippy (#11198)
* Remove older version
* Bump snippy
* VEP: bump major version (#11201)
* VEP: bump major version
* VEP: bumped plugin major version
* VEP: update plugin install
Download and install all plugin modules, instead of just a selection
* Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200)
* Update: PureCN to latest devel (1.11.13); wrapper scripts
PureCN development (https://github.com/lima1/PureCN) has several
improvements over the BioC 3.6 release for handling multiple VCF input
types, and is back compatible with R 3.4.1 so still builds cleanly
with two new dependencies.
Also exposes PureCN wrapper scripts for running from the command line.
Prefixes ambiguous scripts with PureCN_.
* Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet
* add cassiopee release 1.0.9 (#11168)
* add cassiopee release 1.0.9
* update to conda build 3
* remove old version backup and use sha256 for source
* Bump abeona version to 0.26.0 (#11202)
* Bump abeona version to 0.24.0
* Bump abeona version to 0.26.0
* Update LexMapr to v0.1.2 (#11192)
* Update LexMapr to v0.1.2
* Add rdflib dep
* Update svtyper to 0.7.0 (#11196)
* Update svtyper to 0.7.0
* Add recipe for perl-gtdbtk (#11194)
* Add recipe for perl-gtdbtk
* New recipe for RFMix (#11205)
* New recipe for RFMix
* updated version number information
* updated version number information
* updated version number information
* initial purge_haplotigs commit (#11049)
* initial purge_haplotigs commit
* bioconda revisions, updating test commands to run the pipeline on the test dataset
* rolling back test commands
* Add recipe for fsm-lite (#11209)
* Add recipe for fsm-lite
* Add prefix to make
* Remove v from version string
* Updated reparation_blast to version v.1.0.7 (#11210)
* Update sambamba to 0.6.8 (#11212)
* Bump sambamba to 0.6.8
* It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified.
* Set some environment variables
* The compiled binary is in a different place now
* ldc provides some libraries that are linked against.
* mtbseq: update recipe (#11110)
* changed download location/add test
* remove test
* Confindr (#11217)
* Update confindr to 0.4.2
* Fix typo in specifying version of pysam
* Update Genenotebook to v0.1.4 (#11218)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* updating to 0.1.3 (#11221)
* sartools1.6.6 (#11222)
* Perl bio automatedannotation (#11216)
* Initial recipe for Bio-AutomatedAnnotation
* Change URL
* Run cpanm tests
* Temporarily set HOME
* Use cpan version instead
* Add more depencencies
* Set bioperl version
* unset bioperl version, add bioperl-run
* New release including version in modules
* Remove comments
* build -> host
* Upgrade r-biodb to v1.1.2. (#11213)
* Upgrade r-biodb to v1.1.2.
* Remove old versions of r-biodb.
* Comment out libgfortran.
* PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215)
* PeptideShaker: updated to version 1.16.30
- Bugfix: HOME was still being used when folder with customised reports was specified.
- Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line.
* SearchGUI: updated to version 3.3.5.
- BUG FIX: Cleanup of the temp path options when used as options for the other command lines.
- FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2.
- LIBRARY UPDATE: Updated utilities to version 4.12.8.
* Update meta.yaml (#11227)
* Svtools 0.4.0 (#11208)
* Remove directories for old svtools versions
* Update svtools to v0.4.0
* Move build number back to 0
* Anvio 52 (#11230)
* Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software.
* Remove cgat-scripts from blacklist. (#11228)
* Add new formula: bazam 1.0.1 (#11229)
* Update gatk4 to 4.0.10.0 (#11224)
* Add recipe for gtdbtk 0.1.3 (#11211)
* Add recipe for gtdbtk
* Added initial htstream recipe (#11113)
* HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data.
* DeepTools 3.1.3 (#11226)
* PacBio: Update `pbmm2` to version 0.10.0 (#11225)
* fastqc: update to version 0.11.8 (#11214)
* fastqc: update to version 0.11.8
* Update meta.yaml
* Phame (#11223)
* mac recipe and added bioperl
* changing bill number
* added no osx
* adding new version
* removed separate recipe for mac, dont need it
* now running same recipe for mac and linux
* fixed the way fasttrees version was being parsed
* minor change test
* adding detailed description
* restaging the build number
* new version
* Make sure to use bioperl and perl 5.26
* Updated ngs-bits to version 2018_10 (#11235)
* PacBio: Update `pbsv2` to version 2.0.2 (#11236)
* Update VSEARCH to 2.8.5 (#11239)
* Fix shorah recipe and remove from blacklist. (#11241)
* Fix shorah recipe and remove from blacklist.
* Fix blas variant.
* Remove imports from tests.
* unicycler 0.4.7 (#11240)
* unicycler 0.4.7
* unicycler: Work around ValueError: invalid
Unicycler thinks the terminal has 0 columns and produces this error:
File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks
raise ValueError("invalid width %r (must be > 0)" % self.width)
ValueError: invalid width -5 (must be > 0)
* Octopus: update to 0.5.1-beta (#11244)
* New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247)
- PURPLE SV and heterogeneity caller for somatic tumor/normal samples.
- VarDictJava -- 1.5.6 release with fixes for SV calling
- PureCN -- add signature dependency and update with fixes for test
samples.
* Dinucleotide patterns analysis tools v1.0 (#11245)
* Dinucleotide patterns analysis tools v1.0
* Lets try it, it seems to work locally for me.
* Enable SpoTyping_plot.r (#11248)
* rerun again (#11233)
* rerun again
* Update meta.yaml
* Delete build.sh
* Update segway dependency optbuild to 0.2 (#10459)
* Update segway dependency optbuild to 0.2
* Update build and architecture requirements for optbuild 0.2
* Add six as a dependency to the optbuild recipe
* Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249)
* Add prefix dnp- to the package names
* Update build.sh
* Update build.sh
* Bump beast version to 1.10.2 (#11250)
* add maxquant (#11253)
* add mayquant
* relax tests
* PacBio: Update `pbmm2` to version 0.10.1 (#11256)
* PacBio: Update `pbmm2` to version 0.10.1-1 (#11257)
* remove xsv recipe (#11259)
* add blast dependency (#11258)
* Added riborex recipe (#11251)
* Added riborex recipe
* Relaxed version constraints
* Pinned r-core for fdr tools
* fixed the r-base stuff upstream
* Update meta.yaml
* fix graphprot (#11234)
* increase build number
* remove from blacklist
* use cxx instead of c
* move coreutoils to build section
* set additional paths
* patch makefile
* blind try
* update patch
* explicitely copy from src_dir
* update deprecated prefix variable
* Revert "update deprecated prefix variable"
This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d.
* update deprecated prefix variable
* try moving to host section
* Bump mash (#11264)
* Add fmlrc (#11265)
* Add fmlrc
* add doi
* PacBio: Update pb-falcon to 0.2.4. (#11266)
* Add kopt recipe (#11269)
* Genomepy 0.5.2 (#11267)
* release 0.5.2 of genomepy
* trigger new build
* remove genomepy from blacklist
* locale for osx
* updated locale test
* PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275)
* Update mmseqs2 recipe to new release 6-f5a1c (#11272)
* Update yacrd to version 0.4.1 (#11273)
* Add scprep (#11270)
* Add scprep
* All of these should not be needed as host dep
* Metawrap preqs2 (#11242)
* fixed issues
* fixed issues
* added tests
* fixed tab
* gemma 0.98 (#11254)
* gemma 0.98
* gemma 0.98
Leave gsl and zlib out of runtime dependencies
* Add DCA recipe (#11274)
* Add DCA recipe
* add noarch and doi
* remove skip
* Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib
* Various fixes for bulk and trigger a rebuild (#11313)
* Various fixes, at least 4 packages (and their dependencies) should still fail (#11320)
* A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336)
* Fix various recipes (#11354)
* Fix various recipes
* Fix more recipes
* Various CRAN package fixes, since they all lack license files (#11372)
* Various CRAN package fixes, since they all lack license files
* Fix the r-dartr recipe
* There is a light at the end of the tunnel (#11381)
* There is a light at the end of the tunnel
* Licenses no longer exist
* [BULK] Fixes for R/Bioconductor packages (#11406)
* Require `r-base >=3.5` for some packages
* Fix various CRAN packages lacking license file
* Add missing libnetcdf requirement to bioconductor-mzr
* Remove r-alakazam (moved to conda-forge)
Fix linting issue:
```
recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating
```
* [BULK] Many R 3.5 only packages (#11410)
* Update pinning to R>=3.5 and a few runtime dependencies.
* CSAW is R 3.5 only
* Packages using beachmat are 3.5 only
* Packages using bioconductor-singlecellexperiment are R 3.5 only
* [BULK] Don't use r-base >=3.5, use a conda_build_config.yaml instead (#11452)
* Don't use r-base >=3.5, use a conda_build_config.yaml instead
* blacklist r-phangorn
* Update variancepartition
* R 3.5 for packages requiring singlecellexperiment
* Update a few packages
* Update a number of recipes (#11482)
* Update ensemblVEP and derfinder (#11504)
* Bulk update 251018 (#11577)
* [BULK] various package updates
* blacklist bioconductor-mzr
* A couple tweaks
* [BULK] Update 261018 (#11611)
* Apparently the r-rgeos bit works properly now.
* Add tissueenrich and try to fix scpipe on Linux
* A meaningless change just to trigger an update in bulk. (#11618)
* [BULK] update 271018 (#11628)
* Bump bioconductor-esetvis
* Fix yaqcaffy
* Fix more
* Another R 3.5 recipe
* [BULK] update 281018 (#11689)
* Add some files
* Fix arrayexpress
* Fix another 2
* Blacklist a bunch of bioconductor recipes that aren't likely to get built for a variety of reasons (mostly due to mzR). (#11697)
* Update blacklist (#11706)
* [BULK] fix bioconductor-tissueenrich (#11720)
* taxonkit 0.2.5 (#11318)
* Update csvtk (#11319)
* taxonkit 0.2.5
* csvtk 0.15.0
* bumping GROOT to 0.8.1 (#11323)
* HiCMatrix version 3 (#11322)
* Correcting dependencies
* Version 3 of HiCMatrix, the October release
* Update confindr to 0.4.3 (#11330)
* Drop-seq_tools: Version 2.0.0 (#11326)
* Update meta.yaml
* Update build.sh
some tool names changed to fit Camel case
* Update motus to build only for python3 (#11331)
* Update fpa to 0.2 version (#11333)
* update taxonkit to 0.3.0 (#11339)
* ntcard 1.1.0 (#11338)
* Update rgi (#11335)
* first commit
* update dependencies list
* change source to github
* change build number
* testing circleci
* update meta and build
* fix build
* move build script into meta
* remove older recipes
* line fix in bootstrap.py
* change python & matplotlib versions; add build.sh file
* add preprocessing selector to skip python 2.7
* move build script into meta.yaml
* Revert "line fix in bootstrap.py"
This reverts commit 5ac1ecd0142a5cfdfc8499c5b6ef4e1f629cd046.
* Update gmap to version 2018-07-04. (#11332)
MAX_READLENGTH environment variable has been disused since 2016-08-16.
* Upgrade r-biodb to 1.2.0a. (#11341)
* Upgrade r-biodb to 1.2.0a.
* Update meta.yaml
* Updated ont-tombo to version 1.5. (#11329)
* Updated ont-tombo to version 1.5.
* Updated with actual github release version hash.
* remove graphicsmagick (#11342)
* Build kraken2 for osx (#11343)
* First try for a bcalm recipes (#11344)
* New: cgpbigwig (BigWig manipulation); Update: bcbio (#11347)
- cgpbigwig (https://github.com/cancerit/cgpBigWig) provides bigwig
generation and manipulation command line tools including bam to bigwig
conversion.
- bcbio: fixes for QC on variants and peddy for CWL runs
* Try avoid some dependancy (#11349)
* Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8 (#11348)
* Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8
Also add about:home .
* Workaround https://github.com/conda-forge/bison-feedstock/issues/7
* Better bcalm recipes (#11350)
* Try avoid some dependancy
* Correct mess in build number, sorry
* R biodb (#11351)
* rebuild r-biodb
* trigger build
* Add recipe for pypairs (#11356)
* Update smoove to 0.2.1. (#11360)
* Update duphold to 0.0.9. (#11359)
* Update goleft to 0.2.0 (#11361)
* Bump slicedimage to 1.0.0 (#11362)
* Bump slicedimage to 1.0.1 (#11365)
* Added new versions for biopet-sampleconfig (#11268)
* perl-velvetoptimiser: update to 2.2.6 (#11369)
* update to 2.2.6
* remove unneeded patch
* Scanpy upgrade (#11371)
* Bump version
* Upgrade Scanpy
* Bump starfish to 0.0.25 (#11370)
* bumping groot to 0.8.2 (#11374)
* vep: bump subversion (#11367)
* Updated Krocus 1.0.1 (#11355)
* Add tiptoft
* Fix meta.yaml for tiptoft
* Add build script
* Updated krocus 1.0.1
* Add tiptoft 0.1.4 (#11352)
* Add tiptoft
* Fix meta.yaml for tiptoft
* Add build script
* Kodoja v0.0.9 (#11373)
* Add recipe for seer (#11263)
* Add recipe for seer
* lets try this
* Add newer compiler
* Using boost-cpp
* messed up version string
* Attempt building boost
* Use c++11 in boost
* Use python for boost install
* Correct python version spec
* try with different python version
* Fix b2 command
* Fix popd command
* build and link boost program options statically
* Fix tests
* Match dependency order
* Link openblas instead of blas
* Forcing rebuild with openblas
* Don't use armadillo wrapper
* Making review changes. Also trying original tests
* Previous tests were correct
* Add recipe for the translate-gard npm package version 1.0.3 (#11364)
* Fix umi tools (#11376)
umi_tools: clean up dependencies
* add support tools to PATH (#11379)
* Bump to v2.2.1 (#11380)
* Bump starfish to 0.0.26 (#11378)
* Update fpa to 0.3 (#11375)
* Update fpa to 0.3
* Correct error in sha256
* Reset build number
* Update trial to 2.5.5 (#11386)
* Update: bioconductor-titancna; 1.19.1 with hg38 support (#11388)
* Update: bioconductor-titancna; 1.19.1 with hg38 support
* Pin to R 3.4 to avoid pulling in 3.3 and 3.5 during mulled
* Add r-polysat version 1.7-3 (#11384)
* Update biomart version so that compatible with r351 (#11366)
* Update biomart version so that compatible with r351
* Update meta.yaml
reset build number as per https://bioconda.github.io/guidelines.html#buildnum
* Update entrez-direct to 10.0.20180927. (#11387)
* Added recipe for SonicParanoid 1.0.13 (#11271)
* Added recipe for SonicParanoid 1.0.13
* removed 'x.x' for numpy, added basic test
* fixed linter related errors
* compiler set to cxx and added host section (same build error!)
* removed host section
* moved numpy and cython to host section; restored build: noarch: python; added LICENSE.md
* removed build: noarch
* added build and extra sections
* set build number to 0; removed skip build; added python3 minimum version; added test for all executables.
* restored sh python module as requirement
* added Make to run; updated release to latest commit
* remove c compiler from meta.yaml
* modified build.sh to compile source codel added make in build section
* updated to latest commit
* updated to latest version with make included in setup.py
* reverted build.sh to the simplest version (python setup.py install)
* Add perl-json to build requirements to allow meme-chip to run to completion. Change meme-chip to use dreme-py3 instead of dreme if building with python 3. (#11389)
* Bump IgBLAST to 1.9.0 (#11393)
Bump IgBLAST to 1.9.0
Re-package the binary version this time. There are problems building the
source version when the configure script reaches this step:
"trying to build the NCBI SRA/VDB Toolkit from GitHub"
The previous problem about the binaries linking against libbz2.so, for
which we had no conda package, is now solved.
Also, this saves about 45 minutes compilation time.
* Add consan (#11395)
* Add consan
* Skip osx
* Update: vardict, vardict-java 1.5.7 (#11394)
* Update: vardict, vardict-java 1.5.7
Latest vardict-java release and corresponding vardict with bug fixes
after testing with 1.5.6
* Reduce test output to try and fix build problems
* Experiment 2 for build problems: remove r-base from run
* Experiment 3 for build problems: add r-base in host
* update recipe for 3.9.1 (#11397)
* evofold2 (#11396)
* evofold2
* wrapper
* Update meta.yaml
* minor
* Update rnastructure to 6.1. (#11400)
* Ctat mut (#11401)
* updating version number
* correct URL
* proper hash
* Revert "Ctat mut (#11401)" (#11402)
This reverts commit 6db10ac7ffd7abaf8fbf1762b7ea6c63b2585fe0.
* update version (#11403)
* any2fasta 0.4.2 (new formula) (#11407)
* W4mclassfilter v0.98.9 (#11385)
* Added files to build version 0.98.9
* Update meta.yaml
* Update meta.yaml
* updated SonicParanoid recipe to version 1.0.14 (#11409)
* updated SonicParanoid recipe to version 1.0.14
* Update to version 1.0.2 of PopDel (#11398)
* Update to version 1.0.2 of PopDel
Update to version 1.0.2.
* Reset build number to 0
* PacBio: require Meson 0.48.1 for all recipes (#11090)
* Meson 0.47 inserted duplicate RPATHs in
macOS binaries, causing `install_name_tool`
failures when installing the package.
Requiring 0.48.1 ensures we do not run into
these issues anymore in the future.
* rebuild with latest openmpi (#11411)
* Remove kfoots from the blacklist (#11416)
* Update gseapy to 0.9.7 (#11417)
* Update gseapy to 0.9.7
* remove noarch
* Add SC3 as dependency (#11427)
* Add recipe for r-poppr (#11418)
* Update knitr version because of Issue: https://github.com/rstudio/rmarkdown/pull/1271 (#11412)
* Update IQ-TREE to 1.6.7.1 (#11429)
* Update IQ-TREE to 1.6.7.1
* Change build number
* Update: r-deconstructsigs with fixes for hg38 (#11431)
The 1.8.0 release, from 2016, has some issues with hg38 and other
custom genomes that are fixed in development (raerose01/deconstructSigs#27).
There hasn't been a new release pushed so this rolls these into a new
sub-version and makes them available.
* Update entrez-direct to 10.2.20181018. (#11432)
* Add assembly-scan recipe (#11425)
* remove python 2.7 skip (#11424)
Preparation for rnaQUAST
* Add fastq-scan recipe (#11415)
* Add patch to fix racon/rampler path in racon_wrapper. (#11434)
Fixes #11405.
* meme rebuild (#11433)
* Update nanocomp to 0.23.1 (#11436)
* Update nanocomp to 0.23.1
* remove noarch
* Update abricate to 0.8.10 (#11446)
* Update angsd to 0.923 (#11445)
* Update alfred to 0.1.13 (#11444)
* Update alfred to 0.1.13
* Try w/o patch
* Update antarna to 2.0.6 (#11442)
* Update admixtools to 5.1 (#11443)
* Update admixtools to 5.1
* Let makefile choose which bins to install
* Update alignstats to 0.5 (#11441)
* Update xatlas to 0.2.1 (#11437)
* r-gpca (#11428)
* r-gpca
* r-gpca recipe
* Update meta.yaml
* Removed All Comments
* gseapy bump version 0.9.8 (#11440)
* gseapy bump version 0.9.8
* version
* titancna: fix for hg38, remove conda build hacks (#11447)
* titancna: fix for hg38, remove conda build hacks
* Re-add r-base 3.4 pin to avoid 3.5 errors
* Hmmlearn older version (#11450)
* Adding pygtftk
* removed pygtftk from master
* add older version of hmmlearn
* Add card_trick (#11451)
* Add card_trick
* Restrict to py3
* Update checkm-genome to 1.0.12 (#11455)
* Bump drep (#11457)
* Update squid to 1.5 (#11466)
* Update ncbi-ngs-sdk to 2.9.3 (#11467)
* elprep: bumped major version (#11414)
* elprep: bumped major version
* fixed hash
* fix download link, fixed licence
* fixed tests
* skip osx build
* FRED2 as a conda package (#11469)
* Attempt to get FRED2 as a conda package
* SHA update
* 99 little bugs in the code
* Fix things Björn mentioned
* add rnaQUAST recipe (#11470)
* Update bioconda-utils to 0.14.9 (#11454)
* Rapidup (#11474)
* Update to v0.7
* Update Buildnumber
* rapid: update to v0.6
* rapid: update to v0.6
* update grid (#11478)
* Adding biobb_model recipe (#11472)
* Updated wtdbg to v2.1 (#11486)
* update stream to 0.2.6 (#11483)
* update stream to 0.2.2
* update stream to 0.2.3
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.5
* update stream to 0.2.6
* Update meta.yaml (#11487)
* Update connectome-workbench to 1.3.2 (#11468)
Now needs QT 5.7
* Update deblur to 1.1.0 (#11500)
* Update domclust to 1.2.8 (#11498)
* WisecondorX: bump version (#11501)
* Bump as GitHub wasn't working yesterday (#11502)
* Added recipe for Sequenza (#10367)
* Added recipe for Sequenza
* Removed fn entry in source section
* Trying with only one URL
* copynumber is a bioconductor package
* Added missing requirements section
* Removed mailing list address
* Added doi
* Added license_file
* Trying with different license_file path
* Fred2 bump (#11503)
* Bump as GitHub wasn't working yesterday
* Fix licence etc
* Scanpy scripts (#11413)
Doing squash and merge as requested by @nh3
* Bump version
* First implementation of scanpy-scripts bioconda recipe.
* fix path in build.sh
* Remove "noarch" flag as requested by bioconda recipe checklist
* Add a post install notice that post install test needs bats-core.
* Add more dependencies
* Skip building for python versions other than 3.6
* Target v0.0.2 which has non-ascii characters removed
* Lower version requirement for pandas and matplotlib to be the same as scanpy
* Requirement matplotlib>=3.0.0, declare noarch
* New: hmftools-cobalt; Update: hmftools-purple (#11507)
- hmftools-cobalt: Add latest version of PURPLE associated read counter,
COBALT, with support for hg38.
- hmftools-purple: PURPLE release with hg38 support.
* Update Picard to 2.18.15. (#11505)
* Genenotebook (#11476)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* Update pinning (#11514)
* Bump build number for updated dependency (#11510)
* Bump build number for updated dependency
* Try adding r-base to host requirements
* Try adding other requirements to host
* Pin to R version
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Tweak dependency version syntax
* Pin R and package versions correctly
* PacBio: Update pbcore to 1.6.5 (#11513)
* Bump r seurat scripts version (#11292)
* Bump version
* Remove noarch
* Could wrongly quoted version be causing an issue?
* Tweak pinning to try and fix CI error
* seqcluster:fix UMI detection. (#11511)
* seqcluster:fix UMI detection.
* Fix dependency
* quast 5.0.1 (#11479)
* quast 5.0.1
* quast 5.0.1: remove third-party site packages from the distibution pack
* quast 5.0.1: skip Glimmer in test
* quast 5.0.1: joblib and simplejson dependencies added to meta.yaml (Setuptools downloading is disabled in conda build)
* quast 5.0.1: explicit joblib and simplejson dependencies removed (Setuptools downloading is disabled in conda build)
* quast 5.0.1: Python 2 and 3 compatible code in build.sh
* wcX bugfixes (#11508)
* wcX bugfixes
* fixed shasum
* Update fastspar to 0.0.7 (#11515)
* Update iqtree to 1.6.7.2 (#11525)
* Update illumina-interop to 1.1.6 (#11523)
* Update hapbin to 1.3.0 (#11522)
* Update hlama to 3.0.1 (#11520)
* Update gb_taxonomy_tools to 1.0.1 (#11519)
* Update gffcompare to 0.10.5 (#11517)
* Update fast5seek to 0.1.1 (#11516)
* Update deepbinner to 0.2.0 (#11499)
* Update deepbinner to 0.2.0
* Update meta.yaml
Try same fix as in #11240
* Update ncbi-vdb to 2.9.3 (#11550)
* Update mikado to 1.2.4 (#11549)
* Update perl-pcap to 3.5.2 (#11543)
* Update python-hyphy-python to 0.1.9 (#11545)
* Update mlst to 2.15.2 (#11547)
* Update perl-sanger-cgp-vcf to 2.2.1 (#11542)
* Update merfishtools to 1.5.0 (#11537)
* Update perl-sanger-cgp-vagrent to 3.3.3 (#11536)
* Update nonpareil to 3.3.3 (#11535)
* Update prophex to 0.1.1 (#11532)
* Update krakenuniq to 0.5.3 (#11527)
* Update novoplasty to 2.7.2 (#11530)
* Update minced to 0.3.2 (#11529)
* Update mapdamage2 to 2.0.8 (#11528)
* Update perl-sanger-cgp-allelecount to 4.0.0 (#11538)
* Update pyvolve to 0.9.0 (#11531)
* Genenotebook (#11512)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* add plek (#11554)
* Update pyimzml to 1.2.4 (#11534)
* Bump shovill (#11555)
* PacBio: Update minimum pbcore version (#11556)
* We want all users of PacBio tools to be able to
use our utilities with pbmm2 alignments.
* Add recipe for translate-gard v1.0.4 (#11557)
* bioconductor-rnaseqsamplesizedata (#11475)
* Adding Recipe for bioconductor-rnaseqsamplesizedata
* Updated metadata for RnaSeqSampleSizeData
* nextflow 18.10.1 (#11558)
* Update raxml to 8.2.12 (#11567)
* Update r-fgwas to 0.3.6 (#11566)
* Update rapid to 0.7 (#11565)
* Update r-spieceasi to 1.0.2 (#11564)
* Update rcorrector to 1.0.3.1 (#11562)
* Update quicktree to 2.4 (#11560)
* Update paladin to 1.4.4 (#11541)
* Update paladin to 1.4.4
* delete md5
* Update build.sh
* Update build.sh
* Fix and unblacklist Tadarida-D (#11568)
* Add recipe for rgt
* Fix and un-blacklist tadarida-d
* Remove RGT
* bumping groot (#11575)
* update pymzml (#11573)
* Add bioconductor-rnaseqsamplesize (#11559)
* Add bioconductor-rnaseqsamplesize
* Update recipe
* Fixing some URLs
* Update dependencies missing
* Update trumicount to 0.9.11 (#11576)
* Update ConFindr to 0.4.4 (#11578)
* Added new versions for biopet-scatterregions (#11572)
* Added new versions for biopet-bamstats (#11571)
* R ggbiplot (#11584)
* add R -e 'httr::set_config(httr::config(ssl_verifypeer = 0L)); install.packages(devtools, repos=http://mirrors.ebi.ac.uk/CRAN/); library(devtools); install_github(vqv/ggbiplot); library(ggbiplot)'
* add r-ggbiplot
* update meta.yaml
* update meta.yaml
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix errors
* fix errors number 1
* Update rebaler to 0.1.2 (#11563)
* Update rebaler to 0.1.2
* Remove fn
* bump graphclust (#11585)
* Update seqyclean to 1.10.09 (#11589)
* Update stringmlst to 0.5.1 (#11590)
* Update snp-dists to 0.6.2 (#11592)
* Update snippy to 4.3.3 (#11596)
* Update canu to 1.8 (#11600)
* Update starfish to 0.0.27 (#11599)
* Update womtool to 36 (#11594)
* Update telseq to 0.0.2 (#11598)
* Update snp-sites to 2.4.1 (#11588)
* Added recipe for pydemult: Streamed and parallel demultiplexing of fastq files (#11471)
* Added recipe for pydemult
* Bumped version in favor of py3.5
* bump vcf2db to latest commit (#11601)
* bump vcf2db to latest commit
* fix shasum
* Fixing source url
* Update: TitanCNA; hg38 cytoband support and fix for normalization (#11604)
* megan (#11046)
* megan6: initial commit
* megan6: intermediate commit
* megan: made tests work
* megan: doc improvement
* megan: added osx dmg file
* megan: add java to build requirements
* megan: removed new line
* megan: removed osx sources
* Update meta.yaml
* bumping hulk (#11607)
* Update hotspot3d to 1.8.2 (#11521)
* Update hotspot3d to 1.8.2
* Add perl-json as dependency
* Add perl-archive-extract as dependency
* Fqzcomp (#11606)
* Added recipe for fqzcomp
* There is no configure script
* Maybe this works
* Added gcc as build requirement
* Removed gcc again (lint issue)
* Maybe these exports will do the trick
* Nope!
* Added cxx as host requirement
* Compilers are only allowed in build section
* There is no need for make install
* Copy-paste error...
* Add vcf-annotator recipe (#11481)
* Add vcf-annotator recipe
* added pyvcf dependency
* Update meta.yaml
* stacks: fix for @ in exe_path (#11580)
* stacks: fix for @ in exe_path
* stacks: fixed path
* New version with bugfix and different progressiveMauve version. (#11613)
* Sspupdate (#11614)
* New version with bugfix and different progressiveMauve version.
* Keeping old version as folder.
* Push build number.
* Update SVDB to version 1.3.0 (#11506)
* new file: recipes/svdb/1.1.2/meta.yaml
renamed: reipes/svdb/svdb.patch -> recipes/svdb/1.1.2/svdb.patch
modified: recipes/svdb/meta.yaml
* deleted: 1.1.2/meta.yaml
deleted: 1.1.2/svdb.patch
* Bump nanosim (#11608)
* Bump nanosim
* Add scipy as dep
* Add recipe for perl-number-range (#11621)
* New build for grid (#11620)
* update grid
* update build num
* Recipe for das_tool 1.1.1 (#10528)
* recipe for das_tool 1.1.1
* Add recipe for sompy (#11624)
* cmake modified to build with NDEBUG (#11328)
* cmake modified to build with NDEBUG
* Update meta.yaml
* new build with fasta test
* new build with fasta test
* Fix and unblacklist TwoPaCo (#11622)
* Add recipe for TwoPaCo
* Unblacklist twopaco
* Modify and unblacklist recipe for ESTmapper (#11623)
* Modify and unblacklist recipe for ESTmapper
* Add patch
* Modify and unblacklist recipe for Metaseq (#11625)
* Fix recipe for metaseq and remove from blacklist
* Remove build.sh
* nextflow 18.10.1 build 2 (#11630)
* Add Clust (#11619)
* Add clust
* Clean recipe
* Add "noarch"
* Add DOI
* Add build file
* Python 2.7
* Fix scikit-learn dependency
* Trigger new build
* Update: PureCN (multicore) and PURPLE (plotting X libraries) (#11631)
- PureCN: adds support for specifying cores on command line
- PURPLE: adds X library dependencies required for creating
plots
* scripts/travis-run.sh: added a cleaner method to check for env vars (#11612)
* Increase the number of k value usable in bcalm (request by @Malfoy) (#11610)
* Increase the number of k value usable in bcalm (request by @Malfoy)
* Change compilation parameter to reduce memory impact of compilation
* Update anndata to 0.6.11 (#11637)
* Update nglview to 1.1.7 (#11643)
* Update binsanity to 0.2.7.1 (#11644)
* Update cgat-core to 0.5.4 (#11645)
* Update nanosv to 1.2.2 (#11673)
* Update abeona to 0.36.0 (#11670)
* Update pyfaidx to 0.5.5.2 (#11659)
* Update agfusion to 1.23 (#11668)
* Update iqtree to 1.6.8 (#11686)
* update iqtree to 1.6.8
* Trigger rebuild
* Update validators to 0.12.2 (#11672)
* Update python-edlib to 1.2.3.post1 (#11664)
* update for Purge Haplotigs (#11690)
* Update loompy to 2.0.16 (#11667)
* Update loompy to 2.0.16
* Update meta.yaml
* IgBLAST 1.10.0 (#11693)
* Update wtforms-alchemy to 0.16.7 (#11679)
* Update sickle to 0.6.4 (#11663)
* Update sickle to 0.6.4
* Remove fn and libgcc runtime dep
* Update confindr to 0.4.5 (#11696)
* Batvi (#11695)
* batvi initial
* Guideline compatibility..
* Dummy test section..
* Missing java dependency..
* use openjdk instead of java-jdk ..
* source specified in github ..
* trigger build (package did not have batindel directory) ..
* update SHA256 ..
* update SHA256 ..
* Update pythonpy to 0.4.11 (#11661)
* Update cortexpy to 0.45.6 (#11660)
* Update sevenbridges-python to 0.16.0 (#11674)
* Update solvebio to 2.7.0 (#11657)
* Update mathstats to 0.2.6.5 (#11656)
* Update goatools to 0.8.9 (#11641)
* Add gnies (#11627)
* Add gnies
* noarch python
* Update meta.yaml
* Add recipe for SKA v1.0 (#11581)
* Add recipe for SKA v1.0
* Add lib path for zlib
* Older gcc
* Correct install dir
* Try static linking
* Dynamic linking on OS X
* ldd command test
* correct program
* Remove ldd command
* Add recipe for transit version 2.3.1 (#11701)
* Add recipe for transit version 2.3.1
* Use skip, add spaces.
* Update meta.yaml (#11699)
* remove pyqi (#11704)
* Update python-chado to 2.2.0 (#11714)
* update python-chado
* 2.2.1
* Update vcfanno to 0.3.1 (#11710)
* FGMP-1.0.1 (#11278)
* FGMP-1.0.1 recipe
* remove unncessary build info
* add r-nabor (#11716)
* update stream to 0.2.2
* update stream to 0.2.3
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.5
* update stream to 0.2.6
* add r-nabor recipe
* update r-nabor recipe
* update r-nabor recipe
* r-pctgcdata (#11715)
* r-pctgcdata
* r-pctgcdata - fix
* r-pctgcdata - fix
* Update meta.yaml
* Fix plek by a new branch (#11605)
* Modify the PLEK recipe
* Start fixing PLEK, though it requires compilation
* update build.sh
* update yaml
* fix build.sh
* update build.sh
* Update recipe for plek
* add bioconductor-chromvar recipe (#11718)
* add bioconductor-chromvar recipe
* fix bioconductor-tissueenrich
* Apparently the popdel recipe didn't get correctly merged
* Final merge conflicts
* Bioc quick test (#12547)
* Update kallisto to 0.45.0 (#12117)
* Update validators to 0.12.3 (#12116)
* Update illumina-interop to 1.1.7 (#12115)
* Update umi_tools to 0.5.5 (#12123)
* Update tiptoft to 1.0.0 (#12122)
* Update: TitanCNA with fix for hg38 plotting (#12130)
* blockclust (#12111)
* added eden 1.1 version used in blockclust
* Update meta.yaml
* eden checksum and test
* added zlib requirement
* add include and lib paths to build.sh
* add include and lib paths to build.sh
* modify makefile flags using sed
* modify makefile flags using sed
* use c++
* Update build.sh
* Update build.sh
* LDFLAGS not used in makefile
* remove v1.1
* add blockclust 1.1.0 recipe
* skip osx build
* added tarball url and checksum; removed conda_build_config.yaml
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Update chewbbaca to 2.0.16 (#12132)
* Update abeona to 0.40.0 (#12131)
* ping to eden 1.1 (#12134)
* clean swap file (#12137)
* Update corset to 1.07 (#12143)
* Update peddy to 0.4.3 (#12144)
* blockclust latest source and added cloudpickle as requirement (#12142)
* Update nanomath to 0.22.0 (#12149)
* Update pymvpa to 2.6.5 (#12152)
* Updated to version 1.4.0 (#12138)
* Updated to version 1.4.0
* Resetting build number to 0 and build->host
* Update transdecoder to 5.5.0 (#12172)
* Update gridss to 2.0.1 (#12190)
* Update tracer to 1.7.1 (#12189)
* Update flowcraft to 1.4.0 (#12179)
* Update seqbuster to 3.2 (#12182)
* Update perl-io-compress to 2.081 (#12201)
* Update twobitreader to 3.1.6 (#12205)
* Update twobitreader to 3.1.6
* Update meta.yaml
* Update gtfparse to 1.2.0 (#12186)
* Update gtfparse to 1.2.0
* remove compiler
* Update htseq to 0.11.0 (#12177)
* Update htseq to 0.11.0
* add compiler
* Update htseq to 0.11.0 (#12239) [testing co-author]
* Update htseq to 0.11.0
* add compiler
Co-authored-by: Bjoern Gruening <[email protected]>
* alfred v0.1.16 (#12240)
* alfred v0.1.16
* makefile patch
* makefile patch
* Update scrm to 1.7.3 (#12150)
* Update scrm to 1.7.3
* Update scrm to 1.7.3
* Mob suite update 1.4.8 --> 1.4.9 (#12244)
We fixed a small bug related to repetitive elements database reconstruction on each run. Should only run once during the first mob_typer run. Should be good now for parallel runs.
* PeptideShaker updated to v1.16.35 & SearchGUI updated to 3.3.9 (#12241)
* PeptideShaker updated to v1.16.32
SearchGUI updated to v3.3.6
* PeptideShaker updated to v1.16.35
* SearchGUI updated to v3.3.9
* First attempt at a recipe for ncrf (#12101)
* First attempt at a recipe for ncrf
* changed from copies to symlinks
* including absolute path in symlinks
* PacBio: Update `pbmm2` to version 0.11.0 (#12246)
* Gimmemotifs version 0.13.0 (#12245)
* new release to fix numpy incompatibility
* GimmeMotifs 0.13.0 release test
* numpy 1.15
* version 0.13.0
* Fix about:home and extra:
* PacBio: Update `isoseq3` to version 3.1.0 (#12263)
* add python to host section (#12264)
* Update confindr to 0.4.7 (#12266)
* new build of GRiD (#12269)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* peptideshaker, searchgui: version bump (#12136)
* peptideshaker, searchgui: version bump
solving https://github.com/compomics/searchgui/issues/192
* Update peptide-shaker.py
* searchgui: added c compiler for building
test if linking errors go away this way
* searchgui: removed noarch
* Update: bcbio, bcbio-vm with CWL non-human fixes (bcbio/bcbio-nextgen#2473) (#12273)
* Make snakemake a noarch package. (#12274)
* noarch: python in combination with version constraint
* Cleanup deps and simplify version definition.
* Genenotebook v0.1.9 (#12277)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* Create r-airr recipe (#12284)
* Create r-airr recipe using bgruening/conda_r_skeleton_helper
* Update meta.yaml
* Findbin::Real added (#12291)
* Added version bump to 1.3 (#12292)
* ngs-bits 2018_11 (#12262)
* Updated ngs-bits to version 2018_10
* Updated ngs-bits to version 2018_11
* minor edit in grid (#12287)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* minor edit to grid
* Fred2 update (#12259)
* Update FRED2 Recipe
* msstitch version 2.9 (#12296)
* r-mvr (#12300)
This is a non-parametric method for joint adaptive mean-variance regularization and variance sta-
bilization of high-dimensional data.
* Bump to Gromacs 2018.3 + re-enable OSX build (#12299)
* Gromacs 2018.3 + re-enable osx build
See also #7825 on OSX build
Include RRID for Gromacs (see bioconda/bioconda-utils#252)
* disabled ocl-icd on osx; not available (or needed?)
https://anaconda.org/conda-forge/ocl-icd
* pyGenomeTracks update of dependencies (#12279)
* Update pyGenomeTracks recipe to enable py3 support and updating outdated dependecy list
* Increase build number
* Update meta.yaml
* Exclude Python 3.5
* Gromacs 2018.4 (#12302)
* quast 5.0.2 (#12303)
* Update meta.yaml (#12275)
* Update meta.yaml
r-rsqlite version dependency added
* Update meta.yaml
Updated build number to 1
* Use the extended-base container because of wget issues when downloading databases (#12297)
* Update duphold to 0.1.0 (#12257)
* Update flashlfq to 0.1.109 (#12256)
* Update planemo to 0.57.0 (#12251)
* Update meta.yaml (#12258)
* Update scalpel to 0.5.4 (#12249)
* Update scalpel to 0.5.4
* Fix url
* edit grid (#12298)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* minor edit to grid
* minor edit to recipe grid
* added feather to deps (#12293)
* R tigger (#12286)
* Create recipe for r-tigger (#12271)
* Create recipe for r-tigger using bgruening/conda_r_skeleton_helper.
* Delete bld.bat
* Remove windows support
* update scprep to v0.8.1 (#12306)
* Update nanoget to 1.7.5 (#12252)
* Update nanoget to 1.7.5
* Bump to version 1.7.6
should fix the README.md problem
* gffcompare: version bump (#12308)
* Update: cromwell (36), bcbio (Cromwell Docker runs) (#12307)
* Update: cromwell (36), bcbio (Cromwell Docker runs)
* Pin java to 8 to avoid compile errors on 11
* HiCExplorer update to version 2.2-beta (#12309)
* HiCExplorer update to version 2.2-beta
* Remove of '-' from version number
* Numpy set to 1.15
* Update meta.yaml
* upgrade to version 2.8.1 (#12316)
* Create Airr recipe (#12318)
* Create AIRR recipe using conda skeleton pypi.
* Add noarch python
* Clean host requirements
* Added nimnexus [v0.1] (#12133)
* added nimnexus
* Fix sha
* Update build.sh
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* [WIP] Add R-loom (#12320)
* initial WIP skeleton
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* try osx
* Create Changeo recipe (#12321)
* Create changeo recipe using conda skeleton pypi.
* EDIT about section
* ADD noarch generic
* Update noarch to python
* Clean host requirements
* Add test for scripts
* Change requirement to python>=3.4
* Add noarch pyton
* r-corbi (#12325)
* r-nam (#12327)
* Update pybedtools to 0.8.0 (#12324)
* Update pybedtools to 0.8.0
* rm cython requirement
* MSGFplus does not work with newer Java (#12330)
* Trying to not use a very new java version since the latest versions have dropped some classes
* Increment build
* Update atropos to 1.1.21 (#12322)
* Update CONCOCT to 0.4.2 (#12317)
* Update CONCOCT to 0.4.2
* Wrong shasum given
* Reset build number for new version
* New: gvcfgenotyper for joint calling with Illumina strelka2 (#12331)
* Apparently we need openJDK to be below 9, not below 11 as in the previous PR (#12332)
* Update Picard to 2.18.17. (#12333)
* Unblacklist IgDiscover (#12335)
* PacBio: Add missing licenses and post-link message (#12334)
* Bioconductor DEqMS package (#12336)
* Bioconductor DEqMS package
* Limma version could be set lower (checked with the bioconductor recipe page) to include limma in bioconda
* Genenotebook v0.1.10 (#12337)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* v0.1.10
* removed cloudpickle requirement for blockclust (#12242)
* blockclust latest source and added cloudpickle as requirement
* removed cloudpickle requirement for blockclust
* added a tagged release to the source
* back to source url but with release tarball and checksum
* R guilds (#12341)
* Strict rec (#12113)
* added metawrap
* fixed perl and jdk
* added more strict req
* fixed java and perl
* removed extra boost
* Update qcat to v1.0.1 (#12343)
* Add better error checking (#12345)
* Add mhcnames python package (#12349)
* Add MHCflurry pMHC class I binding affinity prediction tool (#12346)
* Bump pilon (#12354)
* Update pronto to 0.11.1 (#12377)
* Update perl-json-xs to 4.0 (#12373)
* Update planemo to 0.57.1 (#12370)
* Update snippy to 4.3.6 (#12372)
* Update intarna to 2.3.1 (#12367)
* Update agfusion to 1.231 (#12366)
* Update bioconda-utils to 0.15.0 (#12359)
* Update mapdamage2 to 2.0.9 (#12358)
* Update scanpy to 1.3.4 (#12357)
* Update goatools to 0.8.11 (#12361)
* Update perl-math-random-mt-auto to 6.23 (#12362)
* Update kipoi to 0.6.3 (#12374)
* Update kipoi_veff to 0.2.1 (#12364)
* Update perl-object-insideout to 4.05 (#12380)
* Update sevenbridges-python to 0.17.1 (#12379)
* Update nanosv to 1.2.3 (#12378)
* Update starfish to 0.0.30 (#12368)
* Update clust to 1.8.10 (#12356)
* Update pypairs to 2.0.6 (#12381)
* Update khmer to 3.0.0a2 (#12360)
* Update flashlfq to 0.1.110 (#12385)
* Update perl-algorithm-cluster to 1.57 (#12384)
* Update arvados-python-client to 1.2.0.20181121194423 (#12382)
* Update avro-cwl to 1.8.9 (#12355)
* Update avro-cwl to 1.8.9
* Set noarch: python
* r-breakaway (#12386)
* R sads (#12388)
* Update python-sortedcontainers to 2.1.0 (#12383)
* r-ebimetagenomics (#12339)
* pin armadilo on major version (#12389)
* IgDiscover version 0.11 (#12351)
* IgDiscover version 0.11
* IgDiscover requires Python 3.6
* Fix build on macOS with a small patch
* Remove unneeded host dependencies
* Update goatools to 0.8.12 (#12391)
* Update bioconda-utils to 0.15.1 (#12390)
* R ebimetagenomics (#12393)
* Add dimspy recipes for reference purposes (#12387)
* Add dimspy recipes for reference purposes
* Remove filename
* remove from blacklist
* Update build-fail-blacklist
* Added BioExcel_SeqQC to bioconda-recipes (#12276)
* PacBio: Update pbalign to 0.3.2 (#12396)
* PacBio: Update pbalign to 0.3.2
Closes: PacificBiosciences/pbbioconda#39
* add bgreat to bioconda (#12350)
* bgreat addition
* zlib in build should not be needed
* btrim integration to conda (#12395)
* Format sleuth recipe. Trigger rebuild because latest version was never uploaded for some reason. (#12399)
* PacBio: Update `pbsv2` to version 2.1.0 (#12400)
* Genenotebook v0.1.11 (#12398)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* v0.1.10
* v0.1.11
* prosolo: new package version 0.6.0 (#12397)
* Update sevenbridges-python to 0.17.2 (#12404)
* Add recipe for ICED (#12406)
* Downgrade version for iced (#12409)
* Update recipe for libstatgen 1.0.5 (#12348)
* Add recipe for libstatgen-1.0.5
* Update iced to 0.5.0 (#12411)
* Update perl-test2-suite to 0.000116 (#12412)
* fix compatibility with other tools (#12415)
* Restore dexseq python helper scripts (#12352)
* Restore dexseq python helper scripts
* Add python requirement for helper scripts
* Add python noarch to build section
* pin it to python2k
* Add htseq requirement, support only python <3 for now
* Genenotebook v0.1.12 (#12418)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* v0.1.10
* v0.1.11
* v0.1.12
* updated source
* added medpy recipe (#12417)
* added medpy recipe
* removed osx from build
* Update meta.yaml
* Update meta.yaml
* add boost and a compiler
* Update meta.yaml
* Update meta.yaml
* add itk
* Updated ddrage to version 1.6.1. (#12421)
* Add r-mcpcounter recipe. (#12261)
* Add MCPcounter recipe.
* fix lint: remove 'fn'
* fix license_file, version number and doi
* Update DEXSeq requirements to force compatible HTSeq version (#12423)
* ARB: Pin glib (#11782)
* Pin glib
* Update meta.yaml
* Update meta.yaml
* Work around CB3 issues
* Work around bioconda-utils lint false positive
* Disable lint check should_not_be_noarch
* Can't reference other packages built in recipe from anything but run
* Move perl to host section. Maybe that helps.
* constraining interpreter version breaks with CB3?
* disable perl version constraint :(
* Update meta.yaml (#12426)
* stacks: fix for fix 'fixing' @ in exe_path (#12420)
* stacks: fix for fix 'fixing' @ in exe_path
the previous fix https://github.com/bioconda/bioconda-recipes/pull/11580
tried to solve the problem with the @ in the exe_path by setting this
variable empty. But the perl scripts
- ap…
dpryan79
added a commit
to bioconda/bioconda-recipes
that referenced
this issue
May 15, 2019
* update mzr as a test
* Begin building for R 3.5.1 (#11252)
* Bump everything for R 3.5.1
* Fix most of the linting issues
* Update blacklist
* Revert "Fix most of the linting issues"
This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5.
* should_not_use_fn
* More fixes
* Fix incorrect yaml
* Should really fix the linting blacklist stuff
* Fix many recipes
* Fix some linting
* Fix r-wicket
* Update derfinder
* Pin to a given bioconductor release.
* Add missing packages
* Restore identifiers to bioconductor packages
* Restore extra information to R packages
* Update R bulk (#11283)
* fixed incorrect doi of publication (#11175)
* Added recipe for kinSimRiboswitch (#10838)
Added recipe for kinSimRiboswitch, a pipeline for simulating the folding
kinetics of RNA switches.
* update multiqc-bcbio (#11187)
* Add recipe for PopDel (#11181)
* Add recipe for PopDel
* Add clang and clangxx to build config
* update seqbuster (#11190)
* update seqbuster
* fix build
* fix test
* Update pyseer to 1.1.2 (#11172)
* bump sourmash (#11197)
* Update BASIC to v1.4.1 (#11195)
* Update BASIC to v1.4.1
* Trigger circleci
* Fix build number
* Update nf-core-1.2 (#11191)
* Update nf-core-1.2
* Update build script
* Update to InterMine 1.11.0 (#11182)
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Add tinyfasta-0.1.0 (#11177)
* Add tinyfasta
* Update build script
* Fix structure of build section
* Bumping snippy (#11198)
* Remove older version
* Bump snippy
* VEP: bump major version (#11201)
* VEP: bump major version
* VEP: bumped plugin major version
* VEP: update plugin install
Download and install all plugin modules, instead of just a selection
* Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200)
* Update: PureCN to latest devel (1.11.13); wrapper scripts
PureCN development (https://github.com/lima1/PureCN) has several
improvements over the BioC 3.6 release for handling multiple VCF input
types, and is back compatible with R 3.4.1 so still builds cleanly
with two new dependencies.
Also exposes PureCN wrapper scripts for running from the command line.
Prefixes ambiguous scripts with PureCN_.
* Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet
* add cassiopee release 1.0.9 (#11168)
* add cassiopee release 1.0.9
* update to conda build 3
* remove old version backup and use sha256 for source
* Bump abeona version to 0.26.0 (#11202)
* Bump abeona version to 0.24.0
* Bump abeona version to 0.26.0
* Update LexMapr to v0.1.2 (#11192)
* Update LexMapr to v0.1.2
* Add rdflib dep
* Update svtyper to 0.7.0 (#11196)
* Update svtyper to 0.7.0
* Add recipe for perl-gtdbtk (#11194)
* Add recipe for perl-gtdbtk
* New recipe for RFMix (#11205)
* New recipe for RFMix
* updated version number information
* updated version number information
* updated version number information
* initial purge_haplotigs commit (#11049)
* initial purge_haplotigs commit
* bioconda revisions, updating test commands to run the pipeline on the test dataset
* rolling back test commands
* Add recipe for fsm-lite (#11209)
* Add recipe for fsm-lite
* Add prefix to make
* Remove v from version string
* Updated reparation_blast to version v.1.0.7 (#11210)
* Update sambamba to 0.6.8 (#11212)
* Bump sambamba to 0.6.8
* It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified.
* Set some environment variables
* The compiled binary is in a different place now
* ldc provides some libraries that are linked against.
* mtbseq: update recipe (#11110)
* changed download location/add test
* remove test
* Confindr (#11217)
* Update confindr to 0.4.2
* Fix typo in specifying version of pysam
* Update Genenotebook to v0.1.4 (#11218)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* updating to 0.1.3 (#11221)
* sartools1.6.6 (#11222)
* Perl bio automatedannotation (#11216)
* Initial recipe for Bio-AutomatedAnnotation
* Change URL
* Run cpanm tests
* Temporarily set HOME
* Use cpan version instead
* Add more depencencies
* Set bioperl version
* unset bioperl version, add bioperl-run
* New release including version in modules
* Remove comments
* build -> host
* Upgrade r-biodb to v1.1.2. (#11213)
* Upgrade r-biodb to v1.1.2.
* Remove old versions of r-biodb.
* Comment out libgfortran.
* PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215)
* PeptideShaker: updated to version 1.16.30
- Bugfix: HOME was still being used when folder with customised reports was specified.
- Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line.
* SearchGUI: updated to version 3.3.5.
- BUG FIX: Cleanup of the temp path options when used as options for the other command lines.
- FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2.
- LIBRARY UPDATE: Updated utilities to version 4.12.8.
* Update meta.yaml (#11227)
* Svtools 0.4.0 (#11208)
* Remove directories for old svtools versions
* Update svtools to v0.4.0
* Move build number back to 0
* Anvio 52 (#11230)
* Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software.
* Remove cgat-scripts from blacklist. (#11228)
* Add new formula: bazam 1.0.1 (#11229)
* Update gatk4 to 4.0.10.0 (#11224)
* Add recipe for gtdbtk 0.1.3 (#11211)
* Add recipe for gtdbtk
* Added initial htstream recipe (#11113)
* HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data.
* DeepTools 3.1.3 (#11226)
* PacBio: Update `pbmm2` to version 0.10.0 (#11225)
* fastqc: update to version 0.11.8 (#11214)
* fastqc: update to version 0.11.8
* Update meta.yaml
* Phame (#11223)
* mac recipe and added bioperl
* changing bill number
* added no osx
* adding new version
* removed separate recipe for mac, dont need it
* now running same recipe for mac and linux
* fixed the way fasttrees version was being parsed
* minor change test
* adding detailed description
* restaging the build number
* new version
* Make sure to use bioperl and perl 5.26
* Updated ngs-bits to version 2018_10 (#11235)
* PacBio: Update `pbsv2` to version 2.0.2 (#11236)
* Update VSEARCH to 2.8.5 (#11239)
* Fix shorah recipe and remove from blacklist. (#11241)
* Fix shorah recipe and remove from blacklist.
* Fix blas variant.
* Remove imports from tests.
* unicycler 0.4.7 (#11240)
* unicycler 0.4.7
* unicycler: Work around ValueError: invalid
Unicycler thinks the terminal has 0 columns and produces this error:
File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks
raise ValueError("invalid width %r (must be > 0)" % self.width)
ValueError: invalid width -5 (must be > 0)
* Octopus: update to 0.5.1-beta (#11244)
* New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247)
- PURPLE SV and heterogeneity caller for somatic tumor/normal samples.
- VarDictJava -- 1.5.6 release with fixes for SV calling
- PureCN -- add signature dependency and update with fixes for test
samples.
* Dinucleotide patterns analysis tools v1.0 (#11245)
* Dinucleotide patterns analysis tools v1.0
* Lets try it, it seems to work locally for me.
* Enable SpoTyping_plot.r (#11248)
* rerun again (#11233)
* rerun again
* Update meta.yaml
* Delete build.sh
* Update segway dependency optbuild to 0.2 (#10459)
* Update segway dependency optbuild to 0.2
* Update build and architecture requirements for optbuild 0.2
* Add six as a dependency to the optbuild recipe
* Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249)
* Add prefix dnp- to the package names
* Update build.sh
* Update build.sh
* Bump beast version to 1.10.2 (#11250)
* add maxquant (#11253)
* add mayquant
* relax tests
* PacBio: Update `pbmm2` to version 0.10.1 (#11256)
* PacBio: Update `pbmm2` to version 0.10.1-1 (#11257)
* remove xsv recipe (#11259)
* add blast dependency (#11258)
* Added riborex recipe (#11251)
* Added riborex recipe
* Relaxed version constraints
* Pinned r-core for fdr tools
* fixed the r-base stuff upstream
* Update meta.yaml
* fix graphprot (#11234)
* increase build number
* remove from blacklist
* use cxx instead of c
* move coreutoils to build section
* set additional paths
* patch makefile
* blind try
* update patch
* explicitely copy from src_dir
* update deprecated prefix variable
* Revert "update deprecated prefix variable"
This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d.
* update deprecated prefix variable
* try moving to host section
* Bump mash (#11264)
* Add fmlrc (#11265)
* Add fmlrc
* add doi
* PacBio: Update pb-falcon to 0.2.4. (#11266)
* Add kopt recipe (#11269)
* Genomepy 0.5.2 (#11267)
* release 0.5.2 of genomepy
* trigger new build
* remove genomepy from blacklist
* locale for osx
* updated locale test
* PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275)
* Update mmseqs2 recipe to new release 6-f5a1c (#11272)
* Update yacrd to version 0.4.1 (#11273)
* Add scprep (#11270)
* Add scprep
* All of these should not be needed as host dep
* Metawrap preqs2 (#11242)
* fixed issues
* fixed issues
* added tests
* fixed tab
* gemma 0.98 (#11254)
* gemma 0.98
* gemma 0.98
Leave gsl and zlib out of runtime dependencies
* Add DCA recipe (#11274)
* Add DCA recipe
* add noarch and doi
* remove skip
* Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib
* Various fixes for bulk and trigger a rebuild (#11313)
* Various fixes, at least 4 packages (and their dependencies) should still fail (#11320)
* A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336)
* Fix various recipes (#11354)
* Fix various recipes
* Fix more recipes
* Various CRAN package fixes, since they all lack license files (#11372)
* Various CRAN package fixes, since they all lack license files
* Fix the r-dartr recipe
* There is a light at the end of the tunnel (#11381)
* There is a light at the end of the tunnel
* Licenses no longer exist
* [BULK] Fixes for R/Bioconductor packages (#11406)
* Require `r-base >=3.5` for some packages
* Fix various CRAN packages lacking license file
* Add missing libnetcdf requirement to bioconductor-mzr
* Remove r-alakazam (moved to conda-forge)
Fix linting issue:
```
recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating
```
* [BULK] Many R 3.5 only packages (#11410)
* [BULK] Bulk update 191018b (#11419)
* update mzr as a test
* Begin building for R 3.5.1 (#11252)
* Bump everything for R 3.5.1
* Fix most of the linting issues
* Update blacklist
* Revert "Fix most of the linting issues"
This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5.
* should_not_use_fn
* More fixes
* Fix incorrect yaml
* Should really fix the linting blacklist stuff
* Fix many recipes
* Fix some linting
* Fix r-wicket
* Update derfinder
* Pin to a given bioconductor release.
* Add missing packages
* Restore identifiers to bioconductor packages
* Restore extra information to R packages
* Update R bulk (#11283)
* fixed incorrect doi of publication (#11175)
* Added recipe for kinSimRiboswitch (#10838)
Added recipe for kinSimRiboswitch, a pipeline for simulating the folding
kinetics of RNA switches.
* update multiqc-bcbio (#11187)
* Add recipe for PopDel (#11181)
* Add recipe for PopDel
* Add clang and clangxx to build config
* update seqbuster (#11190)
* update seqbuster
* fix build
* fix test
* Update pyseer to 1.1.2 (#11172)
* bump sourmash (#11197)
* Update BASIC to v1.4.1 (#11195)
* Update BASIC to v1.4.1
* Trigger circleci
* Fix build number
* Update nf-core-1.2 (#11191)
* Update nf-core-1.2
* Update build script
* Update to InterMine 1.11.0 (#11182)
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Add tinyfasta-0.1.0 (#11177)
* Add tinyfasta
* Update build script
* Fix structure of build section
* Bumping snippy (#11198)
* Remove older version
* Bump snippy
* VEP: bump major version (#11201)
* VEP: bump major version
* VEP: bumped plugin major version
* VEP: update plugin install
Download and install all plugin modules, instead of just a selection
* Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200)
* Update: PureCN to latest devel (1.11.13); wrapper scripts
PureCN development (https://github.com/lima1/PureCN) has several
improvements over the BioC 3.6 release for handling multiple VCF input
types, and is back compatible with R 3.4.1 so still builds cleanly
with two new dependencies.
Also exposes PureCN wrapper scripts for running from the command line.
Prefixes ambiguous scripts with PureCN_.
* Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet
* add cassiopee release 1.0.9 (#11168)
* add cassiopee release 1.0.9
* update to conda build 3
* remove old version backup and use sha256 for source
* Bump abeona version to 0.26.0 (#11202)
* Bump abeona version to 0.24.0
* Bump abeona version to 0.26.0
* Update LexMapr to v0.1.2 (#11192)
* Update LexMapr to v0.1.2
* Add rdflib dep
* Update svtyper to 0.7.0 (#11196)
* Update svtyper to 0.7.0
* Add recipe for perl-gtdbtk (#11194)
* Add recipe for perl-gtdbtk
* New recipe for RFMix (#11205)
* New recipe for RFMix
* updated version number information
* updated version number information
* updated version number information
* initial purge_haplotigs commit (#11049)
* initial purge_haplotigs commit
* bioconda revisions, updating test commands to run the pipeline on the test dataset
* rolling back test commands
* Add recipe for fsm-lite (#11209)
* Add recipe for fsm-lite
* Add prefix to make
* Remove v from version string
* Updated reparation_blast to version v.1.0.7 (#11210)
* Update sambamba to 0.6.8 (#11212)
* Bump sambamba to 0.6.8
* It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified.
* Set some environment variables
* The compiled binary is in a different place now
* ldc provides some libraries that are linked against.
* mtbseq: update recipe (#11110)
* changed download location/add test
* remove test
* Confindr (#11217)
* Update confindr to 0.4.2
* Fix typo in specifying version of pysam
* Update Genenotebook to v0.1.4 (#11218)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* updating to 0.1.3 (#11221)
* sartools1.6.6 (#11222)
* Perl bio automatedannotation (#11216)
* Initial recipe for Bio-AutomatedAnnotation
* Change URL
* Run cpanm tests
* Temporarily set HOME
* Use cpan version instead
* Add more depencencies
* Set bioperl version
* unset bioperl version, add bioperl-run
* New release including version in modules
* Remove comments
* build -> host
* Upgrade r-biodb to v1.1.2. (#11213)
* Upgrade r-biodb to v1.1.2.
* Remove old versions of r-biodb.
* Comment out libgfortran.
* PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215)
* PeptideShaker: updated to version 1.16.30
- Bugfix: HOME was still being used when folder with customised reports was specified.
- Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line.
* SearchGUI: updated to version 3.3.5.
- BUG FIX: Cleanup of the temp path options when used as options for the other command lines.
- FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2.
- LIBRARY UPDATE: Updated utilities to version 4.12.8.
* Update meta.yaml (#11227)
* Svtools 0.4.0 (#11208)
* Remove directories for old svtools versions
* Update svtools to v0.4.0
* Move build number back to 0
* Anvio 52 (#11230)
* Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software.
* Remove cgat-scripts from blacklist. (#11228)
* Add new formula: bazam 1.0.1 (#11229)
* Update gatk4 to 4.0.10.0 (#11224)
* Add recipe for gtdbtk 0.1.3 (#11211)
* Add recipe for gtdbtk
* Added initial htstream recipe (#11113)
* HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data.
* DeepTools 3.1.3 (#11226)
* PacBio: Update `pbmm2` to version 0.10.0 (#11225)
* fastqc: update to version 0.11.8 (#11214)
* fastqc: update to version 0.11.8
* Update meta.yaml
* Phame (#11223)
* mac recipe and added bioperl
* changing bill number
* added no osx
* adding new version
* removed separate recipe for mac, dont need it
* now running same recipe for mac and linux
* fixed the way fasttrees version was being parsed
* minor change test
* adding detailed description
* restaging the build number
* new version
* Make sure to use bioperl and perl 5.26
* Updated ngs-bits to version 2018_10 (#11235)
* PacBio: Update `pbsv2` to version 2.0.2 (#11236)
* Update VSEARCH to 2.8.5 (#11239)
* Fix shorah recipe and remove from blacklist. (#11241)
* Fix shorah recipe and remove from blacklist.
* Fix blas variant.
* Remove imports from tests.
* unicycler 0.4.7 (#11240)
* unicycler 0.4.7
* unicycler: Work around ValueError: invalid
Unicycler thinks the terminal has 0 columns and produces this error:
File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks
raise ValueError("invalid width %r (must be > 0)" % self.width)
ValueError: invalid width -5 (must be > 0)
* Octopus: update to 0.5.1-beta (#11244)
* New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247)
- PURPLE SV and heterogeneity caller for somatic tumor/normal samples.
- VarDictJava -- 1.5.6 release with fixes for SV calling
- PureCN -- add signature dependency and update with fixes for test
samples.
* Dinucleotide patterns analysis tools v1.0 (#11245)
* Dinucleotide patterns analysis tools v1.0
* Lets try it, it seems to work locally for me.
* Enable SpoTyping_plot.r (#11248)
* rerun again (#11233)
* rerun again
* Update meta.yaml
* Delete build.sh
* Update segway dependency optbuild to 0.2 (#10459)
* Update segway dependency optbuild to 0.2
* Update build and architecture requirements for optbuild 0.2
* Add six as a dependency to the optbuild recipe
* Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249)
* Add prefix dnp- to the package names
* Update build.sh
* Update build.sh
* Bump beast version to 1.10.2 (#11250)
* add maxquant (#11253)
* add mayquant
* relax tests
* PacBio: Update `pbmm2` to version 0.10.1 (#11256)
* PacBio: Update `pbmm2` to version 0.10.1-1 (#11257)
* remove xsv recipe (#11259)
* add blast dependency (#11258)
* Added riborex recipe (#11251)
* Added riborex recipe
* Relaxed version constraints
* Pinned r-core for fdr tools
* fixed the r-base stuff upstream
* Update meta.yaml
* fix graphprot (#11234)
* increase build number
* remove from blacklist
* use cxx instead of c
* move coreutoils to build section
* set additional paths
* patch makefile
* blind try
* update patch
* explicitely copy from src_dir
* update deprecated prefix variable
* Revert "update deprecated prefix variable"
This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d.
* update deprecated prefix variable
* try moving to host section
* Bump mash (#11264)
* Add fmlrc (#11265)
* Add fmlrc
* add doi
* PacBio: Update pb-falcon to 0.2.4. (#11266)
* Add kopt recipe (#11269)
* Genomepy 0.5.2 (#11267)
* release 0.5.2 of genomepy
* trigger new build
* remove genomepy from blacklist
* locale for osx
* updated locale test
* PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275)
* Update mmseqs2 recipe to new release 6-f5a1c (#11272)
* Update yacrd to version 0.4.1 (#11273)
* Add scprep (#11270)
* Add scprep
* All of these should not be needed as host dep
* Metawrap preqs2 (#11242)
* fixed issues
* fixed issues
* added tests
* fixed tab
* gemma 0.98 (#11254)
* gemma 0.98
* gemma 0.98
Leave gsl and zlib out of runtime dependencies
* Add DCA recipe (#11274)
* Add DCA recipe
* add noarch and doi
* remove skip
* Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib
* Various fixes for bulk and trigger a rebuild (#11313)
* Various fixes, at least 4 packages (and their dependencies) should still fail (#11320)
* A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336)
* Fix various recipes (#11354)
* Fix various recipes
* Fix more recipes
* Various CRAN package fixes, since they all lack license files (#11372)
* Various CRAN package fixes, since they all lack license files
* Fix the r-dartr recipe
* There is a light at the end of the tunnel (#11381)
* There is a light at the end of the tunnel
* Licenses no longer exist
* [BULK] Fixes for R/Bioconductor packages (#11406)
* Require `r-base >=3.5` for some packages
* Fix various CRAN packages lacking license file
* Add missing libnetcdf requirement to bioconductor-mzr
* Remove r-alakazam (moved to conda-forge)
Fix linting issue:
```
recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating
```
* [BULK] Many R 3.5 only packages (#11410)
* Update pinning to R>=3.5 and a few runtime dependencies.
* CSAW is R 3.5 only
* Packages using beachmat are 3.5 only
* Packages using bioconductor-singlecellexperiment are R 3.5 only
* [BULK] Don't use r-base >=3.5, use a conda_build_config.yaml instead (#11452)
* Don't use r-base >=3.5, use a conda_build_config.yaml instead
* blacklist r-phangorn
* Update variancepartition
* R 3.5 for packages requiring singlecellexperiment
* Update a few packages
* Update a number of recipes (#11482)
* Update ensemblVEP and derfinder (#11504)
* Bulk update 251018 (#11577)
* [BULK] various package updates
* blacklist bioconductor-mzr
* A couple tweaks
* [BULK] Update 261018 (#11611)
* Apparently the r-rgeos bit works properly now.
* Add tissueenrich and try to fix scpipe on Linux
* A meaningless change just to trigger an update in bulk. (#11618)
* [BULK] update 271018 (#11628)
* Bump bioconductor-esetvis
* Fix yaqcaffy
* Fix more
* Another R 3.5 recipe
* [BULK] update 281018 (#11689)
* Add some files
* Fix arrayexpress
* Fix another 2
* Blacklist a bunch of bioconductor recipes that aren't likely to get built for a variety of reasons (mostly due to mzR). (#11697)
* Update blacklist (#11706)
* [BULK] fix bioconductor-tissueenrich (#11720)
* taxonkit 0.2.5 (#11318)
* Update csvtk (#11319)
* taxonkit 0.2.5
* csvtk 0.15.0
* bumping GROOT to 0.8.1 (#11323)
* HiCMatrix version 3 (#11322)
* Correcting dependencies
* Version 3 of HiCMatrix, the October release
* Update confindr to 0.4.3 (#11330)
* Drop-seq_tools: Version 2.0.0 (#11326)
* Update meta.yaml
* Update build.sh
some tool names changed to fit Camel case
* Update motus to build only for python3 (#11331)
* Update fpa to 0.2 version (#11333)
* update taxonkit to 0.3.0 (#11339)
* ntcard 1.1.0 (#11338)
* Update rgi (#11335)
* first commit
* update dependencies list
* change source to github
* change build number
* testing circleci
* update meta and build
* fix build
* move build script into meta
* remove older recipes
* line fix in bootstrap.py
* change python & matplotlib versions; add build.sh file
* add preprocessing selector to skip python 2.7
* move build script into meta.yaml
* Revert "line fix in bootstrap.py"
This reverts commit 5ac1ecd0142a5cfdfc8499c5b6ef4e1f629cd046.
* Update gmap to version 2018-07-04. (#11332)
MAX_READLENGTH environment variable has been disused since 2016-08-16.
* Upgrade r-biodb to 1.2.0a. (#11341)
* Upgrade r-biodb to 1.2.0a.
* Update meta.yaml
* Updated ont-tombo to version 1.5. (#11329)
* Updated ont-tombo to version 1.5.
* Updated with actual github release version hash.
* remove graphicsmagick (#11342)
* Build kraken2 for osx (#11343)
* First try for a bcalm recipes (#11344)
* New: cgpbigwig (BigWig manipulation); Update: bcbio (#11347)
- cgpbigwig (https://github.com/cancerit/cgpBigWig) provides bigwig
generation and manipulation command line tools including bam to bigwig
conversion.
- bcbio: fixes for QC on variants and peddy for CWL runs
* Try avoid some dependancy (#11349)
* Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8 (#11348)
* Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8
Also add about:home .
* Workaround https://github.com/conda-forge/bison-feedstock/issues/7
* Better bcalm recipes (#11350)
* Try avoid some dependancy
* Correct mess in build number, sorry
* R biodb (#11351)
* rebuild r-biodb
* trigger build
* Add recipe for pypairs (#11356)
* Update smoove to 0.2.1. (#11360)
* Update duphold to 0.0.9. (#11359)
* Update goleft to 0.2.0 (#11361)
* Bump slicedimage to 1.0.0 (#11362)
* Bump slicedimage to 1.0.1 (#11365)
* Added new versions for biopet-sampleconfig (#11268)
* perl-velvetoptimiser: update to 2.2.6 (#11369)
* update to 2.2.6
* remove unneeded patch
* Scanpy upgrade (#11371)
* Bump version
* Upgrade Scanpy
* Bump starfish to 0.0.25 (#11370)
* bumping groot to 0.8.2 (#11374)
* vep: bump subversion (#11367)
* Updated Krocus 1.0.1 (#11355)
* Add tiptoft
* Fix meta.yaml for tiptoft
* Add build script
* Updated krocus 1.0.1
* Add tiptoft 0.1.4 (#11352)
* Add tiptoft
* Fix meta.yaml for tiptoft
* Add build script
* Kodoja v0.0.9 (#11373)
* Add recipe for seer (#11263)
* Add recipe for seer
* lets try this
* Add newer compiler
* Using boost-cpp
* messed up version string
* Attempt building boost
* Use c++11 in boost
* Use python for boost install
* Correct python version spec
* try with different python version
* Fix b2 command
* Fix popd command
* build and link boost program options statically
* Fix tests
* Match dependency order
* Link openblas instead of blas
* Forcing rebuild with openblas
* Don't use armadillo wrapper
* Making review changes. Also trying original tests
* Previous tests were correct
* Add recipe for the translate-gard npm package version 1.0.3 (#11364)
* Fix umi tools (#11376)
umi_tools: clean up dependencies
* add support tools to PATH (#11379)
* Bump to v2.2.1 (#11380)
* Bump starfish to 0.0.26 (#11378)
* Update fpa to 0.3 (#11375)
* Update fpa to 0.3
* Correct error in sha256
* Reset build number
* Update trial to 2.5.5 (#11386)
* Update: bioconductor-titancna; 1.19.1 with hg38 support (#11388)
* Update: bioconductor-titancna; 1.19.1 with hg38 support
* Pin to R 3.4 to avoid pulling in 3.3 and 3.5 during mulled
* Add r-polysat version 1.7-3 (#11384)
* Update biomart version so that compatible with r351 (#11366)
* Update biomart version so that compatible with r351
* Update meta.yaml
reset build number as per https://bioconda.github.io/guidelines.html#buildnum
* Update entrez-direct to 10.0.20180927. (#11387)
* Added recipe for SonicParanoid 1.0.13 (#11271)
* Added recipe for SonicParanoid 1.0.13
* removed 'x.x' for numpy, added basic test
* fixed linter related errors
* compiler set to cxx and added host section (same build error!)
* removed host section
* moved numpy and cython to host section; restored build: noarch: python; added LICENSE.md
* removed build: noarch
* added build and extra sections
* set build number to 0; removed skip build; added python3 minimum version; added test for all executables.
* restored sh python module as requirement
* added Make to run; updated release to latest commit
* remove c compiler from meta.yaml
* modified build.sh to compile source codel added make in build section
* updated to latest commit
* updated to latest version with make included in setup.py
* reverted build.sh to the simplest version (python setup.py install)
* Add perl-json to build requirements to allow meme-chip to run to completion. Change meme-chip to use dreme-py3 instead of dreme if building with python 3. (#11389)
* Bump IgBLAST to 1.9.0 (#11393)
Bump IgBLAST to 1.9.0
Re-package the binary version this time. There are problems building the
source version when the configure script reaches this step:
"trying to build the NCBI SRA/VDB Toolkit from GitHub"
The previous problem about the binaries linking against libbz2.so, for
which we had no conda package, is now solved.
Also, this saves about 45 minutes compilation time.
* Add consan (#11395)
* Add consan
* Skip osx
* Update: vardict, vardict-java 1.5.7 (#11394)
* Update: vardict, vardict-java 1.5.7
Latest vardict-java release and corresponding vardict with bug fixes
after testing with 1.5.6
* Reduce test output to try and fix build problems
* Experiment 2 for build problems: remove r-base from run
* Experiment 3 for build problems: add r-base in host
* update recipe for 3.9.1 (#11397)
* evofold2 (#11396)
* evofold2
* wrapper
* Update meta.yaml
* minor
* Update rnastructure to 6.1. (#11400)
* Ctat mut (#11401)
* updating version number
* correct URL
* proper hash
* Revert "Ctat mut (#11401)" (#11402)
This reverts commit 6db10ac7ffd7abaf8fbf1762b7ea6c63b2585fe0.
* update version (#11403)
* any2fasta 0.4.2 (new formula) (#11407)
* W4mclassfilter v0.98.9 (#11385)
* Added files to build version 0.98.9
* Update meta.yaml
* Update meta.yaml
* updated SonicParanoid recipe to version 1.0.14 (#11409)
* updated SonicParanoid recipe to version 1.0.14
* Update to version 1.0.2 of PopDel (#11398)
* Update to version 1.0.2 of PopDel
Update to version 1.0.2.
* Reset build number to 0
* PacBio: require Meson 0.48.1 for all recipes (#11090)
* Meson 0.47 inserted duplicate RPATHs in
macOS binaries, causing `install_name_tool`
failures when installing the package.
Requiring 0.48.1 ensures we do not run into
these issues anymore in the future.
* rebuild with latest openmpi (#11411)
* Remove kfoots from the blacklist (#11416)
* Update gseapy to 0.9.7 (#11417)
* Update gseapy to 0.9.7
* remove noarch
* Add SC3 as dependency (#11427)
* Add recipe for r-poppr (#11418)
* Update knitr version because of Issue: https://github.com/rstudio/rmarkdown/pull/1271 (#11412)
* Update IQ-TREE to 1.6.7.1 (#11429)
* Update IQ-TREE to 1.6.7.1
* Change build number
* Update: r-deconstructsigs with fixes for hg38 (#11431)
The 1.8.0 release, from 2016, has some issues with hg38 and other
custom genomes that are fixed in development (raerose01/deconstructSigs#27).
There hasn't been a new release pushed so this rolls these into a new
sub-version and makes them available.
* Update entrez-direct to 10.2.20181018. (#11432)
* Add assembly-scan recipe (#11425)
* remove python 2.7 skip (#11424)
Preparation for rnaQUAST
* Add fastq-scan recipe (#11415)
* Add patch to fix racon/rampler path in racon_wrapper. (#11434)
Fixes #11405.
* meme rebuild (#11433)
* Update nanocomp to 0.23.1 (#11436)
* Update nanocomp to 0.23.1
* remove noarch
* Update abricate to 0.8.10 (#11446)
* Update angsd to 0.923 (#11445)
* Update alfred to 0.1.13 (#11444)
* Update alfred to 0.1.13
* Try w/o patch
* Update antarna to 2.0.6 (#11442)
* Update admixtools to 5.1 (#11443)
* Update admixtools to 5.1
* Let makefile choose which bins to install
* Update alignstats to 0.5 (#11441)
* Update xatlas to 0.2.1 (#11437)
* r-gpca (#11428)
* r-gpca
* r-gpca recipe
* Update meta.yaml
* Removed All Comments
* gseapy bump version 0.9.8 (#11440)
* gseapy bump version 0.9.8
* version
* titancna: fix for hg38, remove conda build hacks (#11447)
* titancna: fix for hg38, remove conda build hacks
* Re-add r-base 3.4 pin to avoid 3.5 errors
* Hmmlearn older version (#11450)
* Adding pygtftk
* removed pygtftk from master
* add older version of hmmlearn
* Add card_trick (#11451)
* Add card_trick
* Restrict to py3
* Update checkm-genome to 1.0.12 (#11455)
* Bump drep (#11457)
* Update squid to 1.5 (#11466)
* Update ncbi-ngs-sdk to 2.9.3 (#11467)
* elprep: bumped major version (#11414)
* elprep: bumped major version
* fixed hash
* fix download link, fixed licence
* fixed tests
* skip osx build
* FRED2 as a conda package (#11469)
* Attempt to get FRED2 as a conda package
* SHA update
* 99 little bugs in the code
* Fix things Björn mentioned
* add rnaQUAST recipe (#11470)
* Update bioconda-utils to 0.14.9 (#11454)
* Rapidup (#11474)
* Update to v0.7
* Update Buildnumber
* rapid: update to v0.6
* rapid: update to v0.6
* update grid (#11478)
* Adding biobb_model recipe (#11472)
* Updated wtdbg to v2.1 (#11486)
* update stream to 0.2.6 (#11483)
* update stream to 0.2.2
* update stream to 0.2.3
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.5
* update stream to 0.2.6
* Update meta.yaml (#11487)
* Update connectome-workbench to 1.3.2 (#11468)
Now needs QT 5.7
* Update deblur to 1.1.0 (#11500)
* Update domclust to 1.2.8 (#11498)
* WisecondorX: bump version (#11501)
* Bump as GitHub wasn't working yesterday (#11502)
* Added recipe for Sequenza (#10367)
* Added recipe for Sequenza
* Removed fn entry in source section
* Trying with only one URL
* copynumber is a bioconductor package
* Added missing requirements section
* Removed mailing list address
* Added doi
* Added license_file
* Trying with different license_file path
* Fred2 bump (#11503)
* Bump as GitHub wasn't working yesterday
* Fix licence etc
* Scanpy scripts (#11413)
Doing squash and merge as requested by @nh3
* Bump version
* First implementation of scanpy-scripts bioconda recipe.
* fix path in build.sh
* Remove "noarch" flag as requested by bioconda recipe checklist
* Add a post install notice that post install test needs bats-core.
* Add more dependencies
* Skip building for python versions other than 3.6
* Target v0.0.2 which has non-ascii characters removed
* Lower version requirement for pandas and matplotlib to be the same as scanpy
* Requirement matplotlib>=3.0.0, declare noarch
* New: hmftools-cobalt; Update: hmftools-purple (#11507)
- hmftools-cobalt: Add latest version of PURPLE associated read counter,
COBALT, with support for hg38.
- hmftools-purple: PURPLE release with hg38 support.
* Update Picard to 2.18.15. (#11505)
* Genenotebook (#11476)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* Update pinning (#11514)
* Bump build number for updated dependency (#11510)
* Bump build number for updated dependency
* Try adding r-base to host requirements
* Try adding other requirements to host
* Pin to R version
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Tweak dependency version syntax
* Pin R and package versions correctly
* PacBio: Update pbcore to 1.6.5 (#11513)
* Bump r seurat scripts version (#11292)
* Bump version
* Remove noarch
* Could wrongly quoted version be causing an issue?
* Tweak pinning to try and fix CI error
* seqcluster:fix UMI detection. (#11511)
* seqcluster:fix UMI detection.
* Fix dependency
* quast 5.0.1 (#11479)
* quast 5.0.1
* quast 5.0.1: remove third-party site packages from the distibution pack
* quast 5.0.1: skip Glimmer in test
* quast 5.0.1: joblib and simplejson dependencies added to meta.yaml (Setuptools downloading is disabled in conda build)
* quast 5.0.1: explicit joblib and simplejson dependencies removed (Setuptools downloading is disabled in conda build)
* quast 5.0.1: Python 2 and 3 compatible code in build.sh
* wcX bugfixes (#11508)
* wcX bugfixes
* fixed shasum
* Update fastspar to 0.0.7 (#11515)
* Update iqtree to 1.6.7.2 (#11525)
* Update illumina-interop to 1.1.6 (#11523)
* Update hapbin to 1.3.0 (#11522)
* Update hlama to 3.0.1 (#11520)
* Update gb_taxonomy_tools to 1.0.1 (#11519)
* Update gffcompare to 0.10.5 (#11517)
* Update fast5seek to 0.1.1 (#11516)
* Update deepbinner to 0.2.0 (#11499)
* Update deepbinner to 0.2.0
* Update meta.yaml
Try same fix as in #11240
* Update ncbi-vdb to 2.9.3 (#11550)
* Update mikado to 1.2.4 (#11549)
* Update perl-pcap to 3.5.2 (#11543)
* Update python-hyphy-python to 0.1.9 (#11545)
* Update mlst to 2.15.2 (#11547)
* Update perl-sanger-cgp-vcf to 2.2.1 (#11542)
* Update merfishtools to 1.5.0 (#11537)
* Update perl-sanger-cgp-vagrent to 3.3.3 (#11536)
* Update nonpareil to 3.3.3 (#11535)
* Update prophex to 0.1.1 (#11532)
* Update krakenuniq to 0.5.3 (#11527)
* Update novoplasty to 2.7.2 (#11530)
* Update minced to 0.3.2 (#11529)
* Update mapdamage2 to 2.0.8 (#11528)
* Update perl-sanger-cgp-allelecount to 4.0.0 (#11538)
* Update pyvolve to 0.9.0 (#11531)
* Genenotebook (#11512)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* add plek (#11554)
* Update pyimzml to 1.2.4 (#11534)
* Bump shovill (#11555)
* PacBio: Update minimum pbcore version (#11556)
* We want all users of PacBio tools to be able to
use our utilities with pbmm2 alignments.
* Add recipe for translate-gard v1.0.4 (#11557)
* bioconductor-rnaseqsamplesizedata (#11475)
* Adding Recipe for bioconductor-rnaseqsamplesizedata
* Updated metadata for RnaSeqSampleSizeData
* nextflow 18.10.1 (#11558)
* Update raxml to 8.2.12 (#11567)
* Update r-fgwas to 0.3.6 (#11566)
* Update rapid to 0.7 (#11565)
* Update r-spieceasi to 1.0.2 (#11564)
* Update rcorrector to 1.0.3.1 (#11562)
* Update quicktree to 2.4 (#11560)
* Update paladin to 1.4.4 (#11541)
* Update paladin to 1.4.4
* delete md5
* Update build.sh
* Update build.sh
* Fix and unblacklist Tadarida-D (#11568)
* Add recipe for rgt
* Fix and un-blacklist tadarida-d
* Remove RGT
* bumping groot (#11575)
* update pymzml (#11573)
* Add bioconductor-rnaseqsamplesize (#11559)
* Add bioconductor-rnaseqsamplesize
* Update recipe
* Fixing some URLs
* Update dependencies missing
* Update trumicount to 0.9.11 (#11576)
* Update ConFindr to 0.4.4 (#11578)
* Added new versions for biopet-scatterregions (#11572)
* Added new versions for biopet-bamstats (#11571)
* R ggbiplot (#11584)
* add R -e 'httr::set_config(httr::config(ssl_verifypeer = 0L)); install.packages(devtools, repos=http://mirrors.ebi.ac.uk/CRAN/); library(devtools); install_github(vqv/ggbiplot); library(ggbiplot)'
* add r-ggbiplot
* update meta.yaml
* update meta.yaml
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix errors
* fix errors number 1
* Update rebaler to 0.1.2 (#11563)
* Update rebaler to 0.1.2
* Remove fn
* bump graphclust (#11585)
* Update seqyclean to 1.10.09 (#11589)
* Update stringmlst to 0.5.1 (#11590)
* Update snp-dists to 0.6.2 (#11592)
* Update snippy to 4.3.3 (#11596)
* Update canu to 1.8 (#11600)
* Update starfish to 0.0.27 (#11599)
* Update womtool to 36 (#11594)
* Update telseq to 0.0.2 (#11598)
* Update snp-sites to 2.4.1 (#11588)
* Added recipe for pydemult: Streamed and parallel demultiplexing of fastq files (#11471)
* Added recipe for pydemult
* Bumped version in favor of py3.5
* bump vcf2db to latest commit (#11601)
* bump vcf2db to latest commit
* fix shasum
* Fixing source url
* Update: TitanCNA; hg38 cytoband support and fix for normalization (#11604)
* megan (#11046)
* megan6: initial commit
* megan6: intermediate commit
* megan: made tests work
* megan: doc improvement
* megan: added osx dmg file
* megan: add java to build requirements
* megan: removed new line
* megan: removed osx sources
* Update meta.yaml
* bumping hulk (#11607)
* Update hotspot3d to 1.8.2 (#11521)
* Update hotspot3d to 1.8.2
* Add perl-json as dependency
* Add perl-archive-extract as dependency
* Fqzcomp (#11606)
* Added recipe for fqzcomp
* There is no configure script
* Maybe this works
* Added gcc as build requirement
* Removed gcc again (lint issue)
* Maybe these exports will do the trick
* Nope!
* Added cxx as host requirement
* Compilers are only allowed in build section
* There is no need for make install
* Copy-paste error...
* Add vcf-annotator recipe (#11481)
* Add vcf-annotator recipe
* added pyvcf dependency
* Update meta.yaml
* stacks: fix for @ in exe_path (#11580)
* stacks: fix for @ in exe_path
* stacks: fixed path
* New version with bugfix and different progressiveMauve version. (#11613)
* Sspupdate (#11614)
* New version with bugfix and different progressiveMauve version.
* Keeping old version as folder.
* Push build number.
* Update SVDB to version 1.3.0 (#11506)
* new file: recipes/svdb/1.1.2/meta.yaml
renamed: reipes/svdb/svdb.patch -> recipes/svdb/1.1.2/svdb.patch
modified: recipes/svdb/meta.yaml
* deleted: 1.1.2/meta.yaml
deleted: 1.1.2/svdb.patch
* Bump nanosim (#11608)
* Bump nanosim
* Add scipy as dep
* Add recipe for perl-number-range (#11621)
* New build for grid (#11620)
* update grid
* update build num
* Recipe for das_tool 1.1.1 (#10528)
* recipe for das_tool 1.1.1
* Add recipe for sompy (#11624)
* cmake modified to build with NDEBUG (#11328)
* cmake modified to build with NDEBUG
* Update meta.yaml
* new build with fasta test
* new build with fasta test
* Fix and unblacklist TwoPaCo (#11622)
* Add recipe for TwoPaCo
* Unblacklist twopaco
* Modify and unblacklist recipe for ESTmapper (#11623)
* Modify and unblacklist recipe for ESTmapper
* Add patch
* Modify and unblacklist recipe for Metaseq (#11625)
* Fix recipe for metaseq and remove from blacklist
* Remove build.sh
* nextflow 18.10.1 build 2 (#11630)
* Add Clust (#11619)
* Add clust
* Clean recipe
* Add "noarch"
* Add DOI
* Add build file
* Python 2.7
* Fix scikit-learn dependency
* Trigger new build
* Update: PureCN (multicore) and PURPLE (plotting X libraries) (#11631)
- PureCN: adds support for specifying cores on command line
- PURPLE: adds X library dependencies required for creating
plots
* scripts/travis-run.sh: added a cleaner method to check for env vars (#11612)
* Increase the number of k value usable in bcalm (request by @Malfoy) (#11610)
* Increase the number of k value usable in bcalm (request by @Malfoy)
* Change compilation parameter to reduce memory impact of compilation
* Update anndata to 0.6.11 (#11637)
* Update nglview to 1.1.7 (#11643)
* Update binsanity to 0.2.7.1 (#11644)
* Update cgat-core to 0.5.4 (#11645)
* Update nanosv to 1.2.2 (#11673)
* Update abeona to 0.36.0 (#11670)
* Update pyfaidx to 0.5.5.2 (#11659)
* Update agfusion to 1.23 (#11668)
* Update iqtree to 1.6.8 (#11686)
* update iqtree to 1.6.8
* Trigger rebuild
* Update validators to 0.12.2 (#11672)
* Update python-edlib to 1.2.3.post1 (#11664)
* update for Purge Haplotigs (#11690)
* Update loompy to 2.0.16 (#11667)
* Update loompy to 2.0.16
* Update meta.yaml
* IgBLAST 1.10.0 (#11693)
* Update wtforms-alchemy to 0.16.7 (#11679)
* Update sickle to 0.6.4 (#11663)
* Update sickle to 0.6.4
* Remove fn and libgcc runtime dep
* Update confindr to 0.4.5 (#11696)
* Batvi (#11695)
* batvi initial
* Guideline compatibility..
* Dummy test section..
* Missing java dependency..
* use openjdk instead of java-jdk ..
* source specified in github ..
* trigger build (package did not have batindel directory) ..
* update SHA256 ..
* update SHA256 ..
* Update pythonpy to 0.4.11 (#11661)
* Update cortexpy to 0.45.6 (#11660)
* Update sevenbridges-python to 0.16.0 (#11674)
* Update solvebio to 2.7.0 (#11657)
* Update mathstats to 0.2.6.5 (#11656)
* Update goatools to 0.8.9 (#11641)
* Add gnies (#11627)
* Add gnies
* noarch python
* Update meta.yaml
* Add recipe for SKA v1.0 (#11581)
* Add recipe for SKA v1.0
* Add lib path for zlib
* Older gcc
* Correct install dir
* Try static linking
* Dynamic linking on OS X
* ldd command test
* correct program
* Remove ldd command
* Add recipe for transit version 2.3.1 (#11701)
* Add recipe for transit version 2.3.1
* Use skip, add spaces.
* Update meta.yaml (#11699)
* remove pyqi (#11704)
* Update python-chado to 2.2.0 (#11714)
* update python-chado
* 2.2.1
* Update vcfanno to 0.3.1 (#11710)
* FGMP-1.0.1 (#11278)
* FGMP-1.0.1 recipe
* remove unncessary build info
* add r-nabor (#11716)
* update stream to 0.2.2
* update stream to 0.2.3
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.5
* update stream to 0.2.6
* add r-nabor recipe
* update r-nabor recipe
* update r-nabor recipe
* r-pctgcdata (#11715)
* r-pctgcdata
* r-pctgcdata - fix
* r-pctgcdata - fix
* Update meta.yaml
* Fix plek by a new branch (#11605)
* Modify the PLEK recipe
* Start fixing PLEK, though it requires compilation
* update build.sh
* update yaml
* fix build.sh
* update build.sh
* Update recipe for plek
* add bioconductor-chromvar recipe (#11718)
* add bioconductor-chromvar recipe
* fix bioconductor-tissueenrich
* Apparently the popdel recipe didn't get correctly merged
* Final merge conflicts
* Bioc quick test (#12547)
* Update kallisto to 0.45.0 (#12117)
* Update validators to 0.12.3 (#12116)
* Update illumina-interop to 1.1.7 (#12115)
* Update umi_tools to 0.5.5 (#12123)
* Update tiptoft to 1.0.0 (#12122)
* Update: TitanCNA with fix for hg38 plotting (#12130)
* blockclust (#12111)
* added eden 1.1 version used in blockclust
* Update meta.yaml
* eden checksum and test
* added zlib requirement
* add include and lib paths to build.sh
* add include and lib paths to build.sh
* modify makefile flags using sed
* modify makefile flags using sed
* use c++
* Update build.sh
* Update build.sh
* LDFLAGS not used in makefile
* remove v1.1
* add blockclust 1.1.0 recipe
* skip osx build
* added tarball url and checksum; removed conda_build_config.yaml
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Update chewbbaca to 2.0.16 (#12132)
* Update abeona to 0.40.0 (#12131)
* ping to eden 1.1 (#12134)
* clean swap file (#12137)
* Update corset to 1.07 (#12143)
* Update peddy to 0.4.3 (#12144)
* blockclust latest source and added cloudpickle as requirement (#12142)
* Update nanomath to 0.22.0 (#12149)
* Update pymvpa to 2.6.5 (#12152)
* Updated to version 1.4.0 (#12138)
* Updated to version 1.4.0
* Resetting build number to 0 and build->host
* Update transdecoder to 5.5.0 (#12172)
* Update gridss to 2.0.1 (#12190)
* Update tracer to 1.7.1 (#12189)
* Update flowcraft to 1.4.0 (#12179)
* Update seqbuster to 3.2 (#12182)
* Update perl-io-compress to 2.081 (#12201)
* Update twobitreader to 3.1.6 (#12205)
* Update twobitreader to 3.1.6
* Update meta.yaml
* Update gtfparse to 1.2.0 (#12186)
* Update gtfparse to 1.2.0
* remove compiler
* Update htseq to 0.11.0 (#12177)
* Update htseq to 0.11.0
* add compiler
* Update htseq to 0.11.0 (#12239) [testing co-author]
* Update htseq to 0.11.0
* add compiler
Co-authored-by: Bjoern Gruening <[email protected]>
* alfred v0.1.16 (#12240)
* alfred v0.1.16
* makefile patch
* makefile patch
* Update scrm to 1.7.3 (#12150)
* Update scrm to 1.7.3
* Update scrm to 1.7.3
* Mob suite update 1.4.8 --> 1.4.9 (#12244)
We fixed a small bug related to repetitive elements database reconstruction on each run. Should only run once during the first mob_typer run. Should be good now for parallel runs.
* PeptideShaker updated to v1.16.35 & SearchGUI updated to 3.3.9 (#12241)
* PeptideShaker updated to v1.16.32
SearchGUI updated to v3.3.6
* PeptideShaker updated to v1.16.35
* SearchGUI updated to v3.3.9
* First attempt at a recipe for ncrf (#12101)
* First attempt at a recipe for ncrf
* changed from copies to symlinks
* including absolute path in symlinks
* PacBio: Update `pbmm2` to version 0.11.0 (#12246)
* Gimmemotifs version 0.13.0 (#12245)
* new release to fix numpy incompatibility
* GimmeMotifs 0.13.0 release test
* numpy 1.15
* version 0.13.0
* Fix about:home and extra:
* PacBio: Update `isoseq3` to version 3.1.0 (#12263)
* add python to host section (#12264)
* Update confindr to 0.4.7 (#12266)
* new build of GRiD (#12269)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* peptideshaker, searchgui: version bump (#12136)
* peptideshaker, searchgui: version bump
solving https://github.com/compomics/searchgui/issues/192
* Update peptide-shaker.py
* searchgui: added c compiler for building
test if linking errors go away this way
* searchgui: removed noarch
* Update: bcbio, bcbio-vm with CWL non-human fixes (bcbio/bcbio-nextgen#2473) (#12273)
* Make snakemake a noarch package. (#12274)
* noarch: python in combination with version constraint
* Cleanup deps and simplify version definition.
* Genenotebook v0.1.9 (#12277)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* Create r-airr recipe (#12284)
* Create r-airr recipe using bgruening/conda_r_skeleton_helper
* Update meta.yaml
* Findbin::Real added (#12291)
* Added version bump to 1.3 (#12292)
* ngs-bits 2018_11 (#12262)
* Updated ngs-bits to version 2018_10
* Updated ngs-bits to version 2018_11
* minor edit in grid (#12287)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* minor edit to grid
* Fred2 update (#12259)
* Update FRED2 Recipe
* msstitch version 2.9 (#12296)
* r-mvr (#12300)
This is a non-parametric method for joint adaptive mean-variance regularization and variance sta-
bilization of high-dimensional data.
* Bump to Gromacs 2018.3 + re-enable OSX build (#12299)
* Gromacs 2018.3 + re-enable osx build
See also #7825 on OSX build
Include RRID for Gromacs (see bioconda/bioconda-utils#252)
* disabled ocl-icd on osx; not available (or needed?)
https://anaconda.org/conda-forge/ocl-icd
* pyGenomeTracks update of dependencies (#12279)
* Update pyGenomeTracks recipe to enable py3 support and updating outdated dependecy list
* Increase build number
* Update meta.yaml
* Exclude Python 3.5
* Gromacs 2018.4 (#12302)
* quast 5.0.2 (#12303)
* Update meta.yaml (#12275)
* Update meta.yaml
r-rsqlite version dependency added
* Update meta.yaml
Updated build number to 1
* Use the extended-base container because of wget issues when downloading databases (#12297)
* Update duphold to 0.1.0 (#12257)
* Update flashlfq to 0.1.109 (#12256)
* Update planemo to 0.57.0 (#12251)
* Update meta.yaml (#12258)
* Update scalpel to 0.5.4 (#12249)
* Update scalpel to 0.5.4
* Fix url
* edit grid (#12298)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* minor edit to grid
* minor edit to recipe grid
* added feather to deps (#12293)
* R tigger (#12286)
* Create recipe for r-tigger (#12271)
* Create recipe for r-tigger using bgruening/conda_r_skeleton_helper.
* Delete bld.bat
* Remove windows support
* update scprep to v0.8.1 (#12306)
* Update nanoget to 1.7.5 (#12252)
* Update nanoget to 1.7.5
* Bump to version 1.7.6
should fix the README.md problem
* gffcompare: version bump (#12308)
* Update: cromwell (36), bcbio (Cromwell Docker runs) (#12307)
* Update: cromwell (36), bcbio (Cromwell Docker runs)
* Pin java to 8 to avoid compile errors on 11
* HiCExplorer update to version 2.2-beta (#12309)
* HiCExplorer update to version 2.2-beta
* Remove of '-' from version number
* Numpy set to 1.15
* Update meta.yaml
* upgrade to version 2.8.1 (#12316)
* Create Airr recipe (#12318)
* Create AIRR recipe using conda skeleton pypi.
* Add noarch python
* Clean host requirements
* Added nimnexus [v0.1] (#12133)
* added nimnexus
* Fix sha
* Update build.sh
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* [WIP] Add R-loom (#12320)
* initial WIP skeleton
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* try osx
* Create Changeo recipe (#12321)
* Create changeo recipe using conda skeleton pypi.
* EDIT about section
* ADD noarch generic
* Update noarch to python
* Clean host requirements
* Add test for scripts
* Change requirement to python>=3.4
* Add noarch pyton
* r-corbi (#12325)
* r-nam (#12327)
* Update pybedtools to 0.8.0 (#12324)
* Update pybedtools to 0.8.0
* rm cython requirement
* MSGFplus does not work with newer Java (#12330)
* Trying to not use a very new java version since the latest versions have dropped some classes
* Increment build
* Update atropos to 1.1.21 (#12322)
* Update CONCOCT to 0.4.2 (#12317)
* Update CONCOCT to 0.4.2
* Wrong shasum given
* Reset build number for new version
* New: gvcfgenotyper for joint calling with Illumina strelka2 (#12331)
* Apparently we need openJDK to be below 9, not below 11 as in the previous PR (#12332)
* Update Picard to 2.18.17. (#12333)
* Unblacklist IgDiscover (#12335)
* PacBio: Add missing licenses and post-link message (#12334)
* Bioconductor DEqMS package (#12336)
* Bioconductor DEqMS package
* Limma version could be set lower (checked with the bioconductor recipe page) to include limma in bioconda
* Genenotebook v0.1.10 (#12337)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* v0.1.10
* removed cloudpickle requirement for blockclust (#12242)
* blockclust latest source and added cloudpickle as requirement
* removed cloudpickle requirement for blockclust
* added a tagged release to the source
* back to source url but with release tarball and checksum
* R guilds (#12341)
* Strict rec (#12113)
* added metawrap
* fixed perl and jdk
* added more strict req
* fixed java and perl
* removed extra boost
* Update qcat to v1.0.1 (#12343)
* Add better error checking (#12345)
* Add mhcnames python package (#12349)
* Add MHCflurry pMHC class I binding affinity prediction tool (#12346)
* Bump pilon (#12354)
* Update pronto to 0.11.1 (#12377)
* Update perl-json-xs to 4.0 (#12373)
* Update planemo to 0.57.1 (#12370)
* Update snippy to 4.3.6 (#12372)
* Update intarna to 2.3.1 (#12367)
* Update agfusion to 1.231 (#12366)
* Update bioconda-utils to 0.15.0 (#12359)
* Update mapdamage2 to 2.0.9 (#12358)
* Update scanpy to 1.3.4 (#12357)
* Update goatools to 0.8.11 (#12361)
* Update perl-math-random-mt-auto to 6.23 (#12362)
* Update kipoi to 0.6.3 (#12374)
* Update kipoi_veff to 0.2.1 (#12364)
* Update perl-object-insideout to 4.05 (#12380)
* Update sevenbridges-python to 0.17.1 (#12379)
* Update nanosv to 1.2.3 (#12378)
* Update starfish to 0.0.30 (#12368)
* Update clust to 1.8.10 (#12356)
* Update pypairs to 2.0.6 (#12381)
* Update khmer to 3.0.0a2 (#12360)
* Update flashlfq to 0.1.110 (#12385)
* Update perl-algorithm-cluster to 1.57 (#12384)
* Update arvados-python-client to 1.2.0.20181121194423 (#12382)
* Update avro-cwl to 1.8.9 (#12355)
* Update avro-cwl to 1.8.9
* Set noarch: python
* r-breakaway (#12386)
* R sads (#12388)
* Update python-sortedcontainers to 2.1.0 (#12383)
* r-ebimetagenomics (#12339)
* pin armadilo on major version (#12389)
* IgDiscover version 0.11 (#12351)
* IgDiscover version 0.11
* IgDiscover requires Python 3.6
* Fix build on macOS with a small patch
* Remove unneeded host dependencies
* Update goatools to 0.8.12 (#12391)
* Update bioconda-utils to 0.15.1 (#12390)
* R ebimetagenomics (#12393)
* Add dimspy recipes for reference purposes (#12387)
* Add dimspy recipes for reference purposes
* Remove filename
* remove from blacklist
* Update build-fail-blacklist
* Added BioExcel_SeqQC to bioconda-recipes (#12276)
* PacBio: Update pbalign to 0.3.2 (#12396)
* PacBio: Update pbalign to 0.3.2
Closes: PacificBiosciences/pbbioconda#39
* add bgreat to bioconda (#12350)
* bgreat addition
* zlib in build should not be needed
* btrim integration to conda (#12395)
* Format sleuth recipe. Trigger rebuild because latest version was never uploaded for some reason. (#12399)
* PacBio: Update `pbsv2` to version 2.1.0 (#12400)
* Genenotebook v0.1.11 (#12398)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* v0.1.10
* v0.1.11
* prosolo: new package version 0.6.0 (#12397)
* Update sevenbridges-python to 0.17.2 (#12404)
* Add recipe for ICED (#12406)
* Downgrade version for iced (#12409)
* Update recipe for libstatgen 1.0.5 (#12348)
* Add recipe for libstatgen-1.0.5
* Update iced to 0.5.0 (#12411)
* Update perl-test2-suite to 0.000116 (#12412)
* fix compatibility with other tools (#12415)
* Restore dexseq python helper scripts (#12352)
* Restore dexseq python helper scripts
* Add python requirement for helper scripts
* Add python noarch to build section
* pin it to python2k
* Add htseq requirement, support only python <3 for now
* Genenotebook v0.1.12 (#12418)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* v0.1.10
* v0.1.11
* v0.1.12
* updated source
* added medpy recipe (#12417)
* added medpy recipe
* removed osx from build
* Update meta.yaml
* Update meta.yaml
* add boost and a compiler
* Update meta.yaml
* Update meta.yaml
* add itk
* Updated ddrage to version 1.6.1. (#12421)
* Add r-mcpcounter recipe. (#12261)
* Add MCPcounter recipe.
* fix lint: remove 'fn'
* fix license_file, version number and doi
* Update DEXSeq requirements to force compatible HTSeq version (#12423)
* ARB: Pin glib (#11782)
* Pin glib
* Update meta.yaml
* Update meta.yaml
* Work around CB3 issues
* Work around bioconda-utils lint false positive
* Disable lint check should_not_be_noarch
* Can't reference other packages built in recipe from anything but run
* Move perl to host section. Maybe that helps.
* constraining interpreter version breaks with CB3?
* disable perl version constraint :(
* Update meta.yaml (#12426)
* stacks: fix for fix 'fixing' @ in exe_path (#12420)
* stacks: fix for fix 'fixing' @ in exe_path
the previous fix https://github.com/bioconda/bioconda-recipes/pull/11580
tried to solve the problem with the @ in the exe_path by setting this
variable empty. But the perl scripts
- append a / to the empty string an…
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* update mzr as a test
* Begin building for R 3.5.1 (#11252)
* Bump everything for R 3.5.1
* Fix most of the linting issues
* Update blacklist
* Revert "Fix most of the linting issues"
This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5.
* should_not_use_fn
* More fixes
* Fix incorrect yaml
* Should really fix the linting blacklist stuff
* Fix many recipes
* Fix some linting
* Fix r-wicket
* Update derfinder
* Pin to a given bioconductor release.
* Add missing packages
* Restore identifiers to bioconductor packages
* Restore extra information to R packages
* Update R bulk (#11283)
* fixed incorrect doi of publication (#11175)
* Added recipe for kinSimRiboswitch (#10838)
Added recipe for kinSimRiboswitch, a pipeline for simulating the folding
kinetics of RNA switches.
* update multiqc-bcbio (#11187)
* Add recipe for PopDel (#11181)
* Add recipe for PopDel
* Add clang and clangxx to build config
* update seqbuster (#11190)
* update seqbuster
* fix build
* fix test
* Update pyseer to 1.1.2 (#11172)
* bump sourmash (#11197)
* Update BASIC to v1.4.1 (#11195)
* Update BASIC to v1.4.1
* Trigger circleci
* Fix build number
* Update nf-core-1.2 (#11191)
* Update nf-core-1.2
* Update build script
* Update to InterMine 1.11.0 (#11182)
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Add tinyfasta-0.1.0 (#11177)
* Add tinyfasta
* Update build script
* Fix structure of build section
* Bumping snippy (#11198)
* Remove older version
* Bump snippy
* VEP: bump major version (#11201)
* VEP: bump major version
* VEP: bumped plugin major version
* VEP: update plugin install
Download and install all plugin modules, instead of just a selection
* Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200)
* Update: PureCN to latest devel (1.11.13); wrapper scripts
PureCN development (https://github.com/lima1/PureCN) has several
improvements over the BioC 3.6 release for handling multiple VCF input
types, and is back compatible with R 3.4.1 so still builds cleanly
with two new dependencies.
Also exposes PureCN wrapper scripts for running from the command line.
Prefixes ambiguous scripts with PureCN_.
* Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet
* add cassiopee release 1.0.9 (#11168)
* add cassiopee release 1.0.9
* update to conda build 3
* remove old version backup and use sha256 for source
* Bump abeona version to 0.26.0 (#11202)
* Bump abeona version to 0.24.0
* Bump abeona version to 0.26.0
* Update LexMapr to v0.1.2 (#11192)
* Update LexMapr to v0.1.2
* Add rdflib dep
* Update svtyper to 0.7.0 (#11196)
* Update svtyper to 0.7.0
* Add recipe for perl-gtdbtk (#11194)
* Add recipe for perl-gtdbtk
* New recipe for RFMix (#11205)
* New recipe for RFMix
* updated version number information
* updated version number information
* updated version number information
* initial purge_haplotigs commit (#11049)
* initial purge_haplotigs commit
* bioconda revisions, updating test commands to run the pipeline on the test dataset
* rolling back test commands
* Add recipe for fsm-lite (#11209)
* Add recipe for fsm-lite
* Add prefix to make
* Remove v from version string
* Updated reparation_blast to version v.1.0.7 (#11210)
* Update sambamba to 0.6.8 (#11212)
* Bump sambamba to 0.6.8
* It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified.
* Set some environment variables
* The compiled binary is in a different place now
* ldc provides some libraries that are linked against.
* mtbseq: update recipe (#11110)
* changed download location/add test
* remove test
* Confindr (#11217)
* Update confindr to 0.4.2
* Fix typo in specifying version of pysam
* Update Genenotebook to v0.1.4 (#11218)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* updating to 0.1.3 (#11221)
* sartools1.6.6 (#11222)
* Perl bio automatedannotation (#11216)
* Initial recipe for Bio-AutomatedAnnotation
* Change URL
* Run cpanm tests
* Temporarily set HOME
* Use cpan version instead
* Add more depencencies
* Set bioperl version
* unset bioperl version, add bioperl-run
* New release including version in modules
* Remove comments
* build -> host
* Upgrade r-biodb to v1.1.2. (#11213)
* Upgrade r-biodb to v1.1.2.
* Remove old versions of r-biodb.
* Comment out libgfortran.
* PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215)
* PeptideShaker: updated to version 1.16.30
- Bugfix: HOME was still being used when folder with customised reports was specified.
- Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line.
* SearchGUI: updated to version 3.3.5.
- BUG FIX: Cleanup of the temp path options when used as options for the other command lines.
- FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2.
- LIBRARY UPDATE: Updated utilities to version 4.12.8.
* Update meta.yaml (#11227)
* Svtools 0.4.0 (#11208)
* Remove directories for old svtools versions
* Update svtools to v0.4.0
* Move build number back to 0
* Anvio 52 (#11230)
* Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software.
* Remove cgat-scripts from blacklist. (#11228)
* Add new formula: bazam 1.0.1 (#11229)
* Update gatk4 to 4.0.10.0 (#11224)
* Add recipe for gtdbtk 0.1.3 (#11211)
* Add recipe for gtdbtk
* Added initial htstream recipe (#11113)
* HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data.
* DeepTools 3.1.3 (#11226)
* PacBio: Update `pbmm2` to version 0.10.0 (#11225)
* fastqc: update to version 0.11.8 (#11214)
* fastqc: update to version 0.11.8
* Update meta.yaml
* Phame (#11223)
* mac recipe and added bioperl
* changing bill number
* added no osx
* adding new version
* removed separate recipe for mac, dont need it
* now running same recipe for mac and linux
* fixed the way fasttrees version was being parsed
* minor change test
* adding detailed description
* restaging the build number
* new version
* Make sure to use bioperl and perl 5.26
* Updated ngs-bits to version 2018_10 (#11235)
* PacBio: Update `pbsv2` to version 2.0.2 (#11236)
* Update VSEARCH to 2.8.5 (#11239)
* Fix shorah recipe and remove from blacklist. (#11241)
* Fix shorah recipe and remove from blacklist.
* Fix blas variant.
* Remove imports from tests.
* unicycler 0.4.7 (#11240)
* unicycler 0.4.7
* unicycler: Work around ValueError: invalid
Unicycler thinks the terminal has 0 columns and produces this error:
File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks
raise ValueError("invalid width %r (must be > 0)" % self.width)
ValueError: invalid width -5 (must be > 0)
* Octopus: update to 0.5.1-beta (#11244)
* New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247)
- PURPLE SV and heterogeneity caller for somatic tumor/normal samples.
- VarDictJava -- 1.5.6 release with fixes for SV calling
- PureCN -- add signature dependency and update with fixes for test
samples.
* Dinucleotide patterns analysis tools v1.0 (#11245)
* Dinucleotide patterns analysis tools v1.0
* Lets try it, it seems to work locally for me.
* Enable SpoTyping_plot.r (#11248)
* rerun again (#11233)
* rerun again
* Update meta.yaml
* Delete build.sh
* Update segway dependency optbuild to 0.2 (#10459)
* Update segway dependency optbuild to 0.2
* Update build and architecture requirements for optbuild 0.2
* Add six as a dependency to the optbuild recipe
* Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249)
* Add prefix dnp- to the package names
* Update build.sh
* Update build.sh
* Bump beast version to 1.10.2 (#11250)
* add maxquant (#11253)
* add mayquant
* relax tests
* PacBio: Update `pbmm2` to version 0.10.1 (#11256)
* PacBio: Update `pbmm2` to version 0.10.1-1 (#11257)
* remove xsv recipe (#11259)
* add blast dependency (#11258)
* Added riborex recipe (#11251)
* Added riborex recipe
* Relaxed version constraints
* Pinned r-core for fdr tools
* fixed the r-base stuff upstream
* Update meta.yaml
* fix graphprot (#11234)
* increase build number
* remove from blacklist
* use cxx instead of c
* move coreutoils to build section
* set additional paths
* patch makefile
* blind try
* update patch
* explicitely copy from src_dir
* update deprecated prefix variable
* Revert "update deprecated prefix variable"
This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d.
* update deprecated prefix variable
* try moving to host section
* Bump mash (#11264)
* Add fmlrc (#11265)
* Add fmlrc
* add doi
* PacBio: Update pb-falcon to 0.2.4. (#11266)
* Add kopt recipe (#11269)
* Genomepy 0.5.2 (#11267)
* release 0.5.2 of genomepy
* trigger new build
* remove genomepy from blacklist
* locale for osx
* updated locale test
* PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275)
* Update mmseqs2 recipe to new release 6-f5a1c (#11272)
* Update yacrd to version 0.4.1 (#11273)
* Add scprep (#11270)
* Add scprep
* All of these should not be needed as host dep
* Metawrap preqs2 (#11242)
* fixed issues
* fixed issues
* added tests
* fixed tab
* gemma 0.98 (#11254)
* gemma 0.98
* gemma 0.98
Leave gsl and zlib out of runtime dependencies
* Add DCA recipe (#11274)
* Add DCA recipe
* add noarch and doi
* remove skip
* Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib
* Various fixes for bulk and trigger a rebuild (#11313)
* Various fixes, at least 4 packages (and their dependencies) should still fail (#11320)
* A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336)
* Fix various recipes (#11354)
* Fix various recipes
* Fix more recipes
* Various CRAN package fixes, since they all lack license files (#11372)
* Various CRAN package fixes, since they all lack license files
* Fix the r-dartr recipe
* There is a light at the end of the tunnel (#11381)
* There is a light at the end of the tunnel
* Licenses no longer exist
* [BULK] Fixes for R/Bioconductor packages (#11406)
* Require `r-base >=3.5` for some packages
* Fix various CRAN packages lacking license file
* Add missing libnetcdf requirement to bioconductor-mzr
* Remove r-alakazam (moved to conda-forge)
Fix linting issue:
```
recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating
```
* [BULK] Many R 3.5 only packages (#11410)
* [BULK] Bulk update 191018b (#11419)
* update mzr as a test
* Begin building for R 3.5.1 (#11252)
* Bump everything for R 3.5.1
* Fix most of the linting issues
* Update blacklist
* Revert "Fix most of the linting issues"
This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5.
* should_not_use_fn
* More fixes
* Fix incorrect yaml
* Should really fix the linting blacklist stuff
* Fix many recipes
* Fix some linting
* Fix r-wicket
* Update derfinder
* Pin to a given bioconductor release.
* Add missing packages
* Restore identifiers to bioconductor packages
* Restore extra information to R packages
* Update R bulk (#11283)
* fixed incorrect doi of publication (#11175)
* Added recipe for kinSimRiboswitch (#10838)
Added recipe for kinSimRiboswitch, a pipeline for simulating the folding
kinetics of RNA switches.
* update multiqc-bcbio (#11187)
* Add recipe for PopDel (#11181)
* Add recipe for PopDel
* Add clang and clangxx to build config
* update seqbuster (#11190)
* update seqbuster
* fix build
* fix test
* Update pyseer to 1.1.2 (#11172)
* bump sourmash (#11197)
* Update BASIC to v1.4.1 (#11195)
* Update BASIC to v1.4.1
* Trigger circleci
* Fix build number
* Update nf-core-1.2 (#11191)
* Update nf-core-1.2
* Update build script
* Update to InterMine 1.11.0 (#11182)
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Add tinyfasta-0.1.0 (#11177)
* Add tinyfasta
* Update build script
* Fix structure of build section
* Bumping snippy (#11198)
* Remove older version
* Bump snippy
* VEP: bump major version (#11201)
* VEP: bump major version
* VEP: bumped plugin major version
* VEP: update plugin install
Download and install all plugin modules, instead of just a selection
* Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200)
* Update: PureCN to latest devel (1.11.13); wrapper scripts
PureCN development (https://github.com/lima1/PureCN) has several
improvements over the BioC 3.6 release for handling multiple VCF input
types, and is back compatible with R 3.4.1 so still builds cleanly
with two new dependencies.
Also exposes PureCN wrapper scripts for running from the command line.
Prefixes ambiguous scripts with PureCN_.
* Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet
* add cassiopee release 1.0.9 (#11168)
* add cassiopee release 1.0.9
* update to conda build 3
* remove old version backup and use sha256 for source
* Bump abeona version to 0.26.0 (#11202)
* Bump abeona version to 0.24.0
* Bump abeona version to 0.26.0
* Update LexMapr to v0.1.2 (#11192)
* Update LexMapr to v0.1.2
* Add rdflib dep
* Update svtyper to 0.7.0 (#11196)
* Update svtyper to 0.7.0
* Add recipe for perl-gtdbtk (#11194)
* Add recipe for perl-gtdbtk
* New recipe for RFMix (#11205)
* New recipe for RFMix
* updated version number information
* updated version number information
* updated version number information
* initial purge_haplotigs commit (#11049)
* initial purge_haplotigs commit
* bioconda revisions, updating test commands to run the pipeline on the test dataset
* rolling back test commands
* Add recipe for fsm-lite (#11209)
* Add recipe for fsm-lite
* Add prefix to make
* Remove v from version string
* Updated reparation_blast to version v.1.0.7 (#11210)
* Update sambamba to 0.6.8 (#11212)
* Bump sambamba to 0.6.8
* It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified.
* Set some environment variables
* The compiled binary is in a different place now
* ldc provides some libraries that are linked against.
* mtbseq: update recipe (#11110)
* changed download location/add test
* remove test
* Confindr (#11217)
* Update confindr to 0.4.2
* Fix typo in specifying version of pysam
* Update Genenotebook to v0.1.4 (#11218)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* updating to 0.1.3 (#11221)
* sartools1.6.6 (#11222)
* Perl bio automatedannotation (#11216)
* Initial recipe for Bio-AutomatedAnnotation
* Change URL
* Run cpanm tests
* Temporarily set HOME
* Use cpan version instead
* Add more depencencies
* Set bioperl version
* unset bioperl version, add bioperl-run
* New release including version in modules
* Remove comments
* build -> host
* Upgrade r-biodb to v1.1.2. (#11213)
* Upgrade r-biodb to v1.1.2.
* Remove old versions of r-biodb.
* Comment out libgfortran.
* PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215)
* PeptideShaker: updated to version 1.16.30
- Bugfix: HOME was still being used when folder with customised reports was specified.
- Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line.
* SearchGUI: updated to version 3.3.5.
- BUG FIX: Cleanup of the temp path options when used as options for the other command lines.
- FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2.
- LIBRARY UPDATE: Updated utilities to version 4.12.8.
* Update meta.yaml (#11227)
* Svtools 0.4.0 (#11208)
* Remove directories for old svtools versions
* Update svtools to v0.4.0
* Move build number back to 0
* Anvio 52 (#11230)
* Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software.
* Remove cgat-scripts from blacklist. (#11228)
* Add new formula: bazam 1.0.1 (#11229)
* Update gatk4 to 4.0.10.0 (#11224)
* Add recipe for gtdbtk 0.1.3 (#11211)
* Add recipe for gtdbtk
* Added initial htstream recipe (#11113)
* HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data.
* DeepTools 3.1.3 (#11226)
* PacBio: Update `pbmm2` to version 0.10.0 (#11225)
* fastqc: update to version 0.11.8 (#11214)
* fastqc: update to version 0.11.8
* Update meta.yaml
* Phame (#11223)
* mac recipe and added bioperl
* changing bill number
* added no osx
* adding new version
* removed separate recipe for mac, dont need it
* now running same recipe for mac and linux
* fixed the way fasttrees version was being parsed
* minor change test
* adding detailed description
* restaging the build number
* new version
* Make sure to use bioperl and perl 5.26
* Updated ngs-bits to version 2018_10 (#11235)
* PacBio: Update `pbsv2` to version 2.0.2 (#11236)
* Update VSEARCH to 2.8.5 (#11239)
* Fix shorah recipe and remove from blacklist. (#11241)
* Fix shorah recipe and remove from blacklist.
* Fix blas variant.
* Remove imports from tests.
* unicycler 0.4.7 (#11240)
* unicycler 0.4.7
* unicycler: Work around ValueError: invalid
Unicycler thinks the terminal has 0 columns and produces this error:
File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks
raise ValueError("invalid width %r (must be > 0)" % self.width)
ValueError: invalid width -5 (must be > 0)
* Octopus: update to 0.5.1-beta (#11244)
* New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247)
- PURPLE SV and heterogeneity caller for somatic tumor/normal samples.
- VarDictJava -- 1.5.6 release with fixes for SV calling
- PureCN -- add signature dependency and update with fixes for test
samples.
* Dinucleotide patterns analysis tools v1.0 (#11245)
* Dinucleotide patterns analysis tools v1.0
* Lets try it, it seems to work locally for me.
* Enable SpoTyping_plot.r (#11248)
* rerun again (#11233)
* rerun again
* Update meta.yaml
* Delete build.sh
* Update segway dependency optbuild to 0.2 (#10459)
* Update segway dependency optbuild to 0.2
* Update build and architecture requirements for optbuild 0.2
* Add six as a dependency to the optbuild recipe
* Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249)
* Add prefix dnp- to the package names
* Update build.sh
* Update build.sh
* Bump beast version to 1.10.2 (#11250)
* add maxquant (#11253)
* add mayquant
* relax tests
* PacBio: Update `pbmm2` to version 0.10.1 (#11256)
* PacBio: Update `pbmm2` to version 0.10.1-1 (#11257)
* remove xsv recipe (#11259)
* add blast dependency (#11258)
* Added riborex recipe (#11251)
* Added riborex recipe
* Relaxed version constraints
* Pinned r-core for fdr tools
* fixed the r-base stuff upstream
* Update meta.yaml
* fix graphprot (#11234)
* increase build number
* remove from blacklist
* use cxx instead of c
* move coreutoils to build section
* set additional paths
* patch makefile
* blind try
* update patch
* explicitely copy from src_dir
* update deprecated prefix variable
* Revert "update deprecated prefix variable"
This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d.
* update deprecated prefix variable
* try moving to host section
* Bump mash (#11264)
* Add fmlrc (#11265)
* Add fmlrc
* add doi
* PacBio: Update pb-falcon to 0.2.4. (#11266)
* Add kopt recipe (#11269)
* Genomepy 0.5.2 (#11267)
* release 0.5.2 of genomepy
* trigger new build
* remove genomepy from blacklist
* locale for osx
* updated locale test
* PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275)
* Update mmseqs2 recipe to new release 6-f5a1c (#11272)
* Update yacrd to version 0.4.1 (#11273)
* Add scprep (#11270)
* Add scprep
* All of these should not be needed as host dep
* Metawrap preqs2 (#11242)
* fixed issues
* fixed issues
* added tests
* fixed tab
* gemma 0.98 (#11254)
* gemma 0.98
* gemma 0.98
Leave gsl and zlib out of runtime dependencies
* Add DCA recipe (#11274)
* Add DCA recipe
* add noarch and doi
* remove skip
* Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib
* Various fixes for bulk and trigger a rebuild (#11313)
* Various fixes, at least 4 packages (and their dependencies) should still fail (#11320)
* A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336)
* Fix various recipes (#11354)
* Fix various recipes
* Fix more recipes
* Various CRAN package fixes, since they all lack license files (#11372)
* Various CRAN package fixes, since they all lack license files
* Fix the r-dartr recipe
* There is a light at the end of the tunnel (#11381)
* There is a light at the end of the tunnel
* Licenses no longer exist
* [BULK] Fixes for R/Bioconductor packages (#11406)
* Require `r-base >=3.5` for some packages
* Fix various CRAN packages lacking license file
* Add missing libnetcdf requirement to bioconductor-mzr
* Remove r-alakazam (moved to conda-forge)
Fix linting issue:
```
recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating
```
* [BULK] Many R 3.5 only packages (#11410)
* Update pinning to R>=3.5 and a few runtime dependencies.
* CSAW is R 3.5 only
* Packages using beachmat are 3.5 only
* Packages using bioconductor-singlecellexperiment are R 3.5 only
* [BULK] Don't use r-base >=3.5, use a conda_build_config.yaml instead (#11452)
* Don't use r-base >=3.5, use a conda_build_config.yaml instead
* blacklist r-phangorn
* Update variancepartition
* R 3.5 for packages requiring singlecellexperiment
* Update a few packages
* Update a number of recipes (#11482)
* Update ensemblVEP and derfinder (#11504)
* Bulk update 251018 (#11577)
* [BULK] various package updates
* blacklist bioconductor-mzr
* A couple tweaks
* [BULK] Update 261018 (#11611)
* Apparently the r-rgeos bit works properly now.
* Add tissueenrich and try to fix scpipe on Linux
* A meaningless change just to trigger an update in bulk. (#11618)
* [BULK] update 271018 (#11628)
* Bump bioconductor-esetvis
* Fix yaqcaffy
* Fix more
* Another R 3.5 recipe
* [BULK] update 281018 (#11689)
* Add some files
* Fix arrayexpress
* Fix another 2
* Blacklist a bunch of bioconductor recipes that aren't likely to get built for a variety of reasons (mostly due to mzR). (#11697)
* Update blacklist (#11706)
* [BULK] fix bioconductor-tissueenrich (#11720)
* taxonkit 0.2.5 (#11318)
* Update csvtk (#11319)
* taxonkit 0.2.5
* csvtk 0.15.0
* bumping GROOT to 0.8.1 (#11323)
* HiCMatrix version 3 (#11322)
* Correcting dependencies
* Version 3 of HiCMatrix, the October release
* Update confindr to 0.4.3 (#11330)
* Drop-seq_tools: Version 2.0.0 (#11326)
* Update meta.yaml
* Update build.sh
some tool names changed to fit Camel case
* Update motus to build only for python3 (#11331)
* Update fpa to 0.2 version (#11333)
* update taxonkit to 0.3.0 (#11339)
* ntcard 1.1.0 (#11338)
* Update rgi (#11335)
* first commit
* update dependencies list
* change source to github
* change build number
* testing circleci
* update meta and build
* fix build
* move build script into meta
* remove older recipes
* line fix in bootstrap.py
* change python & matplotlib versions; add build.sh file
* add preprocessing selector to skip python 2.7
* move build script into meta.yaml
* Revert "line fix in bootstrap.py"
This reverts commit 5ac1ecd0142a5cfdfc8499c5b6ef4e1f629cd046.
* Update gmap to version 2018-07-04. (#11332)
MAX_READLENGTH environment variable has been disused since 2016-08-16.
* Upgrade r-biodb to 1.2.0a. (#11341)
* Upgrade r-biodb to 1.2.0a.
* Update meta.yaml
* Updated ont-tombo to version 1.5. (#11329)
* Updated ont-tombo to version 1.5.
* Updated with actual github release version hash.
* remove graphicsmagick (#11342)
* Build kraken2 for osx (#11343)
* First try for a bcalm recipes (#11344)
* New: cgpbigwig (BigWig manipulation); Update: bcbio (#11347)
- cgpbigwig (https://github.com/cancerit/cgpBigWig) provides bigwig
generation and manipulation command line tools including bam to bigwig
conversion.
- bcbio: fixes for QC on variants and peddy for CWL runs
* Try avoid some dependancy (#11349)
* Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8 (#11348)
* Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8
Also add about:home .
* Workaround https://github.com/conda-forge/bison-feedstock/issues/7
* Better bcalm recipes (#11350)
* Try avoid some dependancy
* Correct mess in build number, sorry
* R biodb (#11351)
* rebuild r-biodb
* trigger build
* Add recipe for pypairs (#11356)
* Update smoove to 0.2.1. (#11360)
* Update duphold to 0.0.9. (#11359)
* Update goleft to 0.2.0 (#11361)
* Bump slicedimage to 1.0.0 (#11362)
* Bump slicedimage to 1.0.1 (#11365)
* Added new versions for biopet-sampleconfig (#11268)
* perl-velvetoptimiser: update to 2.2.6 (#11369)
* update to 2.2.6
* remove unneeded patch
* Scanpy upgrade (#11371)
* Bump version
* Upgrade Scanpy
* Bump starfish to 0.0.25 (#11370)
* bumping groot to 0.8.2 (#11374)
* vep: bump subversion (#11367)
* Updated Krocus 1.0.1 (#11355)
* Add tiptoft
* Fix meta.yaml for tiptoft
* Add build script
* Updated krocus 1.0.1
* Add tiptoft 0.1.4 (#11352)
* Add tiptoft
* Fix meta.yaml for tiptoft
* Add build script
* Kodoja v0.0.9 (#11373)
* Add recipe for seer (#11263)
* Add recipe for seer
* lets try this
* Add newer compiler
* Using boost-cpp
* messed up version string
* Attempt building boost
* Use c++11 in boost
* Use python for boost install
* Correct python version spec
* try with different python version
* Fix b2 command
* Fix popd command
* build and link boost program options statically
* Fix tests
* Match dependency order
* Link openblas instead of blas
* Forcing rebuild with openblas
* Don't use armadillo wrapper
* Making review changes. Also trying original tests
* Previous tests were correct
* Add recipe for the translate-gard npm package version 1.0.3 (#11364)
* Fix umi tools (#11376)
umi_tools: clean up dependencies
* add support tools to PATH (#11379)
* Bump to v2.2.1 (#11380)
* Bump starfish to 0.0.26 (#11378)
* Update fpa to 0.3 (#11375)
* Update fpa to 0.3
* Correct error in sha256
* Reset build number
* Update trial to 2.5.5 (#11386)
* Update: bioconductor-titancna; 1.19.1 with hg38 support (#11388)
* Update: bioconductor-titancna; 1.19.1 with hg38 support
* Pin to R 3.4 to avoid pulling in 3.3 and 3.5 during mulled
* Add r-polysat version 1.7-3 (#11384)
* Update biomart version so that compatible with r351 (#11366)
* Update biomart version so that compatible with r351
* Update meta.yaml
reset build number as per https://bioconda.github.io/guidelines.html#buildnum
* Update entrez-direct to 10.0.20180927. (#11387)
* Added recipe for SonicParanoid 1.0.13 (#11271)
* Added recipe for SonicParanoid 1.0.13
* removed 'x.x' for numpy, added basic test
* fixed linter related errors
* compiler set to cxx and added host section (same build error!)
* removed host section
* moved numpy and cython to host section; restored build: noarch: python; added LICENSE.md
* removed build: noarch
* added build and extra sections
* set build number to 0; removed skip build; added python3 minimum version; added test for all executables.
* restored sh python module as requirement
* added Make to run; updated release to latest commit
* remove c compiler from meta.yaml
* modified build.sh to compile source codel added make in build section
* updated to latest commit
* updated to latest version with make included in setup.py
* reverted build.sh to the simplest version (python setup.py install)
* Add perl-json to build requirements to allow meme-chip to run to completion. Change meme-chip to use dreme-py3 instead of dreme if building with python 3. (#11389)
* Bump IgBLAST to 1.9.0 (#11393)
Bump IgBLAST to 1.9.0
Re-package the binary version this time. There are problems building the
source version when the configure script reaches this step:
"trying to build the NCBI SRA/VDB Toolkit from GitHub"
The previous problem about the binaries linking against libbz2.so, for
which we had no conda package, is now solved.
Also, this saves about 45 minutes compilation time.
* Add consan (#11395)
* Add consan
* Skip osx
* Update: vardict, vardict-java 1.5.7 (#11394)
* Update: vardict, vardict-java 1.5.7
Latest vardict-java release and corresponding vardict with bug fixes
after testing with 1.5.6
* Reduce test output to try and fix build problems
* Experiment 2 for build problems: remove r-base from run
* Experiment 3 for build problems: add r-base in host
* update recipe for 3.9.1 (#11397)
* evofold2 (#11396)
* evofold2
* wrapper
* Update meta.yaml
* minor
* Update rnastructure to 6.1. (#11400)
* Ctat mut (#11401)
* updating version number
* correct URL
* proper hash
* Revert "Ctat mut (#11401)" (#11402)
This reverts commit 6db10ac7ffd7abaf8fbf1762b7ea6c63b2585fe0.
* update version (#11403)
* any2fasta 0.4.2 (new formula) (#11407)
* W4mclassfilter v0.98.9 (#11385)
* Added files to build version 0.98.9
* Update meta.yaml
* Update meta.yaml
* updated SonicParanoid recipe to version 1.0.14 (#11409)
* updated SonicParanoid recipe to version 1.0.14
* Update to version 1.0.2 of PopDel (#11398)
* Update to version 1.0.2 of PopDel
Update to version 1.0.2.
* Reset build number to 0
* PacBio: require Meson 0.48.1 for all recipes (#11090)
* Meson 0.47 inserted duplicate RPATHs in
macOS binaries, causing `install_name_tool`
failures when installing the package.
Requiring 0.48.1 ensures we do not run into
these issues anymore in the future.
* rebuild with latest openmpi (#11411)
* Remove kfoots from the blacklist (#11416)
* Update gseapy to 0.9.7 (#11417)
* Update gseapy to 0.9.7
* remove noarch
* Add SC3 as dependency (#11427)
* Add recipe for r-poppr (#11418)
* Update knitr version because of Issue: https://github.com/rstudio/rmarkdown/pull/1271 (#11412)
* Update IQ-TREE to 1.6.7.1 (#11429)
* Update IQ-TREE to 1.6.7.1
* Change build number
* Update: r-deconstructsigs with fixes for hg38 (#11431)
The 1.8.0 release, from 2016, has some issues with hg38 and other
custom genomes that are fixed in development (raerose01/deconstructSigs#27).
There hasn't been a new release pushed so this rolls these into a new
sub-version and makes them available.
* Update entrez-direct to 10.2.20181018. (#11432)
* Add assembly-scan recipe (#11425)
* remove python 2.7 skip (#11424)
Preparation for rnaQUAST
* Add fastq-scan recipe (#11415)
* Add patch to fix racon/rampler path in racon_wrapper. (#11434)
Fixes #11405.
* meme rebuild (#11433)
* Update nanocomp to 0.23.1 (#11436)
* Update nanocomp to 0.23.1
* remove noarch
* Update abricate to 0.8.10 (#11446)
* Update angsd to 0.923 (#11445)
* Update alfred to 0.1.13 (#11444)
* Update alfred to 0.1.13
* Try w/o patch
* Update antarna to 2.0.6 (#11442)
* Update admixtools to 5.1 (#11443)
* Update admixtools to 5.1
* Let makefile choose which bins to install
* Update alignstats to 0.5 (#11441)
* Update xatlas to 0.2.1 (#11437)
* r-gpca (#11428)
* r-gpca
* r-gpca recipe
* Update meta.yaml
* Removed All Comments
* gseapy bump version 0.9.8 (#11440)
* gseapy bump version 0.9.8
* version
* titancna: fix for hg38, remove conda build hacks (#11447)
* titancna: fix for hg38, remove conda build hacks
* Re-add r-base 3.4 pin to avoid 3.5 errors
* Hmmlearn older version (#11450)
* Adding pygtftk
* removed pygtftk from master
* add older version of hmmlearn
* Add card_trick (#11451)
* Add card_trick
* Restrict to py3
* Update checkm-genome to 1.0.12 (#11455)
* Bump drep (#11457)
* Update squid to 1.5 (#11466)
* Update ncbi-ngs-sdk to 2.9.3 (#11467)
* elprep: bumped major version (#11414)
* elprep: bumped major version
* fixed hash
* fix download link, fixed licence
* fixed tests
* skip osx build
* FRED2 as a conda package (#11469)
* Attempt to get FRED2 as a conda package
* SHA update
* 99 little bugs in the code
* Fix things Björn mentioned
* add rnaQUAST recipe (#11470)
* Update bioconda-utils to 0.14.9 (#11454)
* Rapidup (#11474)
* Update to v0.7
* Update Buildnumber
* rapid: update to v0.6
* rapid: update to v0.6
* update grid (#11478)
* Adding biobb_model recipe (#11472)
* Updated wtdbg to v2.1 (#11486)
* update stream to 0.2.6 (#11483)
* update stream to 0.2.2
* update stream to 0.2.3
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.5
* update stream to 0.2.6
* Update meta.yaml (#11487)
* Update connectome-workbench to 1.3.2 (#11468)
Now needs QT 5.7
* Update deblur to 1.1.0 (#11500)
* Update domclust to 1.2.8 (#11498)
* WisecondorX: bump version (#11501)
* Bump as GitHub wasn't working yesterday (#11502)
* Added recipe for Sequenza (#10367)
* Added recipe for Sequenza
* Removed fn entry in source section
* Trying with only one URL
* copynumber is a bioconductor package
* Added missing requirements section
* Removed mailing list address
* Added doi
* Added license_file
* Trying with different license_file path
* Fred2 bump (#11503)
* Bump as GitHub wasn't working yesterday
* Fix licence etc
* Scanpy scripts (#11413)
Doing squash and merge as requested by @nh3
* Bump version
* First implementation of scanpy-scripts bioconda recipe.
* fix path in build.sh
* Remove "noarch" flag as requested by bioconda recipe checklist
* Add a post install notice that post install test needs bats-core.
* Add more dependencies
* Skip building for python versions other than 3.6
* Target v0.0.2 which has non-ascii characters removed
* Lower version requirement for pandas and matplotlib to be the same as scanpy
* Requirement matplotlib>=3.0.0, declare noarch
* New: hmftools-cobalt; Update: hmftools-purple (#11507)
- hmftools-cobalt: Add latest version of PURPLE associated read counter,
COBALT, with support for hg38.
- hmftools-purple: PURPLE release with hg38 support.
* Update Picard to 2.18.15. (#11505)
* Genenotebook (#11476)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* Update pinning (#11514)
* Bump build number for updated dependency (#11510)
* Bump build number for updated dependency
* Try adding r-base to host requirements
* Try adding other requirements to host
* Pin to R version
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Tweak dependency version syntax
* Pin R and package versions correctly
* PacBio: Update pbcore to 1.6.5 (#11513)
* Bump r seurat scripts version (#11292)
* Bump version
* Remove noarch
* Could wrongly quoted version be causing an issue?
* Tweak pinning to try and fix CI error
* seqcluster:fix UMI detection. (#11511)
* seqcluster:fix UMI detection.
* Fix dependency
* quast 5.0.1 (#11479)
* quast 5.0.1
* quast 5.0.1: remove third-party site packages from the distibution pack
* quast 5.0.1: skip Glimmer in test
* quast 5.0.1: joblib and simplejson dependencies added to meta.yaml (Setuptools downloading is disabled in conda build)
* quast 5.0.1: explicit joblib and simplejson dependencies removed (Setuptools downloading is disabled in conda build)
* quast 5.0.1: Python 2 and 3 compatible code in build.sh
* wcX bugfixes (#11508)
* wcX bugfixes
* fixed shasum
* Update fastspar to 0.0.7 (#11515)
* Update iqtree to 1.6.7.2 (#11525)
* Update illumina-interop to 1.1.6 (#11523)
* Update hapbin to 1.3.0 (#11522)
* Update hlama to 3.0.1 (#11520)
* Update gb_taxonomy_tools to 1.0.1 (#11519)
* Update gffcompare to 0.10.5 (#11517)
* Update fast5seek to 0.1.1 (#11516)
* Update deepbinner to 0.2.0 (#11499)
* Update deepbinner to 0.2.0
* Update meta.yaml
Try same fix as in #11240
* Update ncbi-vdb to 2.9.3 (#11550)
* Update mikado to 1.2.4 (#11549)
* Update perl-pcap to 3.5.2 (#11543)
* Update python-hyphy-python to 0.1.9 (#11545)
* Update mlst to 2.15.2 (#11547)
* Update perl-sanger-cgp-vcf to 2.2.1 (#11542)
* Update merfishtools to 1.5.0 (#11537)
* Update perl-sanger-cgp-vagrent to 3.3.3 (#11536)
* Update nonpareil to 3.3.3 (#11535)
* Update prophex to 0.1.1 (#11532)
* Update krakenuniq to 0.5.3 (#11527)
* Update novoplasty to 2.7.2 (#11530)
* Update minced to 0.3.2 (#11529)
* Update mapdamage2 to 2.0.8 (#11528)
* Update perl-sanger-cgp-allelecount to 4.0.0 (#11538)
* Update pyvolve to 0.9.0 (#11531)
* Genenotebook (#11512)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* add plek (#11554)
* Update pyimzml to 1.2.4 (#11534)
* Bump shovill (#11555)
* PacBio: Update minimum pbcore version (#11556)
* We want all users of PacBio tools to be able to
use our utilities with pbmm2 alignments.
* Add recipe for translate-gard v1.0.4 (#11557)
* bioconductor-rnaseqsamplesizedata (#11475)
* Adding Recipe for bioconductor-rnaseqsamplesizedata
* Updated metadata for RnaSeqSampleSizeData
* nextflow 18.10.1 (#11558)
* Update raxml to 8.2.12 (#11567)
* Update r-fgwas to 0.3.6 (#11566)
* Update rapid to 0.7 (#11565)
* Update r-spieceasi to 1.0.2 (#11564)
* Update rcorrector to 1.0.3.1 (#11562)
* Update quicktree to 2.4 (#11560)
* Update paladin to 1.4.4 (#11541)
* Update paladin to 1.4.4
* delete md5
* Update build.sh
* Update build.sh
* Fix and unblacklist Tadarida-D (#11568)
* Add recipe for rgt
* Fix and un-blacklist tadarida-d
* Remove RGT
* bumping groot (#11575)
* update pymzml (#11573)
* Add bioconductor-rnaseqsamplesize (#11559)
* Add bioconductor-rnaseqsamplesize
* Update recipe
* Fixing some URLs
* Update dependencies missing
* Update trumicount to 0.9.11 (#11576)
* Update ConFindr to 0.4.4 (#11578)
* Added new versions for biopet-scatterregions (#11572)
* Added new versions for biopet-bamstats (#11571)
* R ggbiplot (#11584)
* add R -e 'httr::set_config(httr::config(ssl_verifypeer = 0L)); install.packages(devtools, repos=http://mirrors.ebi.ac.uk/CRAN/); library(devtools); install_github(vqv/ggbiplot); library(ggbiplot)'
* add r-ggbiplot
* update meta.yaml
* update meta.yaml
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix errors
* fix errors number 1
* Update rebaler to 0.1.2 (#11563)
* Update rebaler to 0.1.2
* Remove fn
* bump graphclust (#11585)
* Update seqyclean to 1.10.09 (#11589)
* Update stringmlst to 0.5.1 (#11590)
* Update snp-dists to 0.6.2 (#11592)
* Update snippy to 4.3.3 (#11596)
* Update canu to 1.8 (#11600)
* Update starfish to 0.0.27 (#11599)
* Update womtool to 36 (#11594)
* Update telseq to 0.0.2 (#11598)
* Update snp-sites to 2.4.1 (#11588)
* Added recipe for pydemult: Streamed and parallel demultiplexing of fastq files (#11471)
* Added recipe for pydemult
* Bumped version in favor of py3.5
* bump vcf2db to latest commit (#11601)
* bump vcf2db to latest commit
* fix shasum
* Fixing source url
* Update: TitanCNA; hg38 cytoband support and fix for normalization (#11604)
* megan (#11046)
* megan6: initial commit
* megan6: intermediate commit
* megan: made tests work
* megan: doc improvement
* megan: added osx dmg file
* megan: add java to build requirements
* megan: removed new line
* megan: removed osx sources
* Update meta.yaml
* bumping hulk (#11607)
* Update hotspot3d to 1.8.2 (#11521)
* Update hotspot3d to 1.8.2
* Add perl-json as dependency
* Add perl-archive-extract as dependency
* Fqzcomp (#11606)
* Added recipe for fqzcomp
* There is no configure script
* Maybe this works
* Added gcc as build requirement
* Removed gcc again (lint issue)
* Maybe these exports will do the trick
* Nope!
* Added cxx as host requirement
* Compilers are only allowed in build section
* There is no need for make install
* Copy-paste error...
* Add vcf-annotator recipe (#11481)
* Add vcf-annotator recipe
* added pyvcf dependency
* Update meta.yaml
* stacks: fix for @ in exe_path (#11580)
* stacks: fix for @ in exe_path
* stacks: fixed path
* New version with bugfix and different progressiveMauve version. (#11613)
* Sspupdate (#11614)
* New version with bugfix and different progressiveMauve version.
* Keeping old version as folder.
* Push build number.
* Update SVDB to version 1.3.0 (#11506)
* new file: recipes/svdb/1.1.2/meta.yaml
renamed: reipes/svdb/svdb.patch -> recipes/svdb/1.1.2/svdb.patch
modified: recipes/svdb/meta.yaml
* deleted: 1.1.2/meta.yaml
deleted: 1.1.2/svdb.patch
* Bump nanosim (#11608)
* Bump nanosim
* Add scipy as dep
* Add recipe for perl-number-range (#11621)
* New build for grid (#11620)
* update grid
* update build num
* Recipe for das_tool 1.1.1 (#10528)
* recipe for das_tool 1.1.1
* Add recipe for sompy (#11624)
* cmake modified to build with NDEBUG (#11328)
* cmake modified to build with NDEBUG
* Update meta.yaml
* new build with fasta test
* new build with fasta test
* Fix and unblacklist TwoPaCo (#11622)
* Add recipe for TwoPaCo
* Unblacklist twopaco
* Modify and unblacklist recipe for ESTmapper (#11623)
* Modify and unblacklist recipe for ESTmapper
* Add patch
* Modify and unblacklist recipe for Metaseq (#11625)
* Fix recipe for metaseq and remove from blacklist
* Remove build.sh
* nextflow 18.10.1 build 2 (#11630)
* Add Clust (#11619)
* Add clust
* Clean recipe
* Add "noarch"
* Add DOI
* Add build file
* Python 2.7
* Fix scikit-learn dependency
* Trigger new build
* Update: PureCN (multicore) and PURPLE (plotting X libraries) (#11631)
- PureCN: adds support for specifying cores on command line
- PURPLE: adds X library dependencies required for creating
plots
* scripts/travis-run.sh: added a cleaner method to check for env vars (#11612)
* Increase the number of k value usable in bcalm (request by @Malfoy) (#11610)
* Increase the number of k value usable in bcalm (request by @Malfoy)
* Change compilation parameter to reduce memory impact of compilation
* Update anndata to 0.6.11 (#11637)
* Update nglview to 1.1.7 (#11643)
* Update binsanity to 0.2.7.1 (#11644)
* Update cgat-core to 0.5.4 (#11645)
* Update nanosv to 1.2.2 (#11673)
* Update abeona to 0.36.0 (#11670)
* Update pyfaidx to 0.5.5.2 (#11659)
* Update agfusion to 1.23 (#11668)
* Update iqtree to 1.6.8 (#11686)
* update iqtree to 1.6.8
* Trigger rebuild
* Update validators to 0.12.2 (#11672)
* Update python-edlib to 1.2.3.post1 (#11664)
* update for Purge Haplotigs (#11690)
* Update loompy to 2.0.16 (#11667)
* Update loompy to 2.0.16
* Update meta.yaml
* IgBLAST 1.10.0 (#11693)
* Update wtforms-alchemy to 0.16.7 (#11679)
* Update sickle to 0.6.4 (#11663)
* Update sickle to 0.6.4
* Remove fn and libgcc runtime dep
* Update confindr to 0.4.5 (#11696)
* Batvi (#11695)
* batvi initial
* Guideline compatibility..
* Dummy test section..
* Missing java dependency..
* use openjdk instead of java-jdk ..
* source specified in github ..
* trigger build (package did not have batindel directory) ..
* update SHA256 ..
* update SHA256 ..
* Update pythonpy to 0.4.11 (#11661)
* Update cortexpy to 0.45.6 (#11660)
* Update sevenbridges-python to 0.16.0 (#11674)
* Update solvebio to 2.7.0 (#11657)
* Update mathstats to 0.2.6.5 (#11656)
* Update goatools to 0.8.9 (#11641)
* Add gnies (#11627)
* Add gnies
* noarch python
* Update meta.yaml
* Add recipe for SKA v1.0 (#11581)
* Add recipe for SKA v1.0
* Add lib path for zlib
* Older gcc
* Correct install dir
* Try static linking
* Dynamic linking on OS X
* ldd command test
* correct program
* Remove ldd command
* Add recipe for transit version 2.3.1 (#11701)
* Add recipe for transit version 2.3.1
* Use skip, add spaces.
* Update meta.yaml (#11699)
* remove pyqi (#11704)
* Update python-chado to 2.2.0 (#11714)
* update python-chado
* 2.2.1
* Update vcfanno to 0.3.1 (#11710)
* FGMP-1.0.1 (#11278)
* FGMP-1.0.1 recipe
* remove unncessary build info
* add r-nabor (#11716)
* update stream to 0.2.2
* update stream to 0.2.3
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.5
* update stream to 0.2.6
* add r-nabor recipe
* update r-nabor recipe
* update r-nabor recipe
* r-pctgcdata (#11715)
* r-pctgcdata
* r-pctgcdata - fix
* r-pctgcdata - fix
* Update meta.yaml
* Fix plek by a new branch (#11605)
* Modify the PLEK recipe
* Start fixing PLEK, though it requires compilation
* update build.sh
* update yaml
* fix build.sh
* update build.sh
* Update recipe for plek
* add bioconductor-chromvar recipe (#11718)
* add bioconductor-chromvar recipe
* fix bioconductor-tissueenrich
* Apparently the popdel recipe didn't get correctly merged
* Final merge conflicts
* Bioc quick test (#12547)
* Update kallisto to 0.45.0 (#12117)
* Update validators to 0.12.3 (#12116)
* Update illumina-interop to 1.1.7 (#12115)
* Update umi_tools to 0.5.5 (#12123)
* Update tiptoft to 1.0.0 (#12122)
* Update: TitanCNA with fix for hg38 plotting (#12130)
* blockclust (#12111)
* added eden 1.1 version used in blockclust
* Update meta.yaml
* eden checksum and test
* added zlib requirement
* add include and lib paths to build.sh
* add include and lib paths to build.sh
* modify makefile flags using sed
* modify makefile flags using sed
* use c++
* Update build.sh
* Update build.sh
* LDFLAGS not used in makefile
* remove v1.1
* add blockclust 1.1.0 recipe
* skip osx build
* added tarball url and checksum; removed conda_build_config.yaml
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Update chewbbaca to 2.0.16 (#12132)
* Update abeona to 0.40.0 (#12131)
* ping to eden 1.1 (#12134)
* clean swap file (#12137)
* Update corset to 1.07 (#12143)
* Update peddy to 0.4.3 (#12144)
* blockclust latest source and added cloudpickle as requirement (#12142)
* Update nanomath to 0.22.0 (#12149)
* Update pymvpa to 2.6.5 (#12152)
* Updated to version 1.4.0 (#12138)
* Updated to version 1.4.0
* Resetting build number to 0 and build->host
* Update transdecoder to 5.5.0 (#12172)
* Update gridss to 2.0.1 (#12190)
* Update tracer to 1.7.1 (#12189)
* Update flowcraft to 1.4.0 (#12179)
* Update seqbuster to 3.2 (#12182)
* Update perl-io-compress to 2.081 (#12201)
* Update twobitreader to 3.1.6 (#12205)
* Update twobitreader to 3.1.6
* Update meta.yaml
* Update gtfparse to 1.2.0 (#12186)
* Update gtfparse to 1.2.0
* remove compiler
* Update htseq to 0.11.0 (#12177)
* Update htseq to 0.11.0
* add compiler
* Update htseq to 0.11.0 (#12239) [testing co-author]
* Update htseq to 0.11.0
* add compiler
Co-authored-by: Bjoern Gruening <[email protected]>
* alfred v0.1.16 (#12240)
* alfred v0.1.16
* makefile patch
* makefile patch
* Update scrm to 1.7.3 (#12150)
* Update scrm to 1.7.3
* Update scrm to 1.7.3
* Mob suite update 1.4.8 --> 1.4.9 (#12244)
We fixed a small bug related to repetitive elements database reconstruction on each run. Should only run once during the first mob_typer run. Should be good now for parallel runs.
* PeptideShaker updated to v1.16.35 & SearchGUI updated to 3.3.9 (#12241)
* PeptideShaker updated to v1.16.32
SearchGUI updated to v3.3.6
* PeptideShaker updated to v1.16.35
* SearchGUI updated to v3.3.9
* First attempt at a recipe for ncrf (#12101)
* First attempt at a recipe for ncrf
* changed from copies to symlinks
* including absolute path in symlinks
* PacBio: Update `pbmm2` to version 0.11.0 (#12246)
* Gimmemotifs version 0.13.0 (#12245)
* new release to fix numpy incompatibility
* GimmeMotifs 0.13.0 release test
* numpy 1.15
* version 0.13.0
* Fix about:home and extra:
* PacBio: Update `isoseq3` to version 3.1.0 (#12263)
* add python to host section (#12264)
* Update confindr to 0.4.7 (#12266)
* new build of GRiD (#12269)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* peptideshaker, searchgui: version bump (#12136)
* peptideshaker, searchgui: version bump
solving https://github.com/compomics/searchgui/issues/192
* Update peptide-shaker.py
* searchgui: added c compiler for building
test if linking errors go away this way
* searchgui: removed noarch
* Update: bcbio, bcbio-vm with CWL non-human fixes (bcbio/bcbio-nextgen#2473) (#12273)
* Make snakemake a noarch package. (#12274)
* noarch: python in combination with version constraint
* Cleanup deps and simplify version definition.
* Genenotebook v0.1.9 (#12277)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* Create r-airr recipe (#12284)
* Create r-airr recipe using bgruening/conda_r_skeleton_helper
* Update meta.yaml
* Findbin::Real added (#12291)
* Added version bump to 1.3 (#12292)
* ngs-bits 2018_11 (#12262)
* Updated ngs-bits to version 2018_10
* Updated ngs-bits to version 2018_11
* minor edit in grid (#12287)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* minor edit to grid
* Fred2 update (#12259)
* Update FRED2 Recipe
* msstitch version 2.9 (#12296)
* r-mvr (#12300)
This is a non-parametric method for joint adaptive mean-variance regularization and variance sta-
bilization of high-dimensional data.
* Bump to Gromacs 2018.3 + re-enable OSX build (#12299)
* Gromacs 2018.3 + re-enable osx build
See also #7825 on OSX build
Include RRID for Gromacs (see bioconda/bioconda-utils#252)
* disabled ocl-icd on osx; not available (or needed?)
https://anaconda.org/conda-forge/ocl-icd
* pyGenomeTracks update of dependencies (#12279)
* Update pyGenomeTracks recipe to enable py3 support and updating outdated dependecy list
* Increase build number
* Update meta.yaml
* Exclude Python 3.5
* Gromacs 2018.4 (#12302)
* quast 5.0.2 (#12303)
* Update meta.yaml (#12275)
* Update meta.yaml
r-rsqlite version dependency added
* Update meta.yaml
Updated build number to 1
* Use the extended-base container because of wget issues when downloading databases (#12297)
* Update duphold to 0.1.0 (#12257)
* Update flashlfq to 0.1.109 (#12256)
* Update planemo to 0.57.0 (#12251)
* Update meta.yaml (#12258)
* Update scalpel to 0.5.4 (#12249)
* Update scalpel to 0.5.4
* Fix url
* edit grid (#12298)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* minor edit to grid
* minor edit to recipe grid
* added feather to deps (#12293)
* R tigger (#12286)
* Create recipe for r-tigger (#12271)
* Create recipe for r-tigger using bgruening/conda_r_skeleton_helper.
* Delete bld.bat
* Remove windows support
* update scprep to v0.8.1 (#12306)
* Update nanoget to 1.7.5 (#12252)
* Update nanoget to 1.7.5
* Bump to version 1.7.6
should fix the README.md problem
* gffcompare: version bump (#12308)
* Update: cromwell (36), bcbio (Cromwell Docker runs) (#12307)
* Update: cromwell (36), bcbio (Cromwell Docker runs)
* Pin java to 8 to avoid compile errors on 11
* HiCExplorer update to version 2.2-beta (#12309)
* HiCExplorer update to version 2.2-beta
* Remove of '-' from version number
* Numpy set to 1.15
* Update meta.yaml
* upgrade to version 2.8.1 (#12316)
* Create Airr recipe (#12318)
* Create AIRR recipe using conda skeleton pypi.
* Add noarch python
* Clean host requirements
* Added nimnexus [v0.1] (#12133)
* added nimnexus
* Fix sha
* Update build.sh
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* [WIP] Add R-loom (#12320)
* initial WIP skeleton
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* try osx
* Create Changeo recipe (#12321)
* Create changeo recipe using conda skeleton pypi.
* EDIT about section
* ADD noarch generic
* Update noarch to python
* Clean host requirements
* Add test for scripts
* Change requirement to python>=3.4
* Add noarch pyton
* r-corbi (#12325)
* r-nam (#12327)
* Update pybedtools to 0.8.0 (#12324)
* Update pybedtools to 0.8.0
* rm cython requirement
* MSGFplus does not work with newer Java (#12330)
* Trying to not use a very new java version since the latest versions have dropped some classes
* Increment build
* Update atropos to 1.1.21 (#12322)
* Update CONCOCT to 0.4.2 (#12317)
* Update CONCOCT to 0.4.2
* Wrong shasum given
* Reset build number for new version
* New: gvcfgenotyper for joint calling with Illumina strelka2 (#12331)
* Apparently we need openJDK to be below 9, not below 11 as in the previous PR (#12332)
* Update Picard to 2.18.17. (#12333)
* Unblacklist IgDiscover (#12335)
* PacBio: Add missing licenses and post-link message (#12334)
* Bioconductor DEqMS package (#12336)
* Bioconductor DEqMS package
* Limma version could be set lower (checked with the bioconductor recipe page) to include limma in bioconda
* Genenotebook v0.1.10 (#12337)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* v0.1.10
* removed cloudpickle requirement for blockclust (#12242)
* blockclust latest source and added cloudpickle as requirement
* removed cloudpickle requirement for blockclust
* added a tagged release to the source
* back to source url but with release tarball and checksum
* R guilds (#12341)
* Strict rec (#12113)
* added metawrap
* fixed perl and jdk
* added more strict req
* fixed java and perl
* removed extra boost
* Update qcat to v1.0.1 (#12343)
* Add better error checking (#12345)
* Add mhcnames python package (#12349)
* Add MHCflurry pMHC class I binding affinity prediction tool (#12346)
* Bump pilon (#12354)
* Update pronto to 0.11.1 (#12377)
* Update perl-json-xs to 4.0 (#12373)
* Update planemo to 0.57.1 (#12370)
* Update snippy to 4.3.6 (#12372)
* Update intarna to 2.3.1 (#12367)
* Update agfusion to 1.231 (#12366)
* Update bioconda-utils to 0.15.0 (#12359)
* Update mapdamage2 to 2.0.9 (#12358)
* Update scanpy to 1.3.4 (#12357)
* Update goatools to 0.8.11 (#12361)
* Update perl-math-random-mt-auto to 6.23 (#12362)
* Update kipoi to 0.6.3 (#12374)
* Update kipoi_veff to 0.2.1 (#12364)
* Update perl-object-insideout to 4.05 (#12380)
* Update sevenbridges-python to 0.17.1 (#12379)
* Update nanosv to 1.2.3 (#12378)
* Update starfish to 0.0.30 (#12368)
* Update clust to 1.8.10 (#12356)
* Update pypairs to 2.0.6 (#12381)
* Update khmer to 3.0.0a2 (#12360)
* Update flashlfq to 0.1.110 (#12385)
* Update perl-algorithm-cluster to 1.57 (#12384)
* Update arvados-python-client to 1.2.0.20181121194423 (#12382)
* Update avro-cwl to 1.8.9 (#12355)
* Update avro-cwl to 1.8.9
* Set noarch: python
* r-breakaway (#12386)
* R sads (#12388)
* Update python-sortedcontainers to 2.1.0 (#12383)
* r-ebimetagenomics (#12339)
* pin armadilo on major version (#12389)
* IgDiscover version 0.11 (#12351)
* IgDiscover version 0.11
* IgDiscover requires Python 3.6
* Fix build on macOS with a small patch
* Remove unneeded host dependencies
* Update goatools to 0.8.12 (#12391)
* Update bioconda-utils to 0.15.1 (#12390)
* R ebimetagenomics (#12393)
* Add dimspy recipes for reference purposes (#12387)
* Add dimspy recipes for reference purposes
* Remove filename
* remove from blacklist
* Update build-fail-blacklist
* Added BioExcel_SeqQC to bioconda-recipes (#12276)
* PacBio: Update pbalign to 0.3.2 (#12396)
* PacBio: Update pbalign to 0.3.2
Closes: PacificBiosciences/pbbioconda#39
* add bgreat to bioconda (#12350)
* bgreat addition
* zlib in build should not be needed
* btrim integration to conda (#12395)
* Format sleuth recipe. Trigger rebuild because latest version was never uploaded for some reason. (#12399)
* PacBio: Update `pbsv2` to version 2.1.0 (#12400)
* Genenotebook v0.1.11 (#12398)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* v0.1.10
* v0.1.11
* prosolo: new package version 0.6.0 (#12397)
* Update sevenbridges-python to 0.17.2 (#12404)
* Add recipe for ICED (#12406)
* Downgrade version for iced (#12409)
* Update recipe for libstatgen 1.0.5 (#12348)
* Add recipe for libstatgen-1.0.5
* Update iced to 0.5.0 (#12411)
* Update perl-test2-suite to 0.000116 (#12412)
* fix compatibility with other tools (#12415)
* Restore dexseq python helper scripts (#12352)
* Restore dexseq python helper scripts
* Add python requirement for helper scripts
* Add python noarch to build section
* pin it to python2k
* Add htseq requirement, support only python <3 for now
* Genenotebook v0.1.12 (#12418)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* v0.1.10
* v0.1.11
* v0.1.12
* updated source
* added medpy recipe (#12417)
* added medpy recipe
* removed osx from build
* Update meta.yaml
* Update meta.yaml
* add boost and a compiler
* Update meta.yaml
* Update meta.yaml
* add itk
* Updated ddrage to version 1.6.1. (#12421)
* Add r-mcpcounter recipe. (#12261)
* Add MCPcounter recipe.
* fix lint: remove 'fn'
* fix license_file, version number and doi
* Update DEXSeq requirements to force compatible HTSeq version (#12423)
* ARB: Pin glib (#11782)
* Pin glib
* Update meta.yaml
* Update meta.yaml
* Work around CB3 issues
* Work around bioconda-utils lint false positive
* Disable lint check should_not_be_noarch
* Can't reference other packages built in recipe from anything but run
* Move perl to host section. Maybe that helps.
* constraining interpreter version breaks with CB3?
* disable perl version constraint :(
* Update meta.yaml (#12426)
* stacks: fix for fix 'fixing' @ in exe_path (#12420)
* stacks: fix for fix 'fixing' @ in exe_path
the previous fix https://github.com/bioconda/bioconda-recipes/pull/11580
tried to solve the problem with the @ in the exe_path by setting this
variable empty. But the perl scripts
- append a / to the empty string an…
kpalin
pushed a commit
to kpalin/bioconda-recipes
that referenced
this issue
Aug 7, 2019
* update mzr as a test
* Begin building for R 3.5.1 (#11252)
* Bump everything for R 3.5.1
* Fix most of the linting issues
* Update blacklist
* Revert "Fix most of the linting issues"
This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5.
* should_not_use_fn
* More fixes
* Fix incorrect yaml
* Should really fix the linting blacklist stuff
* Fix many recipes
* Fix some linting
* Fix r-wicket
* Update derfinder
* Pin to a given bioconductor release.
* Add missing packages
* Restore identifiers to bioconductor packages
* Restore extra information to R packages
* Update R bulk (#11283)
* fixed incorrect doi of publication (#11175)
* Added recipe for kinSimRiboswitch (#10838)
Added recipe for kinSimRiboswitch, a pipeline for simulating the folding
kinetics of RNA switches.
* update multiqc-bcbio (#11187)
* Add recipe for PopDel (#11181)
* Add recipe for PopDel
* Add clang and clangxx to build config
* update seqbuster (#11190)
* update seqbuster
* fix build
* fix test
* Update pyseer to 1.1.2 (#11172)
* bump sourmash (#11197)
* Update BASIC to v1.4.1 (#11195)
* Update BASIC to v1.4.1
* Trigger circleci
* Fix build number
* Update nf-core-1.2 (#11191)
* Update nf-core-1.2
* Update build script
* Update to InterMine 1.11.0 (#11182)
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Add tinyfasta-0.1.0 (#11177)
* Add tinyfasta
* Update build script
* Fix structure of build section
* Bumping snippy (#11198)
* Remove older version
* Bump snippy
* VEP: bump major version (#11201)
* VEP: bump major version
* VEP: bumped plugin major version
* VEP: update plugin install
Download and install all plugin modules, instead of just a selection
* Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200)
* Update: PureCN to latest devel (1.11.13); wrapper scripts
PureCN development (https://github.com/lima1/PureCN) has several
improvements over the BioC 3.6 release for handling multiple VCF input
types, and is back compatible with R 3.4.1 so still builds cleanly
with two new dependencies.
Also exposes PureCN wrapper scripts for running from the command line.
Prefixes ambiguous scripts with PureCN_.
* Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet
* add cassiopee release 1.0.9 (#11168)
* add cassiopee release 1.0.9
* update to conda build 3
* remove old version backup and use sha256 for source
* Bump abeona version to 0.26.0 (#11202)
* Bump abeona version to 0.24.0
* Bump abeona version to 0.26.0
* Update LexMapr to v0.1.2 (#11192)
* Update LexMapr to v0.1.2
* Add rdflib dep
* Update svtyper to 0.7.0 (#11196)
* Update svtyper to 0.7.0
* Add recipe for perl-gtdbtk (#11194)
* Add recipe for perl-gtdbtk
* New recipe for RFMix (#11205)
* New recipe for RFMix
* updated version number information
* updated version number information
* updated version number information
* initial purge_haplotigs commit (#11049)
* initial purge_haplotigs commit
* bioconda revisions, updating test commands to run the pipeline on the test dataset
* rolling back test commands
* Add recipe for fsm-lite (#11209)
* Add recipe for fsm-lite
* Add prefix to make
* Remove v from version string
* Updated reparation_blast to version v.1.0.7 (#11210)
* Update sambamba to 0.6.8 (#11212)
* Bump sambamba to 0.6.8
* It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified.
* Set some environment variables
* The compiled binary is in a different place now
* ldc provides some libraries that are linked against.
* mtbseq: update recipe (#11110)
* changed download location/add test
* remove test
* Confindr (#11217)
* Update confindr to 0.4.2
* Fix typo in specifying version of pysam
* Update Genenotebook to v0.1.4 (#11218)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* updating to 0.1.3 (#11221)
* sartools1.6.6 (#11222)
* Perl bio automatedannotation (#11216)
* Initial recipe for Bio-AutomatedAnnotation
* Change URL
* Run cpanm tests
* Temporarily set HOME
* Use cpan version instead
* Add more depencencies
* Set bioperl version
* unset bioperl version, add bioperl-run
* New release including version in modules
* Remove comments
* build -> host
* Upgrade r-biodb to v1.1.2. (#11213)
* Upgrade r-biodb to v1.1.2.
* Remove old versions of r-biodb.
* Comment out libgfortran.
* PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215)
* PeptideShaker: updated to version 1.16.30
- Bugfix: HOME was still being used when folder with customised reports was specified.
- Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line.
* SearchGUI: updated to version 3.3.5.
- BUG FIX: Cleanup of the temp path options when used as options for the other command lines.
- FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2.
- LIBRARY UPDATE: Updated utilities to version 4.12.8.
* Update meta.yaml (#11227)
* Svtools 0.4.0 (#11208)
* Remove directories for old svtools versions
* Update svtools to v0.4.0
* Move build number back to 0
* Anvio 52 (#11230)
* Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software.
* Remove cgat-scripts from blacklist. (#11228)
* Add new formula: bazam 1.0.1 (#11229)
* Update gatk4 to 4.0.10.0 (#11224)
* Add recipe for gtdbtk 0.1.3 (#11211)
* Add recipe for gtdbtk
* Added initial htstream recipe (#11113)
* HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data.
* DeepTools 3.1.3 (#11226)
* PacBio: Update `pbmm2` to version 0.10.0 (#11225)
* fastqc: update to version 0.11.8 (#11214)
* fastqc: update to version 0.11.8
* Update meta.yaml
* Phame (#11223)
* mac recipe and added bioperl
* changing bill number
* added no osx
* adding new version
* removed separate recipe for mac, dont need it
* now running same recipe for mac and linux
* fixed the way fasttrees version was being parsed
* minor change test
* adding detailed description
* restaging the build number
* new version
* Make sure to use bioperl and perl 5.26
* Updated ngs-bits to version 2018_10 (#11235)
* PacBio: Update `pbsv2` to version 2.0.2 (#11236)
* Update VSEARCH to 2.8.5 (#11239)
* Fix shorah recipe and remove from blacklist. (#11241)
* Fix shorah recipe and remove from blacklist.
* Fix blas variant.
* Remove imports from tests.
* unicycler 0.4.7 (#11240)
* unicycler 0.4.7
* unicycler: Work around ValueError: invalid
Unicycler thinks the terminal has 0 columns and produces this error:
File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks
raise ValueError("invalid width %r (must be > 0)" % self.width)
ValueError: invalid width -5 (must be > 0)
* Octopus: update to 0.5.1-beta (#11244)
* New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247)
- PURPLE SV and heterogeneity caller for somatic tumor/normal samples.
- VarDictJava -- 1.5.6 release with fixes for SV calling
- PureCN -- add signature dependency and update with fixes for test
samples.
* Dinucleotide patterns analysis tools v1.0 (#11245)
* Dinucleotide patterns analysis tools v1.0
* Lets try it, it seems to work locally for me.
* Enable SpoTyping_plot.r (#11248)
* rerun again (#11233)
* rerun again
* Update meta.yaml
* Delete build.sh
* Update segway dependency optbuild to 0.2 (#10459)
* Update segway dependency optbuild to 0.2
* Update build and architecture requirements for optbuild 0.2
* Add six as a dependency to the optbuild recipe
* Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249)
* Add prefix dnp- to the package names
* Update build.sh
* Update build.sh
* Bump beast version to 1.10.2 (#11250)
* add maxquant (#11253)
* add mayquant
* relax tests
* PacBio: Update `pbmm2` to version 0.10.1 (#11256)
* PacBio: Update `pbmm2` to version 0.10.1-1 (#11257)
* remove xsv recipe (#11259)
* add blast dependency (#11258)
* Added riborex recipe (#11251)
* Added riborex recipe
* Relaxed version constraints
* Pinned r-core for fdr tools
* fixed the r-base stuff upstream
* Update meta.yaml
* fix graphprot (#11234)
* increase build number
* remove from blacklist
* use cxx instead of c
* move coreutoils to build section
* set additional paths
* patch makefile
* blind try
* update patch
* explicitely copy from src_dir
* update deprecated prefix variable
* Revert "update deprecated prefix variable"
This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d.
* update deprecated prefix variable
* try moving to host section
* Bump mash (#11264)
* Add fmlrc (#11265)
* Add fmlrc
* add doi
* PacBio: Update pb-falcon to 0.2.4. (#11266)
* Add kopt recipe (#11269)
* Genomepy 0.5.2 (#11267)
* release 0.5.2 of genomepy
* trigger new build
* remove genomepy from blacklist
* locale for osx
* updated locale test
* PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275)
* Update mmseqs2 recipe to new release 6-f5a1c (#11272)
* Update yacrd to version 0.4.1 (#11273)
* Add scprep (#11270)
* Add scprep
* All of these should not be needed as host dep
* Metawrap preqs2 (#11242)
* fixed issues
* fixed issues
* added tests
* fixed tab
* gemma 0.98 (#11254)
* gemma 0.98
* gemma 0.98
Leave gsl and zlib out of runtime dependencies
* Add DCA recipe (#11274)
* Add DCA recipe
* add noarch and doi
* remove skip
* Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib
* Various fixes for bulk and trigger a rebuild (#11313)
* Various fixes, at least 4 packages (and their dependencies) should still fail (#11320)
* A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336)
* Fix various recipes (#11354)
* Fix various recipes
* Fix more recipes
* Various CRAN package fixes, since they all lack license files (#11372)
* Various CRAN package fixes, since they all lack license files
* Fix the r-dartr recipe
* There is a light at the end of the tunnel (#11381)
* There is a light at the end of the tunnel
* Licenses no longer exist
* [BULK] Fixes for R/Bioconductor packages (#11406)
* Require `r-base >=3.5` for some packages
* Fix various CRAN packages lacking license file
* Add missing libnetcdf requirement to bioconductor-mzr
* Remove r-alakazam (moved to conda-forge)
Fix linting issue:
```
recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating
```
* [BULK] Many R 3.5 only packages (#11410)
* [BULK] Bulk update 191018b (#11419)
* update mzr as a test
* Begin building for R 3.5.1 (#11252)
* Bump everything for R 3.5.1
* Fix most of the linting issues
* Update blacklist
* Revert "Fix most of the linting issues"
This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5.
* should_not_use_fn
* More fixes
* Fix incorrect yaml
* Should really fix the linting blacklist stuff
* Fix many recipes
* Fix some linting
* Fix r-wicket
* Update derfinder
* Pin to a given bioconductor release.
* Add missing packages
* Restore identifiers to bioconductor packages
* Restore extra information to R packages
* Update R bulk (#11283)
* fixed incorrect doi of publication (#11175)
* Added recipe for kinSimRiboswitch (#10838)
Added recipe for kinSimRiboswitch, a pipeline for simulating the folding
kinetics of RNA switches.
* update multiqc-bcbio (#11187)
* Add recipe for PopDel (#11181)
* Add recipe for PopDel
* Add clang and clangxx to build config
* update seqbuster (#11190)
* update seqbuster
* fix build
* fix test
* Update pyseer to 1.1.2 (#11172)
* bump sourmash (#11197)
* Update BASIC to v1.4.1 (#11195)
* Update BASIC to v1.4.1
* Trigger circleci
* Fix build number
* Update nf-core-1.2 (#11191)
* Update nf-core-1.2
* Update build script
* Update to InterMine 1.11.0 (#11182)
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Add tinyfasta-0.1.0 (#11177)
* Add tinyfasta
* Update build script
* Fix structure of build section
* Bumping snippy (#11198)
* Remove older version
* Bump snippy
* VEP: bump major version (#11201)
* VEP: bump major version
* VEP: bumped plugin major version
* VEP: update plugin install
Download and install all plugin modules, instead of just a selection
* Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200)
* Update: PureCN to latest devel (1.11.13); wrapper scripts
PureCN development (https://github.com/lima1/PureCN) has several
improvements over the BioC 3.6 release for handling multiple VCF input
types, and is back compatible with R 3.4.1 so still builds cleanly
with two new dependencies.
Also exposes PureCN wrapper scripts for running from the command line.
Prefixes ambiguous scripts with PureCN_.
* Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet
* add cassiopee release 1.0.9 (#11168)
* add cassiopee release 1.0.9
* update to conda build 3
* remove old version backup and use sha256 for source
* Bump abeona version to 0.26.0 (#11202)
* Bump abeona version to 0.24.0
* Bump abeona version to 0.26.0
* Update LexMapr to v0.1.2 (#11192)
* Update LexMapr to v0.1.2
* Add rdflib dep
* Update svtyper to 0.7.0 (#11196)
* Update svtyper to 0.7.0
* Add recipe for perl-gtdbtk (#11194)
* Add recipe for perl-gtdbtk
* New recipe for RFMix (#11205)
* New recipe for RFMix
* updated version number information
* updated version number information
* updated version number information
* initial purge_haplotigs commit (#11049)
* initial purge_haplotigs commit
* bioconda revisions, updating test commands to run the pipeline on the test dataset
* rolling back test commands
* Add recipe for fsm-lite (#11209)
* Add recipe for fsm-lite
* Add prefix to make
* Remove v from version string
* Updated reparation_blast to version v.1.0.7 (#11210)
* Update sambamba to 0.6.8 (#11212)
* Bump sambamba to 0.6.8
* It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified.
* Set some environment variables
* The compiled binary is in a different place now
* ldc provides some libraries that are linked against.
* mtbseq: update recipe (#11110)
* changed download location/add test
* remove test
* Confindr (#11217)
* Update confindr to 0.4.2
* Fix typo in specifying version of pysam
* Update Genenotebook to v0.1.4 (#11218)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* updating to 0.1.3 (#11221)
* sartools1.6.6 (#11222)
* Perl bio automatedannotation (#11216)
* Initial recipe for Bio-AutomatedAnnotation
* Change URL
* Run cpanm tests
* Temporarily set HOME
* Use cpan version instead
* Add more depencencies
* Set bioperl version
* unset bioperl version, add bioperl-run
* New release including version in modules
* Remove comments
* build -> host
* Upgrade r-biodb to v1.1.2. (#11213)
* Upgrade r-biodb to v1.1.2.
* Remove old versions of r-biodb.
* Comment out libgfortran.
* PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215)
* PeptideShaker: updated to version 1.16.30
- Bugfix: HOME was still being used when folder with customised reports was specified.
- Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line.
* SearchGUI: updated to version 3.3.5.
- BUG FIX: Cleanup of the temp path options when used as options for the other command lines.
- FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2.
- LIBRARY UPDATE: Updated utilities to version 4.12.8.
* Update meta.yaml (#11227)
* Svtools 0.4.0 (#11208)
* Remove directories for old svtools versions
* Update svtools to v0.4.0
* Move build number back to 0
* Anvio 52 (#11230)
* Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software.
* Remove cgat-scripts from blacklist. (#11228)
* Add new formula: bazam 1.0.1 (#11229)
* Update gatk4 to 4.0.10.0 (#11224)
* Add recipe for gtdbtk 0.1.3 (#11211)
* Add recipe for gtdbtk
* Added initial htstream recipe (#11113)
* HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data.
* DeepTools 3.1.3 (#11226)
* PacBio: Update `pbmm2` to version 0.10.0 (#11225)
* fastqc: update to version 0.11.8 (#11214)
* fastqc: update to version 0.11.8
* Update meta.yaml
* Phame (#11223)
* mac recipe and added bioperl
* changing bill number
* added no osx
* adding new version
* removed separate recipe for mac, dont need it
* now running same recipe for mac and linux
* fixed the way fasttrees version was being parsed
* minor change test
* adding detailed description
* restaging the build number
* new version
* Make sure to use bioperl and perl 5.26
* Updated ngs-bits to version 2018_10 (#11235)
* PacBio: Update `pbsv2` to version 2.0.2 (#11236)
* Update VSEARCH to 2.8.5 (#11239)
* Fix shorah recipe and remove from blacklist. (#11241)
* Fix shorah recipe and remove from blacklist.
* Fix blas variant.
* Remove imports from tests.
* unicycler 0.4.7 (#11240)
* unicycler 0.4.7
* unicycler: Work around ValueError: invalid
Unicycler thinks the terminal has 0 columns and produces this error:
File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks
raise ValueError("invalid width %r (must be > 0)" % self.width)
ValueError: invalid width -5 (must be > 0)
* Octopus: update to 0.5.1-beta (#11244)
* New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247)
- PURPLE SV and heterogeneity caller for somatic tumor/normal samples.
- VarDictJava -- 1.5.6 release with fixes for SV calling
- PureCN -- add signature dependency and update with fixes for test
samples.
* Dinucleotide patterns analysis tools v1.0 (#11245)
* Dinucleotide patterns analysis tools v1.0
* Lets try it, it seems to work locally for me.
* Enable SpoTyping_plot.r (#11248)
* rerun again (#11233)
* rerun again
* Update meta.yaml
* Delete build.sh
* Update segway dependency optbuild to 0.2 (#10459)
* Update segway dependency optbuild to 0.2
* Update build and architecture requirements for optbuild 0.2
* Add six as a dependency to the optbuild recipe
* Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249)
* Add prefix dnp- to the package names
* Update build.sh
* Update build.sh
* Bump beast version to 1.10.2 (#11250)
* add maxquant (#11253)
* add mayquant
* relax tests
* PacBio: Update `pbmm2` to version 0.10.1 (#11256)
* PacBio: Update `pbmm2` to version 0.10.1-1 (#11257)
* remove xsv recipe (#11259)
* add blast dependency (#11258)
* Added riborex recipe (#11251)
* Added riborex recipe
* Relaxed version constraints
* Pinned r-core for fdr tools
* fixed the r-base stuff upstream
* Update meta.yaml
* fix graphprot (#11234)
* increase build number
* remove from blacklist
* use cxx instead of c
* move coreutoils to build section
* set additional paths
* patch makefile
* blind try
* update patch
* explicitely copy from src_dir
* update deprecated prefix variable
* Revert "update deprecated prefix variable"
This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d.
* update deprecated prefix variable
* try moving to host section
* Bump mash (#11264)
* Add fmlrc (#11265)
* Add fmlrc
* add doi
* PacBio: Update pb-falcon to 0.2.4. (#11266)
* Add kopt recipe (#11269)
* Genomepy 0.5.2 (#11267)
* release 0.5.2 of genomepy
* trigger new build
* remove genomepy from blacklist
* locale for osx
* updated locale test
* PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275)
* Update mmseqs2 recipe to new release 6-f5a1c (#11272)
* Update yacrd to version 0.4.1 (#11273)
* Add scprep (#11270)
* Add scprep
* All of these should not be needed as host dep
* Metawrap preqs2 (#11242)
* fixed issues
* fixed issues
* added tests
* fixed tab
* gemma 0.98 (#11254)
* gemma 0.98
* gemma 0.98
Leave gsl and zlib out of runtime dependencies
* Add DCA recipe (#11274)
* Add DCA recipe
* add noarch and doi
* remove skip
* Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib
* Various fixes for bulk and trigger a rebuild (#11313)
* Various fixes, at least 4 packages (and their dependencies) should still fail (#11320)
* A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336)
* Fix various recipes (#11354)
* Fix various recipes
* Fix more recipes
* Various CRAN package fixes, since they all lack license files (#11372)
* Various CRAN package fixes, since they all lack license files
* Fix the r-dartr recipe
* There is a light at the end of the tunnel (#11381)
* There is a light at the end of the tunnel
* Licenses no longer exist
* [BULK] Fixes for R/Bioconductor packages (#11406)
* Require `r-base >=3.5` for some packages
* Fix various CRAN packages lacking license file
* Add missing libnetcdf requirement to bioconductor-mzr
* Remove r-alakazam (moved to conda-forge)
Fix linting issue:
```
recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating
```
* [BULK] Many R 3.5 only packages (#11410)
* Update pinning to R>=3.5 and a few runtime dependencies.
* CSAW is R 3.5 only
* Packages using beachmat are 3.5 only
* Packages using bioconductor-singlecellexperiment are R 3.5 only
* [BULK] Don't use r-base >=3.5, use a conda_build_config.yaml instead (#11452)
* Don't use r-base >=3.5, use a conda_build_config.yaml instead
* blacklist r-phangorn
* Update variancepartition
* R 3.5 for packages requiring singlecellexperiment
* Update a few packages
* Update a number of recipes (#11482)
* Update ensemblVEP and derfinder (#11504)
* Bulk update 251018 (#11577)
* [BULK] various package updates
* blacklist bioconductor-mzr
* A couple tweaks
* [BULK] Update 261018 (#11611)
* Apparently the r-rgeos bit works properly now.
* Add tissueenrich and try to fix scpipe on Linux
* A meaningless change just to trigger an update in bulk. (#11618)
* [BULK] update 271018 (#11628)
* Bump bioconductor-esetvis
* Fix yaqcaffy
* Fix more
* Another R 3.5 recipe
* [BULK] update 281018 (#11689)
* Add some files
* Fix arrayexpress
* Fix another 2
* Blacklist a bunch of bioconductor recipes that aren't likely to get built for a variety of reasons (mostly due to mzR). (#11697)
* Update blacklist (#11706)
* [BULK] fix bioconductor-tissueenrich (#11720)
* taxonkit 0.2.5 (#11318)
* Update csvtk (#11319)
* taxonkit 0.2.5
* csvtk 0.15.0
* bumping GROOT to 0.8.1 (#11323)
* HiCMatrix version 3 (#11322)
* Correcting dependencies
* Version 3 of HiCMatrix, the October release
* Update confindr to 0.4.3 (#11330)
* Drop-seq_tools: Version 2.0.0 (#11326)
* Update meta.yaml
* Update build.sh
some tool names changed to fit Camel case
* Update motus to build only for python3 (#11331)
* Update fpa to 0.2 version (#11333)
* update taxonkit to 0.3.0 (#11339)
* ntcard 1.1.0 (#11338)
* Update rgi (#11335)
* first commit
* update dependencies list
* change source to github
* change build number
* testing circleci
* update meta and build
* fix build
* move build script into meta
* remove older recipes
* line fix in bootstrap.py
* change python & matplotlib versions; add build.sh file
* add preprocessing selector to skip python 2.7
* move build script into meta.yaml
* Revert "line fix in bootstrap.py"
This reverts commit 5ac1ecd0142a5cfdfc8499c5b6ef4e1f629cd046.
* Update gmap to version 2018-07-04. (#11332)
MAX_READLENGTH environment variable has been disused since 2016-08-16.
* Upgrade r-biodb to 1.2.0a. (#11341)
* Upgrade r-biodb to 1.2.0a.
* Update meta.yaml
* Updated ont-tombo to version 1.5. (#11329)
* Updated ont-tombo to version 1.5.
* Updated with actual github release version hash.
* remove graphicsmagick (#11342)
* Build kraken2 for osx (#11343)
* First try for a bcalm recipes (#11344)
* New: cgpbigwig (BigWig manipulation); Update: bcbio (#11347)
- cgpbigwig (https://github.com/cancerit/cgpBigWig) provides bigwig
generation and manipulation command line tools including bam to bigwig
conversion.
- bcbio: fixes for QC on variants and peddy for CWL runs
* Try avoid some dependancy (#11349)
* Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8 (#11348)
* Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8
Also add about:home .
* Workaround https://github.com/conda-forge/bison-feedstock/issues/7
* Better bcalm recipes (#11350)
* Try avoid some dependancy
* Correct mess in build number, sorry
* R biodb (#11351)
* rebuild r-biodb
* trigger build
* Add recipe for pypairs (#11356)
* Update smoove to 0.2.1. (#11360)
* Update duphold to 0.0.9. (#11359)
* Update goleft to 0.2.0 (#11361)
* Bump slicedimage to 1.0.0 (#11362)
* Bump slicedimage to 1.0.1 (#11365)
* Added new versions for biopet-sampleconfig (#11268)
* perl-velvetoptimiser: update to 2.2.6 (#11369)
* update to 2.2.6
* remove unneeded patch
* Scanpy upgrade (#11371)
* Bump version
* Upgrade Scanpy
* Bump starfish to 0.0.25 (#11370)
* bumping groot to 0.8.2 (#11374)
* vep: bump subversion (#11367)
* Updated Krocus 1.0.1 (#11355)
* Add tiptoft
* Fix meta.yaml for tiptoft
* Add build script
* Updated krocus 1.0.1
* Add tiptoft 0.1.4 (#11352)
* Add tiptoft
* Fix meta.yaml for tiptoft
* Add build script
* Kodoja v0.0.9 (#11373)
* Add recipe for seer (#11263)
* Add recipe for seer
* lets try this
* Add newer compiler
* Using boost-cpp
* messed up version string
* Attempt building boost
* Use c++11 in boost
* Use python for boost install
* Correct python version spec
* try with different python version
* Fix b2 command
* Fix popd command
* build and link boost program options statically
* Fix tests
* Match dependency order
* Link openblas instead of blas
* Forcing rebuild with openblas
* Don't use armadillo wrapper
* Making review changes. Also trying original tests
* Previous tests were correct
* Add recipe for the translate-gard npm package version 1.0.3 (#11364)
* Fix umi tools (#11376)
umi_tools: clean up dependencies
* add support tools to PATH (#11379)
* Bump to v2.2.1 (#11380)
* Bump starfish to 0.0.26 (#11378)
* Update fpa to 0.3 (#11375)
* Update fpa to 0.3
* Correct error in sha256
* Reset build number
* Update trial to 2.5.5 (#11386)
* Update: bioconductor-titancna; 1.19.1 with hg38 support (#11388)
* Update: bioconductor-titancna; 1.19.1 with hg38 support
* Pin to R 3.4 to avoid pulling in 3.3 and 3.5 during mulled
* Add r-polysat version 1.7-3 (#11384)
* Update biomart version so that compatible with r351 (#11366)
* Update biomart version so that compatible with r351
* Update meta.yaml
reset build number as per https://bioconda.github.io/guidelines.html#buildnum
* Update entrez-direct to 10.0.20180927. (#11387)
* Added recipe for SonicParanoid 1.0.13 (#11271)
* Added recipe for SonicParanoid 1.0.13
* removed 'x.x' for numpy, added basic test
* fixed linter related errors
* compiler set to cxx and added host section (same build error!)
* removed host section
* moved numpy and cython to host section; restored build: noarch: python; added LICENSE.md
* removed build: noarch
* added build and extra sections
* set build number to 0; removed skip build; added python3 minimum version; added test for all executables.
* restored sh python module as requirement
* added Make to run; updated release to latest commit
* remove c compiler from meta.yaml
* modified build.sh to compile source codel added make in build section
* updated to latest commit
* updated to latest version with make included in setup.py
* reverted build.sh to the simplest version (python setup.py install)
* Add perl-json to build requirements to allow meme-chip to run to completion. Change meme-chip to use dreme-py3 instead of dreme if building with python 3. (#11389)
* Bump IgBLAST to 1.9.0 (#11393)
Bump IgBLAST to 1.9.0
Re-package the binary version this time. There are problems building the
source version when the configure script reaches this step:
"trying to build the NCBI SRA/VDB Toolkit from GitHub"
The previous problem about the binaries linking against libbz2.so, for
which we had no conda package, is now solved.
Also, this saves about 45 minutes compilation time.
* Add consan (#11395)
* Add consan
* Skip osx
* Update: vardict, vardict-java 1.5.7 (#11394)
* Update: vardict, vardict-java 1.5.7
Latest vardict-java release and corresponding vardict with bug fixes
after testing with 1.5.6
* Reduce test output to try and fix build problems
* Experiment 2 for build problems: remove r-base from run
* Experiment 3 for build problems: add r-base in host
* update recipe for 3.9.1 (#11397)
* evofold2 (#11396)
* evofold2
* wrapper
* Update meta.yaml
* minor
* Update rnastructure to 6.1. (#11400)
* Ctat mut (#11401)
* updating version number
* correct URL
* proper hash
* Revert "Ctat mut (#11401)" (#11402)
This reverts commit 6db10ac7ffd7abaf8fbf1762b7ea6c63b2585fe0.
* update version (#11403)
* any2fasta 0.4.2 (new formula) (#11407)
* W4mclassfilter v0.98.9 (#11385)
* Added files to build version 0.98.9
* Update meta.yaml
* Update meta.yaml
* updated SonicParanoid recipe to version 1.0.14 (#11409)
* updated SonicParanoid recipe to version 1.0.14
* Update to version 1.0.2 of PopDel (#11398)
* Update to version 1.0.2 of PopDel
Update to version 1.0.2.
* Reset build number to 0
* PacBio: require Meson 0.48.1 for all recipes (#11090)
* Meson 0.47 inserted duplicate RPATHs in
macOS binaries, causing `install_name_tool`
failures when installing the package.
Requiring 0.48.1 ensures we do not run into
these issues anymore in the future.
* rebuild with latest openmpi (#11411)
* Remove kfoots from the blacklist (#11416)
* Update gseapy to 0.9.7 (#11417)
* Update gseapy to 0.9.7
* remove noarch
* Add SC3 as dependency (#11427)
* Add recipe for r-poppr (#11418)
* Update knitr version because of Issue: https://github.com/rstudio/rmarkdown/pull/1271 (#11412)
* Update IQ-TREE to 1.6.7.1 (#11429)
* Update IQ-TREE to 1.6.7.1
* Change build number
* Update: r-deconstructsigs with fixes for hg38 (#11431)
The 1.8.0 release, from 2016, has some issues with hg38 and other
custom genomes that are fixed in development (raerose01/deconstructSigs#27).
There hasn't been a new release pushed so this rolls these into a new
sub-version and makes them available.
* Update entrez-direct to 10.2.20181018. (#11432)
* Add assembly-scan recipe (#11425)
* remove python 2.7 skip (#11424)
Preparation for rnaQUAST
* Add fastq-scan recipe (#11415)
* Add patch to fix racon/rampler path in racon_wrapper. (#11434)
Fixes #11405.
* meme rebuild (#11433)
* Update nanocomp to 0.23.1 (#11436)
* Update nanocomp to 0.23.1
* remove noarch
* Update abricate to 0.8.10 (#11446)
* Update angsd to 0.923 (#11445)
* Update alfred to 0.1.13 (#11444)
* Update alfred to 0.1.13
* Try w/o patch
* Update antarna to 2.0.6 (#11442)
* Update admixtools to 5.1 (#11443)
* Update admixtools to 5.1
* Let makefile choose which bins to install
* Update alignstats to 0.5 (#11441)
* Update xatlas to 0.2.1 (#11437)
* r-gpca (#11428)
* r-gpca
* r-gpca recipe
* Update meta.yaml
* Removed All Comments
* gseapy bump version 0.9.8 (#11440)
* gseapy bump version 0.9.8
* version
* titancna: fix for hg38, remove conda build hacks (#11447)
* titancna: fix for hg38, remove conda build hacks
* Re-add r-base 3.4 pin to avoid 3.5 errors
* Hmmlearn older version (#11450)
* Adding pygtftk
* removed pygtftk from master
* add older version of hmmlearn
* Add card_trick (#11451)
* Add card_trick
* Restrict to py3
* Update checkm-genome to 1.0.12 (#11455)
* Bump drep (#11457)
* Update squid to 1.5 (#11466)
* Update ncbi-ngs-sdk to 2.9.3 (#11467)
* elprep: bumped major version (#11414)
* elprep: bumped major version
* fixed hash
* fix download link, fixed licence
* fixed tests
* skip osx build
* FRED2 as a conda package (#11469)
* Attempt to get FRED2 as a conda package
* SHA update
* 99 little bugs in the code
* Fix things Björn mentioned
* add rnaQUAST recipe (#11470)
* Update bioconda-utils to 0.14.9 (#11454)
* Rapidup (#11474)
* Update to v0.7
* Update Buildnumber
* rapid: update to v0.6
* rapid: update to v0.6
* update grid (#11478)
* Adding biobb_model recipe (#11472)
* Updated wtdbg to v2.1 (#11486)
* update stream to 0.2.6 (#11483)
* update stream to 0.2.2
* update stream to 0.2.3
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.5
* update stream to 0.2.6
* Update meta.yaml (#11487)
* Update connectome-workbench to 1.3.2 (#11468)
Now needs QT 5.7
* Update deblur to 1.1.0 (#11500)
* Update domclust to 1.2.8 (#11498)
* WisecondorX: bump version (#11501)
* Bump as GitHub wasn't working yesterday (#11502)
* Added recipe for Sequenza (#10367)
* Added recipe for Sequenza
* Removed fn entry in source section
* Trying with only one URL
* copynumber is a bioconductor package
* Added missing requirements section
* Removed mailing list address
* Added doi
* Added license_file
* Trying with different license_file path
* Fred2 bump (#11503)
* Bump as GitHub wasn't working yesterday
* Fix licence etc
* Scanpy scripts (#11413)
Doing squash and merge as requested by @nh3
* Bump version
* First implementation of scanpy-scripts bioconda recipe.
* fix path in build.sh
* Remove "noarch" flag as requested by bioconda recipe checklist
* Add a post install notice that post install test needs bats-core.
* Add more dependencies
* Skip building for python versions other than 3.6
* Target v0.0.2 which has non-ascii characters removed
* Lower version requirement for pandas and matplotlib to be the same as scanpy
* Requirement matplotlib>=3.0.0, declare noarch
* New: hmftools-cobalt; Update: hmftools-purple (#11507)
- hmftools-cobalt: Add latest version of PURPLE associated read counter,
COBALT, with support for hg38.
- hmftools-purple: PURPLE release with hg38 support.
* Update Picard to 2.18.15. (#11505)
* Genenotebook (#11476)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* Update pinning (#11514)
* Bump build number for updated dependency (#11510)
* Bump build number for updated dependency
* Try adding r-base to host requirements
* Try adding other requirements to host
* Pin to R version
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Tweak dependency version syntax
* Pin R and package versions correctly
* PacBio: Update pbcore to 1.6.5 (#11513)
* Bump r seurat scripts version (#11292)
* Bump version
* Remove noarch
* Could wrongly quoted version be causing an issue?
* Tweak pinning to try and fix CI error
* seqcluster:fix UMI detection. (#11511)
* seqcluster:fix UMI detection.
* Fix dependency
* quast 5.0.1 (#11479)
* quast 5.0.1
* quast 5.0.1: remove third-party site packages from the distibution pack
* quast 5.0.1: skip Glimmer in test
* quast 5.0.1: joblib and simplejson dependencies added to meta.yaml (Setuptools downloading is disabled in conda build)
* quast 5.0.1: explicit joblib and simplejson dependencies removed (Setuptools downloading is disabled in conda build)
* quast 5.0.1: Python 2 and 3 compatible code in build.sh
* wcX bugfixes (#11508)
* wcX bugfixes
* fixed shasum
* Update fastspar to 0.0.7 (#11515)
* Update iqtree to 1.6.7.2 (#11525)
* Update illumina-interop to 1.1.6 (#11523)
* Update hapbin to 1.3.0 (#11522)
* Update hlama to 3.0.1 (#11520)
* Update gb_taxonomy_tools to 1.0.1 (#11519)
* Update gffcompare to 0.10.5 (#11517)
* Update fast5seek to 0.1.1 (#11516)
* Update deepbinner to 0.2.0 (#11499)
* Update deepbinner to 0.2.0
* Update meta.yaml
Try same fix as in #11240
* Update ncbi-vdb to 2.9.3 (#11550)
* Update mikado to 1.2.4 (#11549)
* Update perl-pcap to 3.5.2 (#11543)
* Update python-hyphy-python to 0.1.9 (#11545)
* Update mlst to 2.15.2 (#11547)
* Update perl-sanger-cgp-vcf to 2.2.1 (#11542)
* Update merfishtools to 1.5.0 (#11537)
* Update perl-sanger-cgp-vagrent to 3.3.3 (#11536)
* Update nonpareil to 3.3.3 (#11535)
* Update prophex to 0.1.1 (#11532)
* Update krakenuniq to 0.5.3 (#11527)
* Update novoplasty to 2.7.2 (#11530)
* Update minced to 0.3.2 (#11529)
* Update mapdamage2 to 2.0.8 (#11528)
* Update perl-sanger-cgp-allelecount to 4.0.0 (#11538)
* Update pyvolve to 0.9.0 (#11531)
* Genenotebook (#11512)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* add plek (#11554)
* Update pyimzml to 1.2.4 (#11534)
* Bump shovill (#11555)
* PacBio: Update minimum pbcore version (#11556)
* We want all users of PacBio tools to be able to
use our utilities with pbmm2 alignments.
* Add recipe for translate-gard v1.0.4 (#11557)
* bioconductor-rnaseqsamplesizedata (#11475)
* Adding Recipe for bioconductor-rnaseqsamplesizedata
* Updated metadata for RnaSeqSampleSizeData
* nextflow 18.10.1 (#11558)
* Update raxml to 8.2.12 (#11567)
* Update r-fgwas to 0.3.6 (#11566)
* Update rapid to 0.7 (#11565)
* Update r-spieceasi to 1.0.2 (#11564)
* Update rcorrector to 1.0.3.1 (#11562)
* Update quicktree to 2.4 (#11560)
* Update paladin to 1.4.4 (#11541)
* Update paladin to 1.4.4
* delete md5
* Update build.sh
* Update build.sh
* Fix and unblacklist Tadarida-D (#11568)
* Add recipe for rgt
* Fix and un-blacklist tadarida-d
* Remove RGT
* bumping groot (#11575)
* update pymzml (#11573)
* Add bioconductor-rnaseqsamplesize (#11559)
* Add bioconductor-rnaseqsamplesize
* Update recipe
* Fixing some URLs
* Update dependencies missing
* Update trumicount to 0.9.11 (#11576)
* Update ConFindr to 0.4.4 (#11578)
* Added new versions for biopet-scatterregions (#11572)
* Added new versions for biopet-bamstats (#11571)
* R ggbiplot (#11584)
* add R -e 'httr::set_config(httr::config(ssl_verifypeer = 0L)); install.packages(devtools, repos=http://mirrors.ebi.ac.uk/CRAN/); library(devtools); install_github(vqv/ggbiplot); library(ggbiplot)'
* add r-ggbiplot
* update meta.yaml
* update meta.yaml
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix errors
* fix errors number 1
* Update rebaler to 0.1.2 (#11563)
* Update rebaler to 0.1.2
* Remove fn
* bump graphclust (#11585)
* Update seqyclean to 1.10.09 (#11589)
* Update stringmlst to 0.5.1 (#11590)
* Update snp-dists to 0.6.2 (#11592)
* Update snippy to 4.3.3 (#11596)
* Update canu to 1.8 (#11600)
* Update starfish to 0.0.27 (#11599)
* Update womtool to 36 (#11594)
* Update telseq to 0.0.2 (#11598)
* Update snp-sites to 2.4.1 (#11588)
* Added recipe for pydemult: Streamed and parallel demultiplexing of fastq files (#11471)
* Added recipe for pydemult
* Bumped version in favor of py3.5
* bump vcf2db to latest commit (#11601)
* bump vcf2db to latest commit
* fix shasum
* Fixing source url
* Update: TitanCNA; hg38 cytoband support and fix for normalization (#11604)
* megan (#11046)
* megan6: initial commit
* megan6: intermediate commit
* megan: made tests work
* megan: doc improvement
* megan: added osx dmg file
* megan: add java to build requirements
* megan: removed new line
* megan: removed osx sources
* Update meta.yaml
* bumping hulk (#11607)
* Update hotspot3d to 1.8.2 (#11521)
* Update hotspot3d to 1.8.2
* Add perl-json as dependency
* Add perl-archive-extract as dependency
* Fqzcomp (#11606)
* Added recipe for fqzcomp
* There is no configure script
* Maybe this works
* Added gcc as build requirement
* Removed gcc again (lint issue)
* Maybe these exports will do the trick
* Nope!
* Added cxx as host requirement
* Compilers are only allowed in build section
* There is no need for make install
* Copy-paste error...
* Add vcf-annotator recipe (#11481)
* Add vcf-annotator recipe
* added pyvcf dependency
* Update meta.yaml
* stacks: fix for @ in exe_path (#11580)
* stacks: fix for @ in exe_path
* stacks: fixed path
* New version with bugfix and different progressiveMauve version. (#11613)
* Sspupdate (#11614)
* New version with bugfix and different progressiveMauve version.
* Keeping old version as folder.
* Push build number.
* Update SVDB to version 1.3.0 (#11506)
* new file: recipes/svdb/1.1.2/meta.yaml
renamed: reipes/svdb/svdb.patch -> recipes/svdb/1.1.2/svdb.patch
modified: recipes/svdb/meta.yaml
* deleted: 1.1.2/meta.yaml
deleted: 1.1.2/svdb.patch
* Bump nanosim (#11608)
* Bump nanosim
* Add scipy as dep
* Add recipe for perl-number-range (#11621)
* New build for grid (#11620)
* update grid
* update build num
* Recipe for das_tool 1.1.1 (#10528)
* recipe for das_tool 1.1.1
* Add recipe for sompy (#11624)
* cmake modified to build with NDEBUG (#11328)
* cmake modified to build with NDEBUG
* Update meta.yaml
* new build with fasta test
* new build with fasta test
* Fix and unblacklist TwoPaCo (#11622)
* Add recipe for TwoPaCo
* Unblacklist twopaco
* Modify and unblacklist recipe for ESTmapper (#11623)
* Modify and unblacklist recipe for ESTmapper
* Add patch
* Modify and unblacklist recipe for Metaseq (#11625)
* Fix recipe for metaseq and remove from blacklist
* Remove build.sh
* nextflow 18.10.1 build 2 (#11630)
* Add Clust (#11619)
* Add clust
* Clean recipe
* Add "noarch"
* Add DOI
* Add build file
* Python 2.7
* Fix scikit-learn dependency
* Trigger new build
* Update: PureCN (multicore) and PURPLE (plotting X libraries) (#11631)
- PureCN: adds support for specifying cores on command line
- PURPLE: adds X library dependencies required for creating
plots
* scripts/travis-run.sh: added a cleaner method to check for env vars (#11612)
* Increase the number of k value usable in bcalm (request by @Malfoy) (#11610)
* Increase the number of k value usable in bcalm (request by @Malfoy)
* Change compilation parameter to reduce memory impact of compilation
* Update anndata to 0.6.11 (#11637)
* Update nglview to 1.1.7 (#11643)
* Update binsanity to 0.2.7.1 (#11644)
* Update cgat-core to 0.5.4 (#11645)
* Update nanosv to 1.2.2 (#11673)
* Update abeona to 0.36.0 (#11670)
* Update pyfaidx to 0.5.5.2 (#11659)
* Update agfusion to 1.23 (#11668)
* Update iqtree to 1.6.8 (#11686)
* update iqtree to 1.6.8
* Trigger rebuild
* Update validators to 0.12.2 (#11672)
* Update python-edlib to 1.2.3.post1 (#11664)
* update for Purge Haplotigs (#11690)
* Update loompy to 2.0.16 (#11667)
* Update loompy to 2.0.16
* Update meta.yaml
* IgBLAST 1.10.0 (#11693)
* Update wtforms-alchemy to 0.16.7 (#11679)
* Update sickle to 0.6.4 (#11663)
* Update sickle to 0.6.4
* Remove fn and libgcc runtime dep
* Update confindr to 0.4.5 (#11696)
* Batvi (#11695)
* batvi initial
* Guideline compatibility..
* Dummy test section..
* Missing java dependency..
* use openjdk instead of java-jdk ..
* source specified in github ..
* trigger build (package did not have batindel directory) ..
* update SHA256 ..
* update SHA256 ..
* Update pythonpy to 0.4.11 (#11661)
* Update cortexpy to 0.45.6 (#11660)
* Update sevenbridges-python to 0.16.0 (#11674)
* Update solvebio to 2.7.0 (#11657)
* Update mathstats to 0.2.6.5 (#11656)
* Update goatools to 0.8.9 (#11641)
* Add gnies (#11627)
* Add gnies
* noarch python
* Update meta.yaml
* Add recipe for SKA v1.0 (#11581)
* Add recipe for SKA v1.0
* Add lib path for zlib
* Older gcc
* Correct install dir
* Try static linking
* Dynamic linking on OS X
* ldd command test
* correct program
* Remove ldd command
* Add recipe for transit version 2.3.1 (#11701)
* Add recipe for transit version 2.3.1
* Use skip, add spaces.
* Update meta.yaml (#11699)
* remove pyqi (#11704)
* Update python-chado to 2.2.0 (#11714)
* update python-chado
* 2.2.1
* Update vcfanno to 0.3.1 (#11710)
* FGMP-1.0.1 (#11278)
* FGMP-1.0.1 recipe
* remove unncessary build info
* add r-nabor (#11716)
* update stream to 0.2.2
* update stream to 0.2.3
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.5
* update stream to 0.2.6
* add r-nabor recipe
* update r-nabor recipe
* update r-nabor recipe
* r-pctgcdata (#11715)
* r-pctgcdata
* r-pctgcdata - fix
* r-pctgcdata - fix
* Update meta.yaml
* Fix plek by a new branch (#11605)
* Modify the PLEK recipe
* Start fixing PLEK, though it requires compilation
* update build.sh
* update yaml
* fix build.sh
* update build.sh
* Update recipe for plek
* add bioconductor-chromvar recipe (#11718)
* add bioconductor-chromvar recipe
* fix bioconductor-tissueenrich
* Apparently the popdel recipe didn't get correctly merged
* Final merge conflicts
* Bioc quick test (#12547)
* Update kallisto to 0.45.0 (#12117)
* Update validators to 0.12.3 (#12116)
* Update illumina-interop to 1.1.7 (#12115)
* Update umi_tools to 0.5.5 (#12123)
* Update tiptoft to 1.0.0 (#12122)
* Update: TitanCNA with fix for hg38 plotting (#12130)
* blockclust (#12111)
* added eden 1.1 version used in blockclust
* Update meta.yaml
* eden checksum and test
* added zlib requirement
* add include and lib paths to build.sh
* add include and lib paths to build.sh
* modify makefile flags using sed
* modify makefile flags using sed
* use c++
* Update build.sh
* Update build.sh
* LDFLAGS not used in makefile
* remove v1.1
* add blockclust 1.1.0 recipe
* skip osx build
* added tarball url and checksum; removed conda_build_config.yaml
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Update chewbbaca to 2.0.16 (#12132)
* Update abeona to 0.40.0 (#12131)
* ping to eden 1.1 (#12134)
* clean swap file (#12137)
* Update corset to 1.07 (#12143)
* Update peddy to 0.4.3 (#12144)
* blockclust latest source and added cloudpickle as requirement (#12142)
* Update nanomath to 0.22.0 (#12149)
* Update pymvpa to 2.6.5 (#12152)
* Updated to version 1.4.0 (#12138)
* Updated to version 1.4.0
* Resetting build number to 0 and build->host
* Update transdecoder to 5.5.0 (#12172)
* Update gridss to 2.0.1 (#12190)
* Update tracer to 1.7.1 (#12189)
* Update flowcraft to 1.4.0 (#12179)
* Update seqbuster to 3.2 (#12182)
* Update perl-io-compress to 2.081 (#12201)
* Update twobitreader to 3.1.6 (#12205)
* Update twobitreader to 3.1.6
* Update meta.yaml
* Update gtfparse to 1.2.0 (#12186)
* Update gtfparse to 1.2.0
* remove compiler
* Update htseq to 0.11.0 (#12177)
* Update htseq to 0.11.0
* add compiler
* Update htseq to 0.11.0 (#12239) [testing co-author]
* Update htseq to 0.11.0
* add compiler
Co-authored-by: Bjoern Gruening <[email protected]>
* alfred v0.1.16 (#12240)
* alfred v0.1.16
* makefile patch
* makefile patch
* Update scrm to 1.7.3 (#12150)
* Update scrm to 1.7.3
* Update scrm to 1.7.3
* Mob suite update 1.4.8 --> 1.4.9 (#12244)
We fixed a small bug related to repetitive elements database reconstruction on each run. Should only run once during the first mob_typer run. Should be good now for parallel runs.
* PeptideShaker updated to v1.16.35 & SearchGUI updated to 3.3.9 (#12241)
* PeptideShaker updated to v1.16.32
SearchGUI updated to v3.3.6
* PeptideShaker updated to v1.16.35
* SearchGUI updated to v3.3.9
* First attempt at a recipe for ncrf (#12101)
* First attempt at a recipe for ncrf
* changed from copies to symlinks
* including absolute path in symlinks
* PacBio: Update `pbmm2` to version 0.11.0 (#12246)
* Gimmemotifs version 0.13.0 (#12245)
* new release to fix numpy incompatibility
* GimmeMotifs 0.13.0 release test
* numpy 1.15
* version 0.13.0
* Fix about:home and extra:
* PacBio: Update `isoseq3` to version 3.1.0 (#12263)
* add python to host section (#12264)
* Update confindr to 0.4.7 (#12266)
* new build of GRiD (#12269)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* peptideshaker, searchgui: version bump (#12136)
* peptideshaker, searchgui: version bump
solving https://github.com/compomics/searchgui/issues/192
* Update peptide-shaker.py
* searchgui: added c compiler for building
test if linking errors go away this way
* searchgui: removed noarch
* Update: bcbio, bcbio-vm with CWL non-human fixes (bcbio/bcbio-nextgen#2473) (#12273)
* Make snakemake a noarch package. (#12274)
* noarch: python in combination with version constraint
* Cleanup deps and simplify version definition.
* Genenotebook v0.1.9 (#12277)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* Create r-airr recipe (#12284)
* Create r-airr recipe using bgruening/conda_r_skeleton_helper
* Update meta.yaml
* Findbin::Real added (#12291)
* Added version bump to 1.3 (#12292)
* ngs-bits 2018_11 (#12262)
* Updated ngs-bits to version 2018_10
* Updated ngs-bits to version 2018_11
* minor edit in grid (#12287)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* minor edit to grid
* Fred2 update (#12259)
* Update FRED2 Recipe
* msstitch version 2.9 (#12296)
* r-mvr (#12300)
This is a non-parametric method for joint adaptive mean-variance regularization and variance sta-
bilization of high-dimensional data.
* Bump to Gromacs 2018.3 + re-enable OSX build (#12299)
* Gromacs 2018.3 + re-enable osx build
See also #7825 on OSX build
Include RRID for Gromacs (see bioconda/bioconda-utils#252)
* disabled ocl-icd on osx; not available (or needed?)
https://anaconda.org/conda-forge/ocl-icd
* pyGenomeTracks update of dependencies (#12279)
* Update pyGenomeTracks recipe to enable py3 support and updating outdated dependecy list
* Increase build number
* Update meta.yaml
* Exclude Python 3.5
* Gromacs 2018.4 (#12302)
* quast 5.0.2 (#12303)
* Update meta.yaml (#12275)
* Update meta.yaml
r-rsqlite version dependency added
* Update meta.yaml
Updated build number to 1
* Use the extended-base container because of wget issues when downloading databases (#12297)
* Update duphold to 0.1.0 (#12257)
* Update flashlfq to 0.1.109 (#12256)
* Update planemo to 0.57.0 (#12251)
* Update meta.yaml (#12258)
* Update scalpel to 0.5.4 (#12249)
* Update scalpel to 0.5.4
* Fix url
* edit grid (#12298)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* minor edit to grid
* minor edit to recipe grid
* added feather to deps (#12293)
* R tigger (#12286)
* Create recipe for r-tigger (#12271)
* Create recipe for r-tigger using bgruening/conda_r_skeleton_helper.
* Delete bld.bat
* Remove windows support
* update scprep to v0.8.1 (#12306)
* Update nanoget to 1.7.5 (#12252)
* Update nanoget to 1.7.5
* Bump to version 1.7.6
should fix the README.md problem
* gffcompare: version bump (#12308)
* Update: cromwell (36), bcbio (Cromwell Docker runs) (#12307)
* Update: cromwell (36), bcbio (Cromwell Docker runs)
* Pin java to 8 to avoid compile errors on 11
* HiCExplorer update to version 2.2-beta (#12309)
* HiCExplorer update to version 2.2-beta
* Remove of '-' from version number
* Numpy set to 1.15
* Update meta.yaml
* upgrade to version 2.8.1 (#12316)
* Create Airr recipe (#12318)
* Create AIRR recipe using conda skeleton pypi.
* Add noarch python
* Clean host requirements
* Added nimnexus [v0.1] (#12133)
* added nimnexus
* Fix sha
* Update build.sh
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* [WIP] Add R-loom (#12320)
* initial WIP skeleton
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* try osx
* Create Changeo recipe (#12321)
* Create changeo recipe using conda skeleton pypi.
* EDIT about section
* ADD noarch generic
* Update noarch to python
* Clean host requirements
* Add test for scripts
* Change requirement to python>=3.4
* Add noarch pyton
* r-corbi (#12325)
* r-nam (#12327)
* Update pybedtools to 0.8.0 (#12324)
* Update pybedtools to 0.8.0
* rm cython requirement
* MSGFplus does not work with newer Java (#12330)
* Trying to not use a very new java version since the latest versions have dropped some classes
* Increment build
* Update atropos to 1.1.21 (#12322)
* Update CONCOCT to 0.4.2 (#12317)
* Update CONCOCT to 0.4.2
* Wrong shasum given
* Reset build number for new version
* New: gvcfgenotyper for joint calling with Illumina strelka2 (#12331)
* Apparently we need openJDK to be below 9, not below 11 as in the previous PR (#12332)
* Update Picard to 2.18.17. (#12333)
* Unblacklist IgDiscover (#12335)
* PacBio: Add missing licenses and post-link message (#12334)
* Bioconductor DEqMS package (#12336)
* Bioconductor DEqMS package
* Limma version could be set lower (checked with the bioconductor recipe page) to include limma in bioconda
* Genenotebook v0.1.10 (#12337)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* v0.1.10
* removed cloudpickle requirement for blockclust (#12242)
* blockclust latest source and added cloudpickle as requirement
* removed cloudpickle requirement for blockclust
* added a tagged release to the source
* back to source url but with release tarball and checksum
* R guilds (#12341)
* Strict rec (#12113)
* added metawrap
* fixed perl and jdk
* added more strict req
* fixed java and perl
* removed extra boost
* Update qcat to v1.0.1 (#12343)
* Add better error checking (#12345)
* Add mhcnames python package (#12349)
* Add MHCflurry pMHC class I binding affinity prediction tool (#12346)
* Bump pilon (#12354)
* Update pronto to 0.11.1 (#12377)
* Update perl-json-xs to 4.0 (#12373)
* Update planemo to 0.57.1 (#12370)
* Update snippy to 4.3.6 (#12372)
* Update intarna to 2.3.1 (#12367)
* Update agfusion to 1.231 (#12366)
* Update bioconda-utils to 0.15.0 (#12359)
* Update mapdamage2 to 2.0.9 (#12358)
* Update scanpy to 1.3.4 (#12357)
* Update goatools to 0.8.11 (#12361)
* Update perl-math-random-mt-auto to 6.23 (#12362)
* Update kipoi to 0.6.3 (#12374)
* Update kipoi_veff to 0.2.1 (#12364)
* Update perl-object-insideout to 4.05 (#12380)
* Update sevenbridges-python to 0.17.1 (#12379)
* Update nanosv to 1.2.3 (#12378)
* Update starfish to 0.0.30 (#12368)
* Update clust to 1.8.10 (#12356)
* Update pypairs to 2.0.6 (#12381)
* Update khmer to 3.0.0a2 (#12360)
* Update flashlfq to 0.1.110 (#12385)
* Update perl-algorithm-cluster to 1.57 (#12384)
* Update arvados-python-client to 1.2.0.20181121194423 (#12382)
* Update avro-cwl to 1.8.9 (#12355)
* Update avro-cwl to 1.8.9
* Set noarch: python
* r-breakaway (#12386)
* R sads (#12388)
* Update python-sortedcontainers to 2.1.0 (#12383)
* r-ebimetagenomics (#12339)
* pin armadilo on major version (#12389)
* IgDiscover version 0.11 (#12351)
* IgDiscover version 0.11
* IgDiscover requires Python 3.6
* Fix build on macOS with a small patch
* Remove unneeded host dependencies
* Update goatools to 0.8.12 (#12391)
* Update bioconda-utils to 0.15.1 (#12390)
* R ebimetagenomics (#12393)
* Add dimspy recipes for reference purposes (#12387)
* Add dimspy recipes for reference purposes
* Remove filename
* remove from blacklist
* Update build-fail-blacklist
* Added BioExcel_SeqQC to bioconda-recipes (#12276)
* PacBio: Update pbalign to 0.3.2 (#12396)
* PacBio: Update pbalign to 0.3.2
Closes: PacificBiosciences/pbbioconda#39
* add bgreat to bioconda (#12350)
* bgreat addition
* zlib in build should not be needed
* btrim integration to conda (#12395)
* Format sleuth recipe. Trigger rebuild because latest version was never uploaded for some reason. (#12399)
* PacBio: Update `pbsv2` to version 2.1.0 (#12400)
* Genenotebook v0.1.11 (#12398)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* v0.1.10
* v0.1.11
* prosolo: new package version 0.6.0 (#12397)
* Update sevenbridges-python to 0.17.2 (#12404)
* Add recipe for ICED (#12406)
* Downgrade version for iced (#12409)
* Update recipe for libstatgen 1.0.5 (#12348)
* Add recipe for libstatgen-1.0.5
* Update iced to 0.5.0 (#12411)
* Update perl-test2-suite to 0.000116 (#12412)
* fix compatibility with other tools (#12415)
* Restore dexseq python helper scripts (#12352)
* Restore dexseq python helper scripts
* Add python requirement for helper scripts
* Add python noarch to build section
* pin it to python2k
* Add htseq requirement, support only python <3 for now
* Genenotebook v0.1.12 (#12418)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* v0.1.10
* v0.1.11
* v0.1.12
* updated source
* added medpy recipe (#12417)
* added medpy recipe
* removed osx from build
* Update meta.yaml
* Update meta.yaml
* add boost and a compiler
* Update meta.yaml
* Update meta.yaml
* add itk
* Updated ddrage to version 1.6.1. (#12421)
* Add r-mcpcounter recipe. (#12261)
* Add MCPcounter recipe.
* fix lint: remove 'fn'
* fix license_file, version number and doi
* Update DEXSeq requirements to force compatible HTSeq version (#12423)
* ARB: Pin glib (#11782)
* Pin glib
* Update meta.yaml
* Update meta.yaml
* Work around CB3 issues
* Work around bioconda-utils lint false positive
* Disable lint check should_not_be_noarch
* Can't reference other packages built in recipe from anything but run
* Move perl to host section. Maybe that helps.
* constraining interpreter version breaks with CB3?
* disable perl version constraint :(
* Update meta.yaml (#12426)
* stacks: fix for fix 'fixing' @ in exe_path (#12420)
* stacks: fix for fix 'fixing' @ in exe_path
the previous fix https://github.com/bioconda/bioconda-recipes/pull/11580
tried to solve the problem with the @ in the exe_path by setting this
variable empty. But the perl scripts
- append a / to the empty string an…
kpalin
pushed a commit
to kpalin/bioconda-recipes
that referenced
this issue
Aug 7, 2019
* update mzr as a test
* Begin building for R 3.5.1 (#11252)
* Bump everything for R 3.5.1
* Fix most of the linting issues
* Update blacklist
* Revert "Fix most of the linting issues"
This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5.
* should_not_use_fn
* More fixes
* Fix incorrect yaml
* Should really fix the linting blacklist stuff
* Fix many recipes
* Fix some linting
* Fix r-wicket
* Update derfinder
* Pin to a given bioconductor release.
* Add missing packages
* Restore identifiers to bioconductor packages
* Restore extra information to R packages
* Update R bulk (#11283)
* fixed incorrect doi of publication (#11175)
* Added recipe for kinSimRiboswitch (#10838)
Added recipe for kinSimRiboswitch, a pipeline for simulating the folding
kinetics of RNA switches.
* update multiqc-bcbio (#11187)
* Add recipe for PopDel (#11181)
* Add recipe for PopDel
* Add clang and clangxx to build config
* update seqbuster (#11190)
* update seqbuster
* fix build
* fix test
* Update pyseer to 1.1.2 (#11172)
* bump sourmash (#11197)
* Update BASIC to v1.4.1 (#11195)
* Update BASIC to v1.4.1
* Trigger circleci
* Fix build number
* Update nf-core-1.2 (#11191)
* Update nf-core-1.2
* Update build script
* Update to InterMine 1.11.0 (#11182)
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Add tinyfasta-0.1.0 (#11177)
* Add tinyfasta
* Update build script
* Fix structure of build section
* Bumping snippy (#11198)
* Remove older version
* Bump snippy
* VEP: bump major version (#11201)
* VEP: bump major version
* VEP: bumped plugin major version
* VEP: update plugin install
Download and install all plugin modules, instead of just a selection
* Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200)
* Update: PureCN to latest devel (1.11.13); wrapper scripts
PureCN development (https://github.com/lima1/PureCN) has several
improvements over the BioC 3.6 release for handling multiple VCF input
types, and is back compatible with R 3.4.1 so still builds cleanly
with two new dependencies.
Also exposes PureCN wrapper scripts for running from the command line.
Prefixes ambiguous scripts with PureCN_.
* Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet
* add cassiopee release 1.0.9 (#11168)
* add cassiopee release 1.0.9
* update to conda build 3
* remove old version backup and use sha256 for source
* Bump abeona version to 0.26.0 (#11202)
* Bump abeona version to 0.24.0
* Bump abeona version to 0.26.0
* Update LexMapr to v0.1.2 (#11192)
* Update LexMapr to v0.1.2
* Add rdflib dep
* Update svtyper to 0.7.0 (#11196)
* Update svtyper to 0.7.0
* Add recipe for perl-gtdbtk (#11194)
* Add recipe for perl-gtdbtk
* New recipe for RFMix (#11205)
* New recipe for RFMix
* updated version number information
* updated version number information
* updated version number information
* initial purge_haplotigs commit (#11049)
* initial purge_haplotigs commit
* bioconda revisions, updating test commands to run the pipeline on the test dataset
* rolling back test commands
* Add recipe for fsm-lite (#11209)
* Add recipe for fsm-lite
* Add prefix to make
* Remove v from version string
* Updated reparation_blast to version v.1.0.7 (#11210)
* Update sambamba to 0.6.8 (#11212)
* Bump sambamba to 0.6.8
* It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified.
* Set some environment variables
* The compiled binary is in a different place now
* ldc provides some libraries that are linked against.
* mtbseq: update recipe (#11110)
* changed download location/add test
* remove test
* Confindr (#11217)
* Update confindr to 0.4.2
* Fix typo in specifying version of pysam
* Update Genenotebook to v0.1.4 (#11218)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* updating to 0.1.3 (#11221)
* sartools1.6.6 (#11222)
* Perl bio automatedannotation (#11216)
* Initial recipe for Bio-AutomatedAnnotation
* Change URL
* Run cpanm tests
* Temporarily set HOME
* Use cpan version instead
* Add more depencencies
* Set bioperl version
* unset bioperl version, add bioperl-run
* New release including version in modules
* Remove comments
* build -> host
* Upgrade r-biodb to v1.1.2. (#11213)
* Upgrade r-biodb to v1.1.2.
* Remove old versions of r-biodb.
* Comment out libgfortran.
* PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215)
* PeptideShaker: updated to version 1.16.30
- Bugfix: HOME was still being used when folder with customised reports was specified.
- Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line.
* SearchGUI: updated to version 3.3.5.
- BUG FIX: Cleanup of the temp path options when used as options for the other command lines.
- FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2.
- LIBRARY UPDATE: Updated utilities to version 4.12.8.
* Update meta.yaml (#11227)
* Svtools 0.4.0 (#11208)
* Remove directories for old svtools versions
* Update svtools to v0.4.0
* Move build number back to 0
* Anvio 52 (#11230)
* Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software.
* Remove cgat-scripts from blacklist. (#11228)
* Add new formula: bazam 1.0.1 (#11229)
* Update gatk4 to 4.0.10.0 (#11224)
* Add recipe for gtdbtk 0.1.3 (#11211)
* Add recipe for gtdbtk
* Added initial htstream recipe (#11113)
* HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data.
* DeepTools 3.1.3 (#11226)
* PacBio: Update `pbmm2` to version 0.10.0 (#11225)
* fastqc: update to version 0.11.8 (#11214)
* fastqc: update to version 0.11.8
* Update meta.yaml
* Phame (#11223)
* mac recipe and added bioperl
* changing bill number
* added no osx
* adding new version
* removed separate recipe for mac, dont need it
* now running same recipe for mac and linux
* fixed the way fasttrees version was being parsed
* minor change test
* adding detailed description
* restaging the build number
* new version
* Make sure to use bioperl and perl 5.26
* Updated ngs-bits to version 2018_10 (#11235)
* PacBio: Update `pbsv2` to version 2.0.2 (#11236)
* Update VSEARCH to 2.8.5 (#11239)
* Fix shorah recipe and remove from blacklist. (#11241)
* Fix shorah recipe and remove from blacklist.
* Fix blas variant.
* Remove imports from tests.
* unicycler 0.4.7 (#11240)
* unicycler 0.4.7
* unicycler: Work around ValueError: invalid
Unicycler thinks the terminal has 0 columns and produces this error:
File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks
raise ValueError("invalid width %r (must be > 0)" % self.width)
ValueError: invalid width -5 (must be > 0)
* Octopus: update to 0.5.1-beta (#11244)
* New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247)
- PURPLE SV and heterogeneity caller for somatic tumor/normal samples.
- VarDictJava -- 1.5.6 release with fixes for SV calling
- PureCN -- add signature dependency and update with fixes for test
samples.
* Dinucleotide patterns analysis tools v1.0 (#11245)
* Dinucleotide patterns analysis tools v1.0
* Lets try it, it seems to work locally for me.
* Enable SpoTyping_plot.r (#11248)
* rerun again (#11233)
* rerun again
* Update meta.yaml
* Delete build.sh
* Update segway dependency optbuild to 0.2 (#10459)
* Update segway dependency optbuild to 0.2
* Update build and architecture requirements for optbuild 0.2
* Add six as a dependency to the optbuild recipe
* Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249)
* Add prefix dnp- to the package names
* Update build.sh
* Update build.sh
* Bump beast version to 1.10.2 (#11250)
* add maxquant (#11253)
* add mayquant
* relax tests
* PacBio: Update `pbmm2` to version 0.10.1 (#11256)
* PacBio: Update `pbmm2` to version 0.10.1-1 (#11257)
* remove xsv recipe (#11259)
* add blast dependency (#11258)
* Added riborex recipe (#11251)
* Added riborex recipe
* Relaxed version constraints
* Pinned r-core for fdr tools
* fixed the r-base stuff upstream
* Update meta.yaml
* fix graphprot (#11234)
* increase build number
* remove from blacklist
* use cxx instead of c
* move coreutoils to build section
* set additional paths
* patch makefile
* blind try
* update patch
* explicitely copy from src_dir
* update deprecated prefix variable
* Revert "update deprecated prefix variable"
This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d.
* update deprecated prefix variable
* try moving to host section
* Bump mash (#11264)
* Add fmlrc (#11265)
* Add fmlrc
* add doi
* PacBio: Update pb-falcon to 0.2.4. (#11266)
* Add kopt recipe (#11269)
* Genomepy 0.5.2 (#11267)
* release 0.5.2 of genomepy
* trigger new build
* remove genomepy from blacklist
* locale for osx
* updated locale test
* PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275)
* Update mmseqs2 recipe to new release 6-f5a1c (#11272)
* Update yacrd to version 0.4.1 (#11273)
* Add scprep (#11270)
* Add scprep
* All of these should not be needed as host dep
* Metawrap preqs2 (#11242)
* fixed issues
* fixed issues
* added tests
* fixed tab
* gemma 0.98 (#11254)
* gemma 0.98
* gemma 0.98
Leave gsl and zlib out of runtime dependencies
* Add DCA recipe (#11274)
* Add DCA recipe
* add noarch and doi
* remove skip
* Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib
* Various fixes for bulk and trigger a rebuild (#11313)
* Various fixes, at least 4 packages (and their dependencies) should still fail (#11320)
* A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336)
* Fix various recipes (#11354)
* Fix various recipes
* Fix more recipes
* Various CRAN package fixes, since they all lack license files (#11372)
* Various CRAN package fixes, since they all lack license files
* Fix the r-dartr recipe
* There is a light at the end of the tunnel (#11381)
* There is a light at the end of the tunnel
* Licenses no longer exist
* [BULK] Fixes for R/Bioconductor packages (#11406)
* Require `r-base >=3.5` for some packages
* Fix various CRAN packages lacking license file
* Add missing libnetcdf requirement to bioconductor-mzr
* Remove r-alakazam (moved to conda-forge)
Fix linting issue:
```
recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating
```
* [BULK] Many R 3.5 only packages (#11410)
* [BULK] Bulk update 191018b (#11419)
* update mzr as a test
* Begin building for R 3.5.1 (#11252)
* Bump everything for R 3.5.1
* Fix most of the linting issues
* Update blacklist
* Revert "Fix most of the linting issues"
This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5.
* should_not_use_fn
* More fixes
* Fix incorrect yaml
* Should really fix the linting blacklist stuff
* Fix many recipes
* Fix some linting
* Fix r-wicket
* Update derfinder
* Pin to a given bioconductor release.
* Add missing packages
* Restore identifiers to bioconductor packages
* Restore extra information to R packages
* Update R bulk (#11283)
* fixed incorrect doi of publication (#11175)
* Added recipe for kinSimRiboswitch (#10838)
Added recipe for kinSimRiboswitch, a pipeline for simulating the folding
kinetics of RNA switches.
* update multiqc-bcbio (#11187)
* Add recipe for PopDel (#11181)
* Add recipe for PopDel
* Add clang and clangxx to build config
* update seqbuster (#11190)
* update seqbuster
* fix build
* fix test
* Update pyseer to 1.1.2 (#11172)
* bump sourmash (#11197)
* Update BASIC to v1.4.1 (#11195)
* Update BASIC to v1.4.1
* Trigger circleci
* Fix build number
* Update nf-core-1.2 (#11191)
* Update nf-core-1.2
* Update build script
* Update to InterMine 1.11.0 (#11182)
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Add tinyfasta-0.1.0 (#11177)
* Add tinyfasta
* Update build script
* Fix structure of build section
* Bumping snippy (#11198)
* Remove older version
* Bump snippy
* VEP: bump major version (#11201)
* VEP: bump major version
* VEP: bumped plugin major version
* VEP: update plugin install
Download and install all plugin modules, instead of just a selection
* Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200)
* Update: PureCN to latest devel (1.11.13); wrapper scripts
PureCN development (https://github.com/lima1/PureCN) has several
improvements over the BioC 3.6 release for handling multiple VCF input
types, and is back compatible with R 3.4.1 so still builds cleanly
with two new dependencies.
Also exposes PureCN wrapper scripts for running from the command line.
Prefixes ambiguous scripts with PureCN_.
* Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet
* add cassiopee release 1.0.9 (#11168)
* add cassiopee release 1.0.9
* update to conda build 3
* remove old version backup and use sha256 for source
* Bump abeona version to 0.26.0 (#11202)
* Bump abeona version to 0.24.0
* Bump abeona version to 0.26.0
* Update LexMapr to v0.1.2 (#11192)
* Update LexMapr to v0.1.2
* Add rdflib dep
* Update svtyper to 0.7.0 (#11196)
* Update svtyper to 0.7.0
* Add recipe for perl-gtdbtk (#11194)
* Add recipe for perl-gtdbtk
* New recipe for RFMix (#11205)
* New recipe for RFMix
* updated version number information
* updated version number information
* updated version number information
* initial purge_haplotigs commit (#11049)
* initial purge_haplotigs commit
* bioconda revisions, updating test commands to run the pipeline on the test dataset
* rolling back test commands
* Add recipe for fsm-lite (#11209)
* Add recipe for fsm-lite
* Add prefix to make
* Remove v from version string
* Updated reparation_blast to version v.1.0.7 (#11210)
* Update sambamba to 0.6.8 (#11212)
* Bump sambamba to 0.6.8
* It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified.
* Set some environment variables
* The compiled binary is in a different place now
* ldc provides some libraries that are linked against.
* mtbseq: update recipe (#11110)
* changed download location/add test
* remove test
* Confindr (#11217)
* Update confindr to 0.4.2
* Fix typo in specifying version of pysam
* Update Genenotebook to v0.1.4 (#11218)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* updating to 0.1.3 (#11221)
* sartools1.6.6 (#11222)
* Perl bio automatedannotation (#11216)
* Initial recipe for Bio-AutomatedAnnotation
* Change URL
* Run cpanm tests
* Temporarily set HOME
* Use cpan version instead
* Add more depencencies
* Set bioperl version
* unset bioperl version, add bioperl-run
* New release including version in modules
* Remove comments
* build -> host
* Upgrade r-biodb to v1.1.2. (#11213)
* Upgrade r-biodb to v1.1.2.
* Remove old versions of r-biodb.
* Comment out libgfortran.
* PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215)
* PeptideShaker: updated to version 1.16.30
- Bugfix: HOME was still being used when folder with customised reports was specified.
- Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line.
* SearchGUI: updated to version 3.3.5.
- BUG FIX: Cleanup of the temp path options when used as options for the other command lines.
- FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2.
- LIBRARY UPDATE: Updated utilities to version 4.12.8.
* Update meta.yaml (#11227)
* Svtools 0.4.0 (#11208)
* Remove directories for old svtools versions
* Update svtools to v0.4.0
* Move build number back to 0
* Anvio 52 (#11230)
* Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software.
* Remove cgat-scripts from blacklist. (#11228)
* Add new formula: bazam 1.0.1 (#11229)
* Update gatk4 to 4.0.10.0 (#11224)
* Add recipe for gtdbtk 0.1.3 (#11211)
* Add recipe for gtdbtk
* Added initial htstream recipe (#11113)
* HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data.
* DeepTools 3.1.3 (#11226)
* PacBio: Update `pbmm2` to version 0.10.0 (#11225)
* fastqc: update to version 0.11.8 (#11214)
* fastqc: update to version 0.11.8
* Update meta.yaml
* Phame (#11223)
* mac recipe and added bioperl
* changing bill number
* added no osx
* adding new version
* removed separate recipe for mac, dont need it
* now running same recipe for mac and linux
* fixed the way fasttrees version was being parsed
* minor change test
* adding detailed description
* restaging the build number
* new version
* Make sure to use bioperl and perl 5.26
* Updated ngs-bits to version 2018_10 (#11235)
* PacBio: Update `pbsv2` to version 2.0.2 (#11236)
* Update VSEARCH to 2.8.5 (#11239)
* Fix shorah recipe and remove from blacklist. (#11241)
* Fix shorah recipe and remove from blacklist.
* Fix blas variant.
* Remove imports from tests.
* unicycler 0.4.7 (#11240)
* unicycler 0.4.7
* unicycler: Work around ValueError: invalid
Unicycler thinks the terminal has 0 columns and produces this error:
File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks
raise ValueError("invalid width %r (must be > 0)" % self.width)
ValueError: invalid width -5 (must be > 0)
* Octopus: update to 0.5.1-beta (#11244)
* New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247)
- PURPLE SV and heterogeneity caller for somatic tumor/normal samples.
- VarDictJava -- 1.5.6 release with fixes for SV calling
- PureCN -- add signature dependency and update with fixes for test
samples.
* Dinucleotide patterns analysis tools v1.0 (#11245)
* Dinucleotide patterns analysis tools v1.0
* Lets try it, it seems to work locally for me.
* Enable SpoTyping_plot.r (#11248)
* rerun again (#11233)
* rerun again
* Update meta.yaml
* Delete build.sh
* Update segway dependency optbuild to 0.2 (#10459)
* Update segway dependency optbuild to 0.2
* Update build and architecture requirements for optbuild 0.2
* Add six as a dependency to the optbuild recipe
* Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249)
* Add prefix dnp- to the package names
* Update build.sh
* Update build.sh
* Bump beast version to 1.10.2 (#11250)
* add maxquant (#11253)
* add mayquant
* relax tests
* PacBio: Update `pbmm2` to version 0.10.1 (#11256)
* PacBio: Update `pbmm2` to version 0.10.1-1 (#11257)
* remove xsv recipe (#11259)
* add blast dependency (#11258)
* Added riborex recipe (#11251)
* Added riborex recipe
* Relaxed version constraints
* Pinned r-core for fdr tools
* fixed the r-base stuff upstream
* Update meta.yaml
* fix graphprot (#11234)
* increase build number
* remove from blacklist
* use cxx instead of c
* move coreutoils to build section
* set additional paths
* patch makefile
* blind try
* update patch
* explicitely copy from src_dir
* update deprecated prefix variable
* Revert "update deprecated prefix variable"
This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d.
* update deprecated prefix variable
* try moving to host section
* Bump mash (#11264)
* Add fmlrc (#11265)
* Add fmlrc
* add doi
* PacBio: Update pb-falcon to 0.2.4. (#11266)
* Add kopt recipe (#11269)
* Genomepy 0.5.2 (#11267)
* release 0.5.2 of genomepy
* trigger new build
* remove genomepy from blacklist
* locale for osx
* updated locale test
* PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275)
* Update mmseqs2 recipe to new release 6-f5a1c (#11272)
* Update yacrd to version 0.4.1 (#11273)
* Add scprep (#11270)
* Add scprep
* All of these should not be needed as host dep
* Metawrap preqs2 (#11242)
* fixed issues
* fixed issues
* added tests
* fixed tab
* gemma 0.98 (#11254)
* gemma 0.98
* gemma 0.98
Leave gsl and zlib out of runtime dependencies
* Add DCA recipe (#11274)
* Add DCA recipe
* add noarch and doi
* remove skip
* Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib
* Various fixes for bulk and trigger a rebuild (#11313)
* Various fixes, at least 4 packages (and their dependencies) should still fail (#11320)
* A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336)
* Fix various recipes (#11354)
* Fix various recipes
* Fix more recipes
* Various CRAN package fixes, since they all lack license files (#11372)
* Various CRAN package fixes, since they all lack license files
* Fix the r-dartr recipe
* There is a light at the end of the tunnel (#11381)
* There is a light at the end of the tunnel
* Licenses no longer exist
* [BULK] Fixes for R/Bioconductor packages (#11406)
* Require `r-base >=3.5` for some packages
* Fix various CRAN packages lacking license file
* Add missing libnetcdf requirement to bioconductor-mzr
* Remove r-alakazam (moved to conda-forge)
Fix linting issue:
```
recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating
```
* [BULK] Many R 3.5 only packages (#11410)
* Update pinning to R>=3.5 and a few runtime dependencies.
* CSAW is R 3.5 only
* Packages using beachmat are 3.5 only
* Packages using bioconductor-singlecellexperiment are R 3.5 only
* [BULK] Don't use r-base >=3.5, use a conda_build_config.yaml instead (#11452)
* Don't use r-base >=3.5, use a conda_build_config.yaml instead
* blacklist r-phangorn
* Update variancepartition
* R 3.5 for packages requiring singlecellexperiment
* Update a few packages
* Update a number of recipes (#11482)
* Update ensemblVEP and derfinder (#11504)
* Bulk update 251018 (#11577)
* [BULK] various package updates
* blacklist bioconductor-mzr
* A couple tweaks
* [BULK] Update 261018 (#11611)
* Apparently the r-rgeos bit works properly now.
* Add tissueenrich and try to fix scpipe on Linux
* A meaningless change just to trigger an update in bulk. (#11618)
* [BULK] update 271018 (#11628)
* Bump bioconductor-esetvis
* Fix yaqcaffy
* Fix more
* Another R 3.5 recipe
* [BULK] update 281018 (#11689)
* Add some files
* Fix arrayexpress
* Fix another 2
* Blacklist a bunch of bioconductor recipes that aren't likely to get built for a variety of reasons (mostly due to mzR). (#11697)
* Update blacklist (#11706)
* [BULK] fix bioconductor-tissueenrich (#11720)
* taxonkit 0.2.5 (#11318)
* Update csvtk (#11319)
* taxonkit 0.2.5
* csvtk 0.15.0
* bumping GROOT to 0.8.1 (#11323)
* HiCMatrix version 3 (#11322)
* Correcting dependencies
* Version 3 of HiCMatrix, the October release
* Update confindr to 0.4.3 (#11330)
* Drop-seq_tools: Version 2.0.0 (#11326)
* Update meta.yaml
* Update build.sh
some tool names changed to fit Camel case
* Update motus to build only for python3 (#11331)
* Update fpa to 0.2 version (#11333)
* update taxonkit to 0.3.0 (#11339)
* ntcard 1.1.0 (#11338)
* Update rgi (#11335)
* first commit
* update dependencies list
* change source to github
* change build number
* testing circleci
* update meta and build
* fix build
* move build script into meta
* remove older recipes
* line fix in bootstrap.py
* change python & matplotlib versions; add build.sh file
* add preprocessing selector to skip python 2.7
* move build script into meta.yaml
* Revert "line fix in bootstrap.py"
This reverts commit 5ac1ecd0142a5cfdfc8499c5b6ef4e1f629cd046.
* Update gmap to version 2018-07-04. (#11332)
MAX_READLENGTH environment variable has been disused since 2016-08-16.
* Upgrade r-biodb to 1.2.0a. (#11341)
* Upgrade r-biodb to 1.2.0a.
* Update meta.yaml
* Updated ont-tombo to version 1.5. (#11329)
* Updated ont-tombo to version 1.5.
* Updated with actual github release version hash.
* remove graphicsmagick (#11342)
* Build kraken2 for osx (#11343)
* First try for a bcalm recipes (#11344)
* New: cgpbigwig (BigWig manipulation); Update: bcbio (#11347)
- cgpbigwig (https://github.com/cancerit/cgpBigWig) provides bigwig
generation and manipulation command line tools including bam to bigwig
conversion.
- bcbio: fixes for QC on variants and peddy for CWL runs
* Try avoid some dependancy (#11349)
* Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8 (#11348)
* Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8
Also add about:home .
* Workaround https://github.com/conda-forge/bison-feedstock/issues/7
* Better bcalm recipes (#11350)
* Try avoid some dependancy
* Correct mess in build number, sorry
* R biodb (#11351)
* rebuild r-biodb
* trigger build
* Add recipe for pypairs (#11356)
* Update smoove to 0.2.1. (#11360)
* Update duphold to 0.0.9. (#11359)
* Update goleft to 0.2.0 (#11361)
* Bump slicedimage to 1.0.0 (#11362)
* Bump slicedimage to 1.0.1 (#11365)
* Added new versions for biopet-sampleconfig (#11268)
* perl-velvetoptimiser: update to 2.2.6 (#11369)
* update to 2.2.6
* remove unneeded patch
* Scanpy upgrade (#11371)
* Bump version
* Upgrade Scanpy
* Bump starfish to 0.0.25 (#11370)
* bumping groot to 0.8.2 (#11374)
* vep: bump subversion (#11367)
* Updated Krocus 1.0.1 (#11355)
* Add tiptoft
* Fix meta.yaml for tiptoft
* Add build script
* Updated krocus 1.0.1
* Add tiptoft 0.1.4 (#11352)
* Add tiptoft
* Fix meta.yaml for tiptoft
* Add build script
* Kodoja v0.0.9 (#11373)
* Add recipe for seer (#11263)
* Add recipe for seer
* lets try this
* Add newer compiler
* Using boost-cpp
* messed up version string
* Attempt building boost
* Use c++11 in boost
* Use python for boost install
* Correct python version spec
* try with different python version
* Fix b2 command
* Fix popd command
* build and link boost program options statically
* Fix tests
* Match dependency order
* Link openblas instead of blas
* Forcing rebuild with openblas
* Don't use armadillo wrapper
* Making review changes. Also trying original tests
* Previous tests were correct
* Add recipe for the translate-gard npm package version 1.0.3 (#11364)
* Fix umi tools (#11376)
umi_tools: clean up dependencies
* add support tools to PATH (#11379)
* Bump to v2.2.1 (#11380)
* Bump starfish to 0.0.26 (#11378)
* Update fpa to 0.3 (#11375)
* Update fpa to 0.3
* Correct error in sha256
* Reset build number
* Update trial to 2.5.5 (#11386)
* Update: bioconductor-titancna; 1.19.1 with hg38 support (#11388)
* Update: bioconductor-titancna; 1.19.1 with hg38 support
* Pin to R 3.4 to avoid pulling in 3.3 and 3.5 during mulled
* Add r-polysat version 1.7-3 (#11384)
* Update biomart version so that compatible with r351 (#11366)
* Update biomart version so that compatible with r351
* Update meta.yaml
reset build number as per https://bioconda.github.io/guidelines.html#buildnum
* Update entrez-direct to 10.0.20180927. (#11387)
* Added recipe for SonicParanoid 1.0.13 (#11271)
* Added recipe for SonicParanoid 1.0.13
* removed 'x.x' for numpy, added basic test
* fixed linter related errors
* compiler set to cxx and added host section (same build error!)
* removed host section
* moved numpy and cython to host section; restored build: noarch: python; added LICENSE.md
* removed build: noarch
* added build and extra sections
* set build number to 0; removed skip build; added python3 minimum version; added test for all executables.
* restored sh python module as requirement
* added Make to run; updated release to latest commit
* remove c compiler from meta.yaml
* modified build.sh to compile source codel added make in build section
* updated to latest commit
* updated to latest version with make included in setup.py
* reverted build.sh to the simplest version (python setup.py install)
* Add perl-json to build requirements to allow meme-chip to run to completion. Change meme-chip to use dreme-py3 instead of dreme if building with python 3. (#11389)
* Bump IgBLAST to 1.9.0 (#11393)
Bump IgBLAST to 1.9.0
Re-package the binary version this time. There are problems building the
source version when the configure script reaches this step:
"trying to build the NCBI SRA/VDB Toolkit from GitHub"
The previous problem about the binaries linking against libbz2.so, for
which we had no conda package, is now solved.
Also, this saves about 45 minutes compilation time.
* Add consan (#11395)
* Add consan
* Skip osx
* Update: vardict, vardict-java 1.5.7 (#11394)
* Update: vardict, vardict-java 1.5.7
Latest vardict-java release and corresponding vardict with bug fixes
after testing with 1.5.6
* Reduce test output to try and fix build problems
* Experiment 2 for build problems: remove r-base from run
* Experiment 3 for build problems: add r-base in host
* update recipe for 3.9.1 (#11397)
* evofold2 (#11396)
* evofold2
* wrapper
* Update meta.yaml
* minor
* Update rnastructure to 6.1. (#11400)
* Ctat mut (#11401)
* updating version number
* correct URL
* proper hash
* Revert "Ctat mut (#11401)" (#11402)
This reverts commit 6db10ac7ffd7abaf8fbf1762b7ea6c63b2585fe0.
* update version (#11403)
* any2fasta 0.4.2 (new formula) (#11407)
* W4mclassfilter v0.98.9 (#11385)
* Added files to build version 0.98.9
* Update meta.yaml
* Update meta.yaml
* updated SonicParanoid recipe to version 1.0.14 (#11409)
* updated SonicParanoid recipe to version 1.0.14
* Update to version 1.0.2 of PopDel (#11398)
* Update to version 1.0.2 of PopDel
Update to version 1.0.2.
* Reset build number to 0
* PacBio: require Meson 0.48.1 for all recipes (#11090)
* Meson 0.47 inserted duplicate RPATHs in
macOS binaries, causing `install_name_tool`
failures when installing the package.
Requiring 0.48.1 ensures we do not run into
these issues anymore in the future.
* rebuild with latest openmpi (#11411)
* Remove kfoots from the blacklist (#11416)
* Update gseapy to 0.9.7 (#11417)
* Update gseapy to 0.9.7
* remove noarch
* Add SC3 as dependency (#11427)
* Add recipe for r-poppr (#11418)
* Update knitr version because of Issue: https://github.com/rstudio/rmarkdown/pull/1271 (#11412)
* Update IQ-TREE to 1.6.7.1 (#11429)
* Update IQ-TREE to 1.6.7.1
* Change build number
* Update: r-deconstructsigs with fixes for hg38 (#11431)
The 1.8.0 release, from 2016, has some issues with hg38 and other
custom genomes that are fixed in development (raerose01/deconstructSigs#27).
There hasn't been a new release pushed so this rolls these into a new
sub-version and makes them available.
* Update entrez-direct to 10.2.20181018. (#11432)
* Add assembly-scan recipe (#11425)
* remove python 2.7 skip (#11424)
Preparation for rnaQUAST
* Add fastq-scan recipe (#11415)
* Add patch to fix racon/rampler path in racon_wrapper. (#11434)
Fixes #11405.
* meme rebuild (#11433)
* Update nanocomp to 0.23.1 (#11436)
* Update nanocomp to 0.23.1
* remove noarch
* Update abricate to 0.8.10 (#11446)
* Update angsd to 0.923 (#11445)
* Update alfred to 0.1.13 (#11444)
* Update alfred to 0.1.13
* Try w/o patch
* Update antarna to 2.0.6 (#11442)
* Update admixtools to 5.1 (#11443)
* Update admixtools to 5.1
* Let makefile choose which bins to install
* Update alignstats to 0.5 (#11441)
* Update xatlas to 0.2.1 (#11437)
* r-gpca (#11428)
* r-gpca
* r-gpca recipe
* Update meta.yaml
* Removed All Comments
* gseapy bump version 0.9.8 (#11440)
* gseapy bump version 0.9.8
* version
* titancna: fix for hg38, remove conda build hacks (#11447)
* titancna: fix for hg38, remove conda build hacks
* Re-add r-base 3.4 pin to avoid 3.5 errors
* Hmmlearn older version (#11450)
* Adding pygtftk
* removed pygtftk from master
* add older version of hmmlearn
* Add card_trick (#11451)
* Add card_trick
* Restrict to py3
* Update checkm-genome to 1.0.12 (#11455)
* Bump drep (#11457)
* Update squid to 1.5 (#11466)
* Update ncbi-ngs-sdk to 2.9.3 (#11467)
* elprep: bumped major version (#11414)
* elprep: bumped major version
* fixed hash
* fix download link, fixed licence
* fixed tests
* skip osx build
* FRED2 as a conda package (#11469)
* Attempt to get FRED2 as a conda package
* SHA update
* 99 little bugs in the code
* Fix things Björn mentioned
* add rnaQUAST recipe (#11470)
* Update bioconda-utils to 0.14.9 (#11454)
* Rapidup (#11474)
* Update to v0.7
* Update Buildnumber
* rapid: update to v0.6
* rapid: update to v0.6
* update grid (#11478)
* Adding biobb_model recipe (#11472)
* Updated wtdbg to v2.1 (#11486)
* update stream to 0.2.6 (#11483)
* update stream to 0.2.2
* update stream to 0.2.3
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.5
* update stream to 0.2.6
* Update meta.yaml (#11487)
* Update connectome-workbench to 1.3.2 (#11468)
Now needs QT 5.7
* Update deblur to 1.1.0 (#11500)
* Update domclust to 1.2.8 (#11498)
* WisecondorX: bump version (#11501)
* Bump as GitHub wasn't working yesterday (#11502)
* Added recipe for Sequenza (#10367)
* Added recipe for Sequenza
* Removed fn entry in source section
* Trying with only one URL
* copynumber is a bioconductor package
* Added missing requirements section
* Removed mailing list address
* Added doi
* Added license_file
* Trying with different license_file path
* Fred2 bump (#11503)
* Bump as GitHub wasn't working yesterday
* Fix licence etc
* Scanpy scripts (#11413)
Doing squash and merge as requested by @nh3
* Bump version
* First implementation of scanpy-scripts bioconda recipe.
* fix path in build.sh
* Remove "noarch" flag as requested by bioconda recipe checklist
* Add a post install notice that post install test needs bats-core.
* Add more dependencies
* Skip building for python versions other than 3.6
* Target v0.0.2 which has non-ascii characters removed
* Lower version requirement for pandas and matplotlib to be the same as scanpy
* Requirement matplotlib>=3.0.0, declare noarch
* New: hmftools-cobalt; Update: hmftools-purple (#11507)
- hmftools-cobalt: Add latest version of PURPLE associated read counter,
COBALT, with support for hg38.
- hmftools-purple: PURPLE release with hg38 support.
* Update Picard to 2.18.15. (#11505)
* Genenotebook (#11476)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* Update pinning (#11514)
* Bump build number for updated dependency (#11510)
* Bump build number for updated dependency
* Try adding r-base to host requirements
* Try adding other requirements to host
* Pin to R version
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Tweak dependency version syntax
* Pin R and package versions correctly
* PacBio: Update pbcore to 1.6.5 (#11513)
* Bump r seurat scripts version (#11292)
* Bump version
* Remove noarch
* Could wrongly quoted version be causing an issue?
* Tweak pinning to try and fix CI error
* seqcluster:fix UMI detection. (#11511)
* seqcluster:fix UMI detection.
* Fix dependency
* quast 5.0.1 (#11479)
* quast 5.0.1
* quast 5.0.1: remove third-party site packages from the distibution pack
* quast 5.0.1: skip Glimmer in test
* quast 5.0.1: joblib and simplejson dependencies added to meta.yaml (Setuptools downloading is disabled in conda build)
* quast 5.0.1: explicit joblib and simplejson dependencies removed (Setuptools downloading is disabled in conda build)
* quast 5.0.1: Python 2 and 3 compatible code in build.sh
* wcX bugfixes (#11508)
* wcX bugfixes
* fixed shasum
* Update fastspar to 0.0.7 (#11515)
* Update iqtree to 1.6.7.2 (#11525)
* Update illumina-interop to 1.1.6 (#11523)
* Update hapbin to 1.3.0 (#11522)
* Update hlama to 3.0.1 (#11520)
* Update gb_taxonomy_tools to 1.0.1 (#11519)
* Update gffcompare to 0.10.5 (#11517)
* Update fast5seek to 0.1.1 (#11516)
* Update deepbinner to 0.2.0 (#11499)
* Update deepbinner to 0.2.0
* Update meta.yaml
Try same fix as in #11240
* Update ncbi-vdb to 2.9.3 (#11550)
* Update mikado to 1.2.4 (#11549)
* Update perl-pcap to 3.5.2 (#11543)
* Update python-hyphy-python to 0.1.9 (#11545)
* Update mlst to 2.15.2 (#11547)
* Update perl-sanger-cgp-vcf to 2.2.1 (#11542)
* Update merfishtools to 1.5.0 (#11537)
* Update perl-sanger-cgp-vagrent to 3.3.3 (#11536)
* Update nonpareil to 3.3.3 (#11535)
* Update prophex to 0.1.1 (#11532)
* Update krakenuniq to 0.5.3 (#11527)
* Update novoplasty to 2.7.2 (#11530)
* Update minced to 0.3.2 (#11529)
* Update mapdamage2 to 2.0.8 (#11528)
* Update perl-sanger-cgp-allelecount to 4.0.0 (#11538)
* Update pyvolve to 0.9.0 (#11531)
* Genenotebook (#11512)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* add plek (#11554)
* Update pyimzml to 1.2.4 (#11534)
* Bump shovill (#11555)
* PacBio: Update minimum pbcore version (#11556)
* We want all users of PacBio tools to be able to
use our utilities with pbmm2 alignments.
* Add recipe for translate-gard v1.0.4 (#11557)
* bioconductor-rnaseqsamplesizedata (#11475)
* Adding Recipe for bioconductor-rnaseqsamplesizedata
* Updated metadata for RnaSeqSampleSizeData
* nextflow 18.10.1 (#11558)
* Update raxml to 8.2.12 (#11567)
* Update r-fgwas to 0.3.6 (#11566)
* Update rapid to 0.7 (#11565)
* Update r-spieceasi to 1.0.2 (#11564)
* Update rcorrector to 1.0.3.1 (#11562)
* Update quicktree to 2.4 (#11560)
* Update paladin to 1.4.4 (#11541)
* Update paladin to 1.4.4
* delete md5
* Update build.sh
* Update build.sh
* Fix and unblacklist Tadarida-D (#11568)
* Add recipe for rgt
* Fix and un-blacklist tadarida-d
* Remove RGT
* bumping groot (#11575)
* update pymzml (#11573)
* Add bioconductor-rnaseqsamplesize (#11559)
* Add bioconductor-rnaseqsamplesize
* Update recipe
* Fixing some URLs
* Update dependencies missing
* Update trumicount to 0.9.11 (#11576)
* Update ConFindr to 0.4.4 (#11578)
* Added new versions for biopet-scatterregions (#11572)
* Added new versions for biopet-bamstats (#11571)
* R ggbiplot (#11584)
* add R -e 'httr::set_config(httr::config(ssl_verifypeer = 0L)); install.packages(devtools, repos=http://mirrors.ebi.ac.uk/CRAN/); library(devtools); install_github(vqv/ggbiplot); library(ggbiplot)'
* add r-ggbiplot
* update meta.yaml
* update meta.yaml
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix errors
* fix errors number 1
* Update rebaler to 0.1.2 (#11563)
* Update rebaler to 0.1.2
* Remove fn
* bump graphclust (#11585)
* Update seqyclean to 1.10.09 (#11589)
* Update stringmlst to 0.5.1 (#11590)
* Update snp-dists to 0.6.2 (#11592)
* Update snippy to 4.3.3 (#11596)
* Update canu to 1.8 (#11600)
* Update starfish to 0.0.27 (#11599)
* Update womtool to 36 (#11594)
* Update telseq to 0.0.2 (#11598)
* Update snp-sites to 2.4.1 (#11588)
* Added recipe for pydemult: Streamed and parallel demultiplexing of fastq files (#11471)
* Added recipe for pydemult
* Bumped version in favor of py3.5
* bump vcf2db to latest commit (#11601)
* bump vcf2db to latest commit
* fix shasum
* Fixing source url
* Update: TitanCNA; hg38 cytoband support and fix for normalization (#11604)
* megan (#11046)
* megan6: initial commit
* megan6: intermediate commit
* megan: made tests work
* megan: doc improvement
* megan: added osx dmg file
* megan: add java to build requirements
* megan: removed new line
* megan: removed osx sources
* Update meta.yaml
* bumping hulk (#11607)
* Update hotspot3d to 1.8.2 (#11521)
* Update hotspot3d to 1.8.2
* Add perl-json as dependency
* Add perl-archive-extract as dependency
* Fqzcomp (#11606)
* Added recipe for fqzcomp
* There is no configure script
* Maybe this works
* Added gcc as build requirement
* Removed gcc again (lint issue)
* Maybe these exports will do the trick
* Nope!
* Added cxx as host requirement
* Compilers are only allowed in build section
* There is no need for make install
* Copy-paste error...
* Add vcf-annotator recipe (#11481)
* Add vcf-annotator recipe
* added pyvcf dependency
* Update meta.yaml
* stacks: fix for @ in exe_path (#11580)
* stacks: fix for @ in exe_path
* stacks: fixed path
* New version with bugfix and different progressiveMauve version. (#11613)
* Sspupdate (#11614)
* New version with bugfix and different progressiveMauve version.
* Keeping old version as folder.
* Push build number.
* Update SVDB to version 1.3.0 (#11506)
* new file: recipes/svdb/1.1.2/meta.yaml
renamed: reipes/svdb/svdb.patch -> recipes/svdb/1.1.2/svdb.patch
modified: recipes/svdb/meta.yaml
* deleted: 1.1.2/meta.yaml
deleted: 1.1.2/svdb.patch
* Bump nanosim (#11608)
* Bump nanosim
* Add scipy as dep
* Add recipe for perl-number-range (#11621)
* New build for grid (#11620)
* update grid
* update build num
* Recipe for das_tool 1.1.1 (#10528)
* recipe for das_tool 1.1.1
* Add recipe for sompy (#11624)
* cmake modified to build with NDEBUG (#11328)
* cmake modified to build with NDEBUG
* Update meta.yaml
* new build with fasta test
* new build with fasta test
* Fix and unblacklist TwoPaCo (#11622)
* Add recipe for TwoPaCo
* Unblacklist twopaco
* Modify and unblacklist recipe for ESTmapper (#11623)
* Modify and unblacklist recipe for ESTmapper
* Add patch
* Modify and unblacklist recipe for Metaseq (#11625)
* Fix recipe for metaseq and remove from blacklist
* Remove build.sh
* nextflow 18.10.1 build 2 (#11630)
* Add Clust (#11619)
* Add clust
* Clean recipe
* Add "noarch"
* Add DOI
* Add build file
* Python 2.7
* Fix scikit-learn dependency
* Trigger new build
* Update: PureCN (multicore) and PURPLE (plotting X libraries) (#11631)
- PureCN: adds support for specifying cores on command line
- PURPLE: adds X library dependencies required for creating
plots
* scripts/travis-run.sh: added a cleaner method to check for env vars (#11612)
* Increase the number of k value usable in bcalm (request by @Malfoy) (#11610)
* Increase the number of k value usable in bcalm (request by @Malfoy)
* Change compilation parameter to reduce memory impact of compilation
* Update anndata to 0.6.11 (#11637)
* Update nglview to 1.1.7 (#11643)
* Update binsanity to 0.2.7.1 (#11644)
* Update cgat-core to 0.5.4 (#11645)
* Update nanosv to 1.2.2 (#11673)
* Update abeona to 0.36.0 (#11670)
* Update pyfaidx to 0.5.5.2 (#11659)
* Update agfusion to 1.23 (#11668)
* Update iqtree to 1.6.8 (#11686)
* update iqtree to 1.6.8
* Trigger rebuild
* Update validators to 0.12.2 (#11672)
* Update python-edlib to 1.2.3.post1 (#11664)
* update for Purge Haplotigs (#11690)
* Update loompy to 2.0.16 (#11667)
* Update loompy to 2.0.16
* Update meta.yaml
* IgBLAST 1.10.0 (#11693)
* Update wtforms-alchemy to 0.16.7 (#11679)
* Update sickle to 0.6.4 (#11663)
* Update sickle to 0.6.4
* Remove fn and libgcc runtime dep
* Update confindr to 0.4.5 (#11696)
* Batvi (#11695)
* batvi initial
* Guideline compatibility..
* Dummy test section..
* Missing java dependency..
* use openjdk instead of java-jdk ..
* source specified in github ..
* trigger build (package did not have batindel directory) ..
* update SHA256 ..
* update SHA256 ..
* Update pythonpy to 0.4.11 (#11661)
* Update cortexpy to 0.45.6 (#11660)
* Update sevenbridges-python to 0.16.0 (#11674)
* Update solvebio to 2.7.0 (#11657)
* Update mathstats to 0.2.6.5 (#11656)
* Update goatools to 0.8.9 (#11641)
* Add gnies (#11627)
* Add gnies
* noarch python
* Update meta.yaml
* Add recipe for SKA v1.0 (#11581)
* Add recipe for SKA v1.0
* Add lib path for zlib
* Older gcc
* Correct install dir
* Try static linking
* Dynamic linking on OS X
* ldd command test
* correct program
* Remove ldd command
* Add recipe for transit version 2.3.1 (#11701)
* Add recipe for transit version 2.3.1
* Use skip, add spaces.
* Update meta.yaml (#11699)
* remove pyqi (#11704)
* Update python-chado to 2.2.0 (#11714)
* update python-chado
* 2.2.1
* Update vcfanno to 0.3.1 (#11710)
* FGMP-1.0.1 (#11278)
* FGMP-1.0.1 recipe
* remove unncessary build info
* add r-nabor (#11716)
* update stream to 0.2.2
* update stream to 0.2.3
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.4
* update stream to 0.2.5
* update stream to 0.2.6
* add r-nabor recipe
* update r-nabor recipe
* update r-nabor recipe
* r-pctgcdata (#11715)
* r-pctgcdata
* r-pctgcdata - fix
* r-pctgcdata - fix
* Update meta.yaml
* Fix plek by a new branch (#11605)
* Modify the PLEK recipe
* Start fixing PLEK, though it requires compilation
* update build.sh
* update yaml
* fix build.sh
* update build.sh
* Update recipe for plek
* add bioconductor-chromvar recipe (#11718)
* add bioconductor-chromvar recipe
* fix bioconductor-tissueenrich
* Apparently the popdel recipe didn't get correctly merged
* Final merge conflicts
* Bioc quick test (#12547)
* Update kallisto to 0.45.0 (#12117)
* Update validators to 0.12.3 (#12116)
* Update illumina-interop to 1.1.7 (#12115)
* Update umi_tools to 0.5.5 (#12123)
* Update tiptoft to 1.0.0 (#12122)
* Update: TitanCNA with fix for hg38 plotting (#12130)
* blockclust (#12111)
* added eden 1.1 version used in blockclust
* Update meta.yaml
* eden checksum and test
* added zlib requirement
* add include and lib paths to build.sh
* add include and lib paths to build.sh
* modify makefile flags using sed
* modify makefile flags using sed
* use c++
* Update build.sh
* Update build.sh
* LDFLAGS not used in makefile
* remove v1.1
* add blockclust 1.1.0 recipe
* skip osx build
* added tarball url and checksum; removed conda_build_config.yaml
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* Update chewbbaca to 2.0.16 (#12132)
* Update abeona to 0.40.0 (#12131)
* ping to eden 1.1 (#12134)
* clean swap file (#12137)
* Update corset to 1.07 (#12143)
* Update peddy to 0.4.3 (#12144)
* blockclust latest source and added cloudpickle as requirement (#12142)
* Update nanomath to 0.22.0 (#12149)
* Update pymvpa to 2.6.5 (#12152)
* Updated to version 1.4.0 (#12138)
* Updated to version 1.4.0
* Resetting build number to 0 and build->host
* Update transdecoder to 5.5.0 (#12172)
* Update gridss to 2.0.1 (#12190)
* Update tracer to 1.7.1 (#12189)
* Update flowcraft to 1.4.0 (#12179)
* Update seqbuster to 3.2 (#12182)
* Update perl-io-compress to 2.081 (#12201)
* Update twobitreader to 3.1.6 (#12205)
* Update twobitreader to 3.1.6
* Update meta.yaml
* Update gtfparse to 1.2.0 (#12186)
* Update gtfparse to 1.2.0
* remove compiler
* Update htseq to 0.11.0 (#12177)
* Update htseq to 0.11.0
* add compiler
* Update htseq to 0.11.0 (#12239) [testing co-author]
* Update htseq to 0.11.0
* add compiler
Co-authored-by: Bjoern Gruening <[email protected]>
* alfred v0.1.16 (#12240)
* alfred v0.1.16
* makefile patch
* makefile patch
* Update scrm to 1.7.3 (#12150)
* Update scrm to 1.7.3
* Update scrm to 1.7.3
* Mob suite update 1.4.8 --> 1.4.9 (#12244)
We fixed a small bug related to repetitive elements database reconstruction on each run. Should only run once during the first mob_typer run. Should be good now for parallel runs.
* PeptideShaker updated to v1.16.35 & SearchGUI updated to 3.3.9 (#12241)
* PeptideShaker updated to v1.16.32
SearchGUI updated to v3.3.6
* PeptideShaker updated to v1.16.35
* SearchGUI updated to v3.3.9
* First attempt at a recipe for ncrf (#12101)
* First attempt at a recipe for ncrf
* changed from copies to symlinks
* including absolute path in symlinks
* PacBio: Update `pbmm2` to version 0.11.0 (#12246)
* Gimmemotifs version 0.13.0 (#12245)
* new release to fix numpy incompatibility
* GimmeMotifs 0.13.0 release test
* numpy 1.15
* version 0.13.0
* Fix about:home and extra:
* PacBio: Update `isoseq3` to version 3.1.0 (#12263)
* add python to host section (#12264)
* Update confindr to 0.4.7 (#12266)
* new build of GRiD (#12269)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* peptideshaker, searchgui: version bump (#12136)
* peptideshaker, searchgui: version bump
solving https://github.com/compomics/searchgui/issues/192
* Update peptide-shaker.py
* searchgui: added c compiler for building
test if linking errors go away this way
* searchgui: removed noarch
* Update: bcbio, bcbio-vm with CWL non-human fixes (bcbio/bcbio-nextgen#2473) (#12273)
* Make snakemake a noarch package. (#12274)
* noarch: python in combination with version constraint
* Cleanup deps and simplify version definition.
* Genenotebook v0.1.9 (#12277)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* Create r-airr recipe (#12284)
* Create r-airr recipe using bgruening/conda_r_skeleton_helper
* Update meta.yaml
* Findbin::Real added (#12291)
* Added version bump to 1.3 (#12292)
* ngs-bits 2018_11 (#12262)
* Updated ngs-bits to version 2018_10
* Updated ngs-bits to version 2018_11
* minor edit in grid (#12287)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* minor edit to grid
* Fred2 update (#12259)
* Update FRED2 Recipe
* msstitch version 2.9 (#12296)
* r-mvr (#12300)
This is a non-parametric method for joint adaptive mean-variance regularization and variance sta-
bilization of high-dimensional data.
* Bump to Gromacs 2018.3 + re-enable OSX build (#12299)
* Gromacs 2018.3 + re-enable osx build
See also #7825 on OSX build
Include RRID for Gromacs (see bioconda/bioconda-utils#252)
* disabled ocl-icd on osx; not available (or needed?)
https://anaconda.org/conda-forge/ocl-icd
* pyGenomeTracks update of dependencies (#12279)
* Update pyGenomeTracks recipe to enable py3 support and updating outdated dependecy list
* Increase build number
* Update meta.yaml
* Exclude Python 3.5
* Gromacs 2018.4 (#12302)
* quast 5.0.2 (#12303)
* Update meta.yaml (#12275)
* Update meta.yaml
r-rsqlite version dependency added
* Update meta.yaml
Updated build number to 1
* Use the extended-base container because of wget issues when downloading databases (#12297)
* Update duphold to 0.1.0 (#12257)
* Update flashlfq to 0.1.109 (#12256)
* Update planemo to 0.57.0 (#12251)
* Update meta.yaml (#12258)
* Update scalpel to 0.5.4 (#12249)
* Update scalpel to 0.5.4
* Fix url
* edit grid (#12298)
* update grid
* update build num
* edit grid to use mosdepth for depth coverage
* edit grid to use mosdepth for depth coverage
* Update meta.yaml
* new build for grid
* Update meta.yaml
* minor edit to grid
* minor edit to recipe grid
* added feather to deps (#12293)
* R tigger (#12286)
* Create recipe for r-tigger (#12271)
* Create recipe for r-tigger using bgruening/conda_r_skeleton_helper.
* Delete bld.bat
* Remove windows support
* update scprep to v0.8.1 (#12306)
* Update nanoget to 1.7.5 (#12252)
* Update nanoget to 1.7.5
* Bump to version 1.7.6
should fix the README.md problem
* gffcompare: version bump (#12308)
* Update: cromwell (36), bcbio (Cromwell Docker runs) (#12307)
* Update: cromwell (36), bcbio (Cromwell Docker runs)
* Pin java to 8 to avoid compile errors on 11
* HiCExplorer update to version 2.2-beta (#12309)
* HiCExplorer update to version 2.2-beta
* Remove of '-' from version number
* Numpy set to 1.15
* Update meta.yaml
* upgrade to version 2.8.1 (#12316)
* Create Airr recipe (#12318)
* Create AIRR recipe using conda skeleton pypi.
* Add noarch python
* Clean host requirements
* Added nimnexus [v0.1] (#12133)
* added nimnexus
* Fix sha
* Update build.sh
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* [WIP] Add R-loom (#12320)
* initial WIP skeleton
* Update meta.yaml
* Update meta.yaml
* Update meta.yaml
* try osx
* Create Changeo recipe (#12321)
* Create changeo recipe using conda skeleton pypi.
* EDIT about section
* ADD noarch generic
* Update noarch to python
* Clean host requirements
* Add test for scripts
* Change requirement to python>=3.4
* Add noarch pyton
* r-corbi (#12325)
* r-nam (#12327)
* Update pybedtools to 0.8.0 (#12324)
* Update pybedtools to 0.8.0
* rm cython requirement
* MSGFplus does not work with newer Java (#12330)
* Trying to not use a very new java version since the latest versions have dropped some classes
* Increment build
* Update atropos to 1.1.21 (#12322)
* Update CONCOCT to 0.4.2 (#12317)
* Update CONCOCT to 0.4.2
* Wrong shasum given
* Reset build number for new version
* New: gvcfgenotyper for joint calling with Illumina strelka2 (#12331)
* Apparently we need openJDK to be below 9, not below 11 as in the previous PR (#12332)
* Update Picard to 2.18.17. (#12333)
* Unblacklist IgDiscover (#12335)
* PacBio: Add missing licenses and post-link message (#12334)
* Bioconductor DEqMS package (#12336)
* Bioconductor DEqMS package
* Limma version could be set lower (checked with the bioconductor recipe page) to include limma in bioconda
* Genenotebook v0.1.10 (#12337)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* v0.1.10
* removed cloudpickle requirement for blockclust (#12242)
* blockclust latest source and added cloudpickle as requirement
* removed cloudpickle requirement for blockclust
* added a tagged release to the source
* back to source url but with release tarball and checksum
* R guilds (#12341)
* Strict rec (#12113)
* added metawrap
* fixed perl and jdk
* added more strict req
* fixed java and perl
* removed extra boost
* Update qcat to v1.0.1 (#12343)
* Add better error checking (#12345)
* Add mhcnames python package (#12349)
* Add MHCflurry pMHC class I binding affinity prediction tool (#12346)
* Bump pilon (#12354)
* Update pronto to 0.11.1 (#12377)
* Update perl-json-xs to 4.0 (#12373)
* Update planemo to 0.57.1 (#12370)
* Update snippy to 4.3.6 (#12372)
* Update intarna to 2.3.1 (#12367)
* Update agfusion to 1.231 (#12366)
* Update bioconda-utils to 0.15.0 (#12359)
* Update mapdamage2 to 2.0.9 (#12358)
* Update scanpy to 1.3.4 (#12357)
* Update goatools to 0.8.11 (#12361)
* Update perl-math-random-mt-auto to 6.23 (#12362)
* Update kipoi to 0.6.3 (#12374)
* Update kipoi_veff to 0.2.1 (#12364)
* Update perl-object-insideout to 4.05 (#12380)
* Update sevenbridges-python to 0.17.1 (#12379)
* Update nanosv to 1.2.3 (#12378)
* Update starfish to 0.0.30 (#12368)
* Update clust to 1.8.10 (#12356)
* Update pypairs to 2.0.6 (#12381)
* Update khmer to 3.0.0a2 (#12360)
* Update flashlfq to 0.1.110 (#12385)
* Update perl-algorithm-cluster to 1.57 (#12384)
* Update arvados-python-client to 1.2.0.20181121194423 (#12382)
* Update avro-cwl to 1.8.9 (#12355)
* Update avro-cwl to 1.8.9
* Set noarch: python
* r-breakaway (#12386)
* R sads (#12388)
* Update python-sortedcontainers to 2.1.0 (#12383)
* r-ebimetagenomics (#12339)
* pin armadilo on major version (#12389)
* IgDiscover version 0.11 (#12351)
* IgDiscover version 0.11
* IgDiscover requires Python 3.6
* Fix build on macOS with a small patch
* Remove unneeded host dependencies
* Update goatools to 0.8.12 (#12391)
* Update bioconda-utils to 0.15.1 (#12390)
* R ebimetagenomics (#12393)
* Add dimspy recipes for reference purposes (#12387)
* Add dimspy recipes for reference purposes
* Remove filename
* remove from blacklist
* Update build-fail-blacklist
* Added BioExcel_SeqQC to bioconda-recipes (#12276)
* PacBio: Update pbalign to 0.3.2 (#12396)
* PacBio: Update pbalign to 0.3.2
Closes: PacificBiosciences/pbbioconda#39
* add bgreat to bioconda (#12350)
* bgreat addition
* zlib in build should not be needed
* btrim integration to conda (#12395)
* Format sleuth recipe. Trigger rebuild because latest version was never uploaded for some reason. (#12399)
* PacBio: Update `pbsv2` to version 2.1.0 (#12400)
* Genenotebook v0.1.11 (#12398)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* v0.1.10
* v0.1.11
* prosolo: new package version 0.6.0 (#12397)
* Update sevenbridges-python to 0.17.2 (#12404)
* Add recipe for ICED (#12406)
* Downgrade version for iced (#12409)
* Update recipe for libstatgen 1.0.5 (#12348)
* Add recipe for libstatgen-1.0.5
* Update iced to 0.5.0 (#12411)
* Update perl-test2-suite to 0.000116 (#12412)
* fix compatibility with other tools (#12415)
* Restore dexseq python helper scripts (#12352)
* Restore dexseq python helper scripts
* Add python requirement for helper scripts
* Add python noarch to build section
* pin it to python2k
* Add htseq requirement, support only python <3 for now
* Genenotebook v0.1.12 (#12418)
* genenotebook recipe
* About
* Package name
* License
* sha256sum
* Update build.sh
* Make bin dir
* Change ln to cp
* New symlink strategy
* Build from prebundled tarball
* genenotebook v0.1.2
* version fix
* retry
* fix
* build number
* genenotebook v0.1.3
* genenotebook v0.1.3
* new build procedure
* change run dependencies
* build
* restore build procedure
* Fix summary
* dependency versions
* v0.1.5
* version fix
* v0.1.6
* reset build number
* build number
* genenotebook v0.1.7
* v0.1.8
* v0.1.9
* v0.1.10
* v0.1.11
* v0.1.12
* updated source
* added medpy recipe (#12417)
* added medpy recipe
* removed osx from build
* Update meta.yaml
* Update meta.yaml
* add boost and a compiler
* Update meta.yaml
* Update meta.yaml
* add itk
* Updated ddrage to version 1.6.1. (#12421)
* Add r-mcpcounter recipe. (#12261)
* Add MCPcounter recipe.
* fix lint: remove 'fn'
* fix license_file, version number and doi
* Update DEXSeq requirements to force compatible HTSeq version (#12423)
* ARB: Pin glib (#11782)
* Pin glib
* Update meta.yaml
* Update meta.yaml
* Work around CB3 issues
* Work around bioconda-utils lint false positive
* Disable lint check should_not_be_noarch
* Can't reference other packages built in recipe from anything but run
* Move perl to host section. Maybe that helps.
* constraining interpreter version breaks with CB3?
* disable perl version constraint :(
* Update meta.yaml (#12426)
* stacks: fix for fix 'fixing' @ in exe_path (#12420)
* stacks: fix for fix 'fixing' @ in exe_path
the previous fix https://github.com/bioconda/bioconda-recipes/pull/11580
tried to solve the problem with the @ in the exe_path by setting this
variable empty. But the perl scripts
- append a / to the empty string an…
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Hello,
After upgrading to the latest development version, the logs and joint VCF file generation don't seem to work properly anymore. Debug messages don't get printed anymore (neither on stdout, nor in the log file), and the
bcbio-nextgen-debug.logfile is pretty much identical withbcbio-nextgen.log. The only difference is the resource requests messages which appear in the debug log:The multi-sample
<batch>-gatk-haplotype-joint-annotated.vcf.gzdid not get generated, even though the sample-specific VCF files are where they should be.Furthermore,
bcbio-nextgen-commands.logis completely empty.To test all of this, I've run a simple variant calling job that worked flawlessly a few days ago, before upgrading Bcbio-nextgen.
The text was updated successfully, but these errors were encountered: