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update #1

Merged
merged 54 commits into from
Sep 22, 2022
Merged

update #1

merged 54 commits into from
Sep 22, 2022

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marcDabad
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Describe your pull request here

Please read the guidelines for Bioconda recipes before opening a pull request (PR).

  • If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
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BiocondaBot and others added 30 commits September 16, 2022 08:18
@BiocondaBot
[ci skip] Merge PR 36986
7e4cc9f 
Merge PR #36986, commits were: 
 * Update metabinner to 1.4.4
@BiocondaBot
[ci skip] Merge PR 36975
0cab53e 
Merge PR #36975, commits were: 
 * Update prot-scriber to 0.1.4
 * Update prot-scriber to 0.1.4
@BiocondaBot
[ci skip] Merge PR 36988
5bb0e71 
Merge PR #36988, commits were: 
 * Update crispresso2 to 2.2.10
@BiocondaBot
[ci skip] Merge PR 36951
f18a1eb 
Merge PR #36951, commits were: 
 * Update crispritz to 2.6.6
@BiocondaBot
[ci skip] Merge PR 36949
e78c0c7 
Merge PR #36949, commits were: 
 * Update kneaddata to 0.12.0
@BiocondaBot
Update regenie to 3.2.1 (#37006)
919b5c4
@guilhermesena1
[ci skip] Merge PR 37008
e78ca69 
Merge PR #37008, commits were: 
 * Merge branch 'master' into master
 * changing falco's meta to a (hopefully) fixed version of falco that runs properly on conda
@BiocondaBot
[ci skip] Merge PR 37016
afd924c 
Merge PR #37016, commits were: 
 * Update svim-asm to 1.0.3
@jameshadfield
[ci skip] Merge PR 36997
fd0d633 
Merge PR #36997, commits were: 
 * Update build.sh
 * Update build.sh
 * Update meta.yaml
 * Update build-fail-blacklist
 * Merge remote-tracking branch 'upstream/master' into patch-1
 * Merge branch 'master' into patch-1
 * Update nextstrain/auspice to 2.38.0

GitHub release notes: https://github.com/nextstrain/auspice/releases/tag/v2.38.0
@nh13
[ci skip] Merge PR 37011
7e12505 
Merge PR #37011, commits were: 
 * Update meta.yaml
 * Merge branch 'master' into add/fgsv
 * Add fgsv
@BiocondaBot
[ci skip] Merge PR 37014
763b5c9 
Merge PR #37014, commits were: 
 * Update hmnfusion to 1.2.6
@BiocondaBot
Update r-fastbaps to 1.0.8 (#37021)
331ed0a
@guilhermesena1
[ci skip] Merge PR 37018
90d095f 
Merge PR #37018, commits were: 
 * Merge branch 'master' into master
 * removing zlib and htslib restrictions until there is evidence of incompatibility at some point
 * adding a function to remove zero bytes from conda install path
 * hard-writing the name 'falco' for the opt directory since conda variable seem to be adding special characters that are causing compilation problems
 * update falco release and build instructions
@PauAndrio
Add concoord recipe (#37026)
55c38f9 
* Add concoord recipe

* Adding lisence

* Fixing OS selectors

* Adding the skip-lints

* Remove the https from source url to avoid certificate problems

* Remove build.sh file

* Remove reference to the name of the package in cp script

* Fix typo in binary name
@dnbenso
[ci skip] Merge PR 36999
e8d9107 
Merge PR #36999, commits were: 
 * Update meta.yaml
 * Merge branch 'master' into add_phip-stat
 * Adding phip-stat to bioconda - processing raw PhIP-seq data into analysis-ready enrichment scores
@BiocondaBot
[ci skip] Merge PR 37010
f8b44e1 
Merge PR #37010, commits were: 
 * Update meta.yaml
 * Update synapseclient to 2.7.0
@BiocondaBot
Update das_tool to 1.1.5 (#37023)
948cf25
@trishorts
[ci skip] Merge PR 37030
1e41bd9 
Merge PR #37030, commits were: 
 * Update meta.yaml FlashLFQ new release v 1.2.4
@prihoda
[ci skip] Merge PR 37024
c5e7e4e 
Merge PR #37024, commits were: 
 * Use older protobuf version in DeepBGC
@BiocondaBot
[ci skip] Merge PR 36787
5384883 
Merge PR #36787, commits were: 
 * fix quote
 * quiet down curl
 * update patch files for v2
 * Update sra-human-scrubber to 2.0.0
 * Update sra-human-scrubber to 1.1.0
@BiocondaBot
[ci skip] Merge PR 37036
652819b 
Merge PR #37036, commits were: 
 * add dependency
 * Update pbptyper to 1.0.3
@AlessioMilanese
Add stag (#36974)
0f451d7 
Add `stag` to bioconda:

* Create meta.yaml for stag

* add maintainer

* add space

* remove reference to `LICENCE`

* Update meta.yaml

* trying to add installation
@BiocondaBot
[ci skip] Merge PR 37032
5fb75c5 
Merge PR #37032, commits were: 
 * Update snipit to 1.0.7
@PauAndrio
Update adding CONCOORDLIB env var Concoord (#37028)
c36d8be 
* Add concoord recipe

* Adding lisence

* Fixing OS selectors

* Adding the skip-lints

* Remove the https from source url to avoid certificate problems

* Remove build.sh file

* Remove reference to the name of the package in cp script

* Fix typo in binary name

* Adding CONCOORDLIB env var

* Bumping build number

* Fix Typo in script

* adding -h option to test
@wernerkrampl
[ci skip] Merge PR 36779
2abeed1 
Merge PR #36779, commits were: 
 * Merge branch 'master' into update_snakelines
 * Merge branch 'master' into update_snakelines
 * Merge branch 'master' into update_snakelines
 * Update meta.yaml
 * Fixed error in build.sh.
 * Updated Snakelines to version 1.1.0
@BiocondaBot
Update zdb to 1.0.3 (#36752)
3894d8c
@adamhospital
new biobb_godmd package (#37043)
c8d8c00 
Co-authored-by: Adam Hospital Gasch <[email protected]>
@BiocondaBot
[ci skip] Merge PR 37044
466a50e 
Merge PR #37044, commits were: 
 * Update bakta to 1.5.1
@guillaume-gricourt
[ci skip] Merge PR 36885
aeae9d9 
Merge PR #36885, commits were: 
 * Merge branch 'straindesign' of github.com:brsynth/bioconda-recipes into straindesign
 * refactor(recipes): straindesign, rm extra space
 * Merge branch 'bioconda:master' into straindesign
 * Merge branch 'master' into straindesign
 * fix(recipes): straindesign, random space
 * fix(recipes): straindesign, shasum
 * feat(recipes): rename "rpfbagr" to "straindesign"
@BiocondaBot
[ci skip] Merge PR 37034
04c1a8f 
Merge PR #37034, commits were: 
 * Update run_test.sh
 * Update run_test.sh

Disable pipe tests (and GRCh38 download/indexing)
 * Update meta.yaml
 * Update microhapulator to 0.7
Colelyman and others added 24 commits September 20, 2022 15:43
@Colelyman
[ci skip] Merge PR 37033
4bbaa8a 
Merge PR #37033, commits were: 
 * Update meta.yaml
 * Have CRISPResso2 depend on seaborn-base instead of seaborn
@BiocondaBot
[ci skip] Merge PR 37052
1a42176 
Merge PR #37052, commits were: 
 * Update build.sh
 * Update meta.yaml
 * Update pbptyper to 1.0.4
@rpetit3
[ci skip] Merge PR 36582
743f833 
Merge PR #36582, commits were: 
 * fix log write to read only directory
 * fix typo in patch file
 * play nice with sed on mac
 * add version to test command
 * rearange build
 * fix string in patch
 * update meta yaml
 * fix typo
 * add version to test command
 * add patch files
 * Merge remote-tracking branch 'upstream/master' into rp3-add-nextpolish
 * Merge remote-tracking branch 'upstream/master' into rp3-add-nextpolish
 * Update build.sh
 * Update build.sh
 * Update build.sh
 * Update build.sh
 * Update build.sh
 * Update meta.yaml
 * 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 build.sh
 * Update build.sh
 * Merge branch 'master' into rp3-add-nextpolish
 * add recipe for nanopolish
@BiocondaBot
[ci skip] Merge PR 37053
67b1d87 
Merge PR #37053, commits were: 
 * Update igv-reports to 1.6.1
 * Update igv-reports to 1.6.0
@lldelisle
[ci skip] Merge PR 36872
c2a448c 
Merge PR #36872, commits were: 
 * Update meta.yaml
 * Merge branch 'master' into update_hicup_dep
 * require high version of stringi
 * try to fix stringi
 * fix typo
 * prevent failing stringi
 * add pandoc
 * update dependencies and test
@BiocondaBot
[ci skip] Merge PR 37055
26ccaa5 
Merge PR #37055, commits were: 
 * Update semibin to 1.1.0
@BiocondaBot
Update atlas-fastq-provider to 0.4.4 (#37062)
b33e155
@PauAndrio
Update env_vars in Concoord (#37064)
a2f5797 
* Add concoord recipe

* Adding lisence

* Fixing OS selectors

* Adding the skip-lints

* Remove the https from source url to avoid certificate problems

* Remove build.sh file

* Remove reference to the name of the package in cp script

* Fix typo in binary name

* Adding CONCOORDLIB env var

* Bumping build number

* Fix Typo in script

* adding -h option to test

* Managing env vars
@BiocondaBot
[ci skip] Merge PR 37065
fa45f5b 
Merge PR #37065, commits were: 
 * Update treetime to 0.9.4
@BiocondaBot
[ci skip] Merge PR 37050
9220c7a 
Merge PR #37050, commits were: 
 * Update bbmap to 39.00
@BiocondaBot
[ci skip] Merge PR 37015
4cc2280 
Merge PR #37015, commits were: 
 * Update seqscreen to 4.0
 * Update seqscreen to 4.0
 * Update seqscreen to 4.0
@BiocondaBot
[ci skip] Merge PR 37042
5344880 
Merge PR #37042, commits were: 
 * Update proteinortho to 6.1.1
@BiocondaBot
Update thapbi-pict to 0.13.1 (#37067)
e97c41f
@wernerkrampl
[ci skip] Merge PR 37060
89c4704 
Merge PR #37060, commits were: 
 * Fixed a typo.
 * Fixed sh256.
 * Updated Snakelines to version 1.1.3. Added missing dependency.
@fredericlemoine
[ci skip] Merge PR 37058
66e9e05 
Merge PR #37058, commits were: 
 * Corrected package version in gotree
@ashotmarg
[ci skip] Merge PR 37057
04f9966 
Merge PR #37057, commits were: 
 * Merge branch 'master' into master
 * added the hap-ibd
@BiocondaBot
[ci skip] Merge PR 36989
7d372d2 
Merge PR #36989, commits were: 
 * Update jbrowse2 to 2.1.4
 * Update jbrowse2 to 2.1.3
@victorlin
[ci skip] Merge PR 37071
f2886c3 
Merge PR #37071, commits were: 
 * Reset build number
 * Update augur to 18.0.0

Update dependency list to reflect new changes to setup.py [1].

[1]: nextstrain/augur@17.1.0...18.0.0
@BiocondaBot
[ci skip] Merge PR 37012
c12d3bf 
Merge PR #37012, commits were: 
 * Update grafimo to 1.1.6
@BiocondaBot
[ci skip] Merge PR 37074
4b567a0 
Merge PR #37074, commits were: 
 * Update cellxgene to 1.1.1
@BiocondaBot
[ci skip] Merge PR 37073
315385c 
Merge PR #37073, commits were: 
 * Update meta.yaml
 * Update r-signac to 1.8.0
@rpetit3
[ci skip] Merge PR 37070
9503cb4 
Merge PR #37070, commits were: 
 * github dev, don't use CRLF please
 * Helps if you put patches in right place
 * add tempfile patches
 * update license
 * Update meta.yaml
 * add recipe for pHierCC
@BiocondaBot
[ci skip] Merge PR 37077
1b2d180 
Merge PR #37077, commits were: 
 * Update meta.yaml
 * Update arvados-python-client to 2.4.3
@J35P312
[ci skip] Merge PR 36976
ad44b24 
Merge PR #36976, commits were: 
 * 	modified:   meta.yaml
@marcDabad marcDabad merged commit 3bd5708 into marcDabad:master Sep 22, 2022
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