Merge pull request #1242 from ComparativeGenomicsToolkit/docker-fixes

prep release 2.7.0

BIN-INSTALL.md

@@ -6,17 +6,17 @@ pre-compile binary, static linked distribution.
 ## Extracting
 If you have not already extract the distribution and cd into the cactus directory:
 ```
-tar -xzf cactus-bin-v2.6.13.tar.gz
-cd cactus-bin-v2.6.13
+tar -xzf cactus-bin-v2.7.0.tar.gz
+cd cactus-bin-v2.7.0
 ```
 
 ## Setup
 
 To build a python virtualenv and activate, do the following steps. This requires Python version >= 3.7 (so Ubuntu 18.04 users should use `-p python3.8` below):
 ```
-virtualenv -p python3 venv-cactus-v2.6.13
-printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.6.13/bin/activate
-source venv-cactus-v2.6.13/bin/activate
+virtualenv -p python3 venv-cactus-v2.7.0
+printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.7.0/bin/activate
+source venv-cactus-v2.7.0/bin/activate
 python3 -m pip install -U setuptools pip wheel
 python3 -m pip install -U .
 python3 -m pip install -U -r ./toil-requirement.txt

ReleaseNotes.md

@@ -1,7 +1,11 @@
-# Release 2.7.0 2023-??-??
+# Release 2.7.0 2023-12-05
 
-This release changes how outgroups are used during chaining:
+This release changes how outgroups are used during chaining during progressive alignment, and adds some pangenome options 
 
+- Add `--xg` option for `xg` pangenome output.
+- Add (experimental) `cactus-pagnenome --noSplit` option in order to bypass reference chromosome splitting. This was previously only possible by running step-by-step and not using `cactus-graphmap-join`.
+- Add pangenome tutorial (developed for recent hackathon) to documentation.
+- Update to `vg` version [1.53.0](https://github.com/vgteam/vg/releases/tag/v1.53.0). 
 - Updated local alignment selection criteria. At each internal node of the guide tree Cactus picks a set of pairwise local alignments between the genomes being aligned to construct an initial sequence graph representing the whole genome alignment. This sequence graph is then refined and an ancestral sequence inferred to complete the alignment process for the internal node. The pairwise local alignments are generated with LASTZ (or SegAlign if using the GPU mode). To create a reliable subset of local alignments Cactus employs a chaining process that organizes the pairwise local alignments into pairwise chains of syntenic alignments, using a process akin to the chains and nets procedure used by the UCSC Browser. Previously, each genome being aligned, including both ingroup and outgroup genomes, was used to select a set of primary chains. That is, for each genome sequence non-overlapping chains of pairwise alignments were chosen, each of which could be to any of the other genomes in the set. Only these primary chains were then fed into the Cactus process to construct the sequence graph. This heuristic works reasonably well, in effect it allows each subsequence to choose a sequence in another genome with which it shares a most recent common ancestor. In the new, updated version we tweak this process slightly to avoid rare edge cases. Now each sequence in each ingroup genome picks primary chains only to other ingroup genomes. Thus the set of primary chains for ingroup genomes does not include any outgroup alignments. The outgroup genomes then get to pick primary chains to the ingroups, effectively voting on which parts of the ingroups they are syntenic too. The result of this change is that the outgroups are effectively only used to determine ancestral orderings and do not ever prevent the syntenic portions of two ingroups from aligning together.
 
 # Release 2.6.13 2023-11-15

doc/progressive.md

@@ -170,12 +170,12 @@ The Cactus Docker image contains everything you need to run Cactus (python envir
 
 ```
 wget -q https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/master/examples/evolverMammals.txt -O evolverMammals.txt
-docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.13 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.7.0 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
 ```
 
 Or you can proceed interactively by running
 ```
-docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.13 bash
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.7.0 bash
 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
 
 ```
@@ -221,7 +221,7 @@ You cannot run `cactus --batchSystem slurm` from *inside* the Cactus docker cont
 To run Progressive Cactus with CPU (default) lastz, you should increase the chunk size.  This will divide the input assemblies into fewer pieces, resulting in fewer jobs on the cluster.
 
 ```
-cp cactus-bin-v2.6.13/src/cactus/cactus_progressive_config.xml ./config-slurm.xml
+cp cactus-bin-v2.7.0/src/cactus/cactus_progressive_config.xml ./config-slurm.xml
 sed -i config-slurm.xml -e 's/blast chunkSize="30000000"/blast chunkSize="90000000"/g'
 sed -i config-slurm.xml -e 's/dechunkBatchSize="1000"/dechunkBatchSize="200"/g'
 ```

setup.py

@@ -24,7 +24,7 @@ def run(self):
 
 setup(
     name = "Cactus",
-    version = "2.6.13",
+    version = "2.7.0",
     author = "Benedict Paten",
     package_dir = {'': 'src'},
     packages = find_packages(where='src'),

src/cactus/shared/common.py

@@ -305,7 +305,7 @@ def getDockerTag(gpu=False):
         return "latest"    
     else:
         # must be manually kept current with each release        
-        return 'v2.6.13' + ('-gpu' if gpu else '')
+        return 'v2.7.0' + ('-gpu' if gpu else '')
 
 def getDockerImage(gpu=False):
     """Get fully specified Docker image name."""