Merge pull request #1179 from ComparativeGenomicsToolkit/docker-fixes

prep release v2.6.8

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-v2.6.7.tar.gz
-cd cactus-bin-v2.6.7
+tar -xzf cactus-bin-v2.6.8.tar.gz
+cd cactus-bin-v2.6.8
 ```
 
 ## 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-v2.6.7
-printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.6.7/bin/activate
-source venv-cactus-v2.6.7/bin/activate
+virtualenv -p python3 venv-cactus-v2.6.8
+printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.6.8/bin/activate
+source venv-cactus-v2.6.8/bin/activate
 python3 -m pip install -U setuptools pip
 python3 -m pip install -U .
 python3 -m pip install -U -r ./toil-requirement.txt

ReleaseNotes.md

@@ -1,3 +1,17 @@
+# Release 2.6.8 2023-09-28
+
+This release includes several bug fixes for the pangenome pipeline
+
+- Fix bug where mash distances used to determine minigraph construction order could be wrong when input sample names differ by only their last character
+- Fix some job memory specifications to better support slurm environments
+- Guarantee that pangenome components have exactly two tips (one for each reference path endpoint). This is required for vg's now haplotype sampling logic.
+- Add warning message when genomes that are too diverse are input to `cactus-pangenome`
+- Update hal
+- `--consMemory` option now overrides memory for hal export, in addition to `cactus_consolidated`
+- Update `vg` to v1.51.0
+- Fix bug where samples passed in to `--reference` (except the first) could be dropped as reference in the final output if they are missing from the first chromosome
+- Port CI to OpenStack
+
 # Release 2.6.7 2023-08-16
 
 This release includes a patched vg and gfaffix

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:v2.6.7 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.8 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:v2.6.7 bash
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.8 bash
 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
 
 ```
@@ -211,7 +211,7 @@ 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-v2.6.7/src/cactus/cactus_progressive_config.xml ./config-slurm.xml
+cp cactus-bin-v2.6.8/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 = "2.6.7",
+    version = "2.6.8",
     author = "Benedict Paten",
     package_dir = {'': 'src'},
     packages = find_packages(where='src'),

src/cactus/shared/common.py

@@ -305,7 +305,7 @@ def getDockerImage():
 
 def getDockerRelease(gpu=False):
     """Get the most recent docker release."""
-    r = "quay.io/comparative-genomics-toolkit/cactus:v2.6.7"
+    r = "quay.io/comparative-genomics-toolkit/cactus:v2.6.8"
     if gpu:
         r += "-gpu"
     return r