Merge pull request #1229 from ComparativeGenomicsToolkit/docker-fixes

prep release v2.6.13

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-v2.6.12.tar.gz
-cd cactus-bin-v2.6.12
+tar -xzf cactus-bin-v2.6.13.tar.gz
+cd cactus-bin-v2.6.13
 ```
 
 ## 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-v2.6.12
-printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.6.12/bin/activate
-source venv-cactus-v2.6.12/bin/activate
+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
 python3 -m pip install -U setuptools pip wheel
 python3 -m pip install -U .
 python3 -m pip install -U -r ./toil-requirement.txt

ReleaseNotes.md

@@ -1,3 +1,12 @@
+# Release 2.6.13 2023-11-15
+
+This release fixes an issue where Toil can ask for way too much memory for minigraph construction
+- Cut default minigraph construction memory estimate by half
+- Add `--mgMemory` option to override minigraph construction memory estimate no matter what
+- Exit with a clear error message (instead of more cryptic crash) when user tries to run container binaries in a container
+- Fix double Toil delete that seems to cause fatal error in some environments
+- Fix `gfaffix` regular expression bug that could cause paths other than the reference to be protoected from collapse.
+
 # Release 2.6.12 2023-11-07
 
 The release contains fixes some recent regressions:

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:v2.6.12 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
+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
 ```
 
 Or you can proceed interactively by running
 ```
-docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.12 bash
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.13 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-v2.6.12/src/cactus/cactus_progressive_config.xml ./config-slurm.xml
+cp cactus-bin-v2.6.13/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 = "2.6.12",
+    version = "2.6.13",
     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 'v2.6.12' + ('-gpu' if gpu else '')
+        return 'v2.6.13' + ('-gpu' if gpu else '')
 
 def getDockerImage(gpu=False):
     """Get fully specified Docker image name."""