Merge pull request #1084 from ComparativeGenomicsToolkit/oneshot

prep release 2.6.2

ReleaseNotes.md

@@ -1,3 +1,11 @@
+# Release 2.6.2 2023-06-28
+
+This release patches a few bugs introduced or found in v2.6.1
+
+- Docker container fixed to include runtime libatomic dependency for odgi
+- `--refContigs` option fixed in `cactus-graphmap-split`
+- `cactus-pangenome` fixed to properly output intermediate GAF and unfiltered PAF alignment files
+
 # Release 2.6.1 2023-06-27
 
 This Release adds SLURM cluster support for Cactus (both progressive and pangenome). It also adds some new visualization features to the pangenome pipeline, along with several bugfixes.

doc/progressive.md

@@ -169,12 +169,12 @@ Conservation scores can be computed using [phast](http://compgen.cshl.edu/phast/
 The Cactus Docker image contains everything you need to run Cactus (python environment, all binaries, system dependencies). For example, to run the test data:
 
 ```
-docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.1 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.2 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:v2.6.1 bash
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.2 bash
 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
 
 ```
@@ -210,7 +210,7 @@ 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-v2.6.1/src/cactus/cactus_progressive_config.xml ./config-slurm.xml
+cp cactus-bin-v2.6.2/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 = "2.6.1",
+    version = "2.6.2",
     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:v2.6.1"
+    r = "quay.io/comparative-genomics-toolkit/cactus:v2.6.2"
     if gpu:
         r += "-gpu"
     return r