Merge pull request #997 from ComparativeGenomicsToolkit/oneshot

prep release v2.5.1
ComparativeGenomicsToolkit · Apr 19, 2023 · 4823037 · 4823037
2 parents 7b1e644 + 7375539
commit 4823037
Show file tree

Hide file tree

Showing 4 changed files with 15 additions and 4 deletions.
diff --git a/ReleaseNotes.md b/ReleaseNotes.md
@@ -1,3 +1,14 @@
+# Release 2.5.1 2023-04-19
+
+This Release mostly patches some bugs in the pangenome pipeline
+
+- `cactus-pangenome` now saves PAF file in the output directory
+- Ship version of `vg` that is patched to not make too-slow `giraffe` indexes for some complex graphs
+- Fix bug where `.` characters in reference sample name could lead to strange errors at end of pipeline
+- Better sample name validation for all pangenome tools to prevent confusion around `.`s.
+- Update `taffy` to fix issues where `--filterGapCausingDupes` could lead to crashes in `cactus-hal2maf`
+- Strip defaults of `taffy` commands from being specified in `cactus-hal2maf` -- they are now taken from `taffy`
+
 # Release 2.5.0 2023-04-03
 
 This Release greatly simplifies the interface for building pangenomes

diff --git a/doc/progressive.md b/doc/progressive.md
@@ -164,12 +164,12 @@ 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:v2.5.0 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.5.1 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:v2.5.0 bash
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.5.1 bash
 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
 
 ```

diff --git a/setup.py b/setup.py
@@ -24,7 +24,7 @@ def run(self):
 
 setup(
     name = "Cactus",
-    version = "2.5.0",
+    version = "2.5.1",
     author = "Benedict Paten",
     package_dir = {'': 'src'},
     packages = find_packages(where='src'),

diff --git a/src/cactus/shared/common.py b/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:v2.5.0"
+    r = "quay.io/comparative-genomics-toolkit/cactus:v2.5.1"
     if gpu:
         r += "-gpu"
     return r