Merge pull request #769 from ComparativeGenomicsToolkit/docker-fixes

prep release v2.2.0

README.md

@@ -42,10 +42,10 @@ There are many different ways to install and run Cactus:
 
 #### Docker Image
 
-Cactus docker images are hosted on [quay](https://quay.io/repository/comparative-genomics-toolkit/cactus).  The image for the latest release is listed on the [Releases Page](https://github.com/ComparativeGenomicsToolkit/cactus/releases).  Here is an command line to run the included evolver mammals example with release 2.1.1
+Cactus docker images are hosted on [quay](https://quay.io/repository/comparative-genomics-toolkit/cactus).  The image for the latest release is listed on the [Releases Page](https://github.com/ComparativeGenomicsToolkit/cactus/releases).  Here is an command line to run the included evolver mammals example with release 2.2.0
 ```
 wget https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/master/examples/evolverMammals.txt
-docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.1.1 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal --root mr --binariesMode local
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.2.0 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal --root mr --binariesMode local
 
 ```
 
@@ -129,7 +129,7 @@ Cactus can be setup and used in a virtual environment as in the [previous sectio
 
 Singularity binaries can be used in place of docker binaries with the `--binariesMode singularity` flag.  Note, you must use Singularity 2.3 - 2.6 or Singularity 3.1.0+. Singularity 3 versions below 3.1.0 are incompatible with cactus (see [issue #55](https://github.com/ComparativeGenomicsToolkit/cactus/issues/55) and [issue #60](https://github.com/ComparativeGenomicsToolkit/cactus/issues/60)).
 
-By default, cactus will use the image, `quay.io/comparative-genomics-toolkit/cactus:<CACTUS_COMMIT>` when running binaries. This is usually okay, but can be overridden with the `CACTUS_DOCKER_ORG` and `CACTUS_DOCKER_TAG` environment variables.  For example, to use GPU release 2.1.1, run `export CACTUS_DOCKER_TAG=v2.1.1-gpu` before running cactus.  
+By default, cactus will use the image, `quay.io/comparative-genomics-toolkit/cactus:<CACTUS_COMMIT>` when running binaries. This is usually okay, but can be overridden with the `CACTUS_DOCKER_ORG` and `CACTUS_DOCKER_TAG` environment variables.  For example, to use GPU release 2.2.0, run `export CACTUS_DOCKER_TAG=v2.2.0-gpu` before running cactus.  
 
 The `--binariesMode local` flag can be used to force `cactus` to run local binaries -- this is the default behavior if they are found.
 

ReleaseNotes.md

@@ -1,3 +1,21 @@
+# Release 2.2.0 2022-08-19
+
+This release contains a major update to the "blast" phase, where chaining logic is introduced to select lastz anchors, replacing the old quality-based heuristic. It also uses 1 fewer outgroup (2 instead of 3) by default, and no longer explicitly computes self-alignments, which should result in faster runtimes. 
+
+Other changes include:
+
+- Complete rewrite and drastic simplification of all code used to genereate lastz anchors
+- PAF format now used natively throughout Cactus (replacing lastz cigars)
+- Major refactor and cleanup of the "progressive" python module, removing vestiges of old Progressive Cactus repo
+- Rewrite and simplifcation of the "Cactus Workflow" Python code.
+- Intermediate files (project, multicactus project, experiment XML) all done away with.
+- More explicit error message for "illegal instruction" signal (which commonly confused people trying to run on older CPUs)
+- Fasta contig name checking and prefixing done at beginning of each tool (this should prevent cryptic `halAppendSubtree` errors in the pangenome pipeline)
+- Update to newest SegAlign, which should fix an overflow bug that occurs when repeatmasking some data.
+- Increase binary compatibility by linking with newer libxml2
+- Add `cactus-terra-helper` tool to force-resume Terra workflows (when its own call caching fails)
+- Small cleanup of `cactus-preprocess` interface
+
 # Release 2.1.1 2022-06-15
 
 This release includes:

setup.py

@@ -24,7 +24,7 @@ def run(self):
 
 setup(
     name = "Cactus",
-    version = "2.1.1",
+    version = "2.2.0",
     author = "Benedict Paten",
     package_dir = {'': 'src'},
     packages = find_packages(where='src'),

src/cactus/shared/common.py

@@ -280,7 +280,7 @@ def getDockerImage():
 
 def getDockerRelease(gpu=False):
     """Get the most recent docker release."""
-    r = "quay.io/comparative-genomics-toolkit/cactus:v2.1.1"
+    r = "quay.io/comparative-genomics-toolkit/cactus:v2.2.0"
     if gpu:
         r += "-gpu"
     return r