From 1bdf98adce828e143aa93649bd00e2ad26e7de25 Mon Sep 17 00:00:00 2001 From: Glenn Hickey Date: Wed, 16 Aug 2023 09:03:32 -0400 Subject: [PATCH 1/2] prep release 2.6.7 --- BIN-INSTALL.md | 6 +++--- ReleaseNotes.md | 9 +++++++++ doc/progressive.md | 6 +++--- setup.py | 2 +- src/cactus/shared/common.py | 2 +- 5 files changed, 17 insertions(+), 8 deletions(-) diff --git a/BIN-INSTALL.md b/BIN-INSTALL.md index b8e37dabd..200534449 100644 --- a/BIN-INSTALL.md +++ b/BIN-INSTALL.md @@ -14,9 +14,9 @@ cd "cactus-bin-${REL_TAG}" To build a python virtualenv and activate, do the following steps. This requires Python version >= 3.7 (so Ubuntu 18.04 users should use `-p python3.8` below): ``` -virtualenv -p python3 venv-cactus-v2.6.6 -printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.6.6/bin/activate -source venv-cactus-v2.6.6/bin/activate +virtualenv -p python3 venv-cactus-v2.6.7 +printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.6.7/bin/activate +source venv-cactus-v2.6.7/bin/activate python3 -m pip install -U setuptools pip python3 -m pip install -U . python3 -m pip install -U -r ./toil-requirement.txt diff --git a/ReleaseNotes.md b/ReleaseNotes.md index 20827a423..3952f4dd4 100644 --- a/ReleaseNotes.md +++ b/ReleaseNotes.md @@ -1,3 +1,12 @@ +# Release 2.6.7 2023-08-16 + +This release includes a patched vg and gfaffix + +- Update to `vg` version `1.50.1` which patches the path name incompatibility bug in `1.50.0` +- Revert minigraph-cactus Reference path name convention introduced in v2.6.6 (ie haplotypes can be left unspecified) +- Upgrade to GFAffix 0.1.5 which fixes a crash among other things (thanks @danydoerr!) +- Fix bug where large input contig sizes (>2Gb) would break the pangenome pipeline with some versions of `awk`. + # Release 2.6.6 2023-08-03 This release fixes a compatibility problem between Cactus and the newly released `vg` version `1.50.0`. diff --git a/doc/progressive.md b/doc/progressive.md index 75665d7db..22c135e92 100644 --- a/doc/progressive.md +++ b/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:v2.6.6 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal +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 ``` Or you can proceed interactively by running ``` -docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.6 bash +docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.7 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-v2.6.6/src/cactus/cactus_progressive_config.xml ./config-slurm.xml +cp cactus-bin-v2.6.7/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' ``` diff --git a/setup.py b/setup.py index 5e008b1e7..0d52396a1 100644 --- a/setup.py +++ b/setup.py @@ -24,7 +24,7 @@ def run(self): setup( name = "Cactus", - version = "2.6.6", + version = "2.6.7", 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 index f485ef29d..74c8b577c 100644 --- 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:v2.6.6" + r = "quay.io/comparative-genomics-toolkit/cactus:v2.6.7" if gpu: r += "-gpu" return r From e63be989e9636192cb2703b80681edb2fba6db35 Mon Sep 17 00:00:00 2001 From: Glenn Hickey Date: Wed, 16 Aug 2023 17:24:28 -0400 Subject: [PATCH 2/2] add tag --- BIN-INSTALL.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/BIN-INSTALL.md b/BIN-INSTALL.md index 200534449..24d9b96e6 100644 --- a/BIN-INSTALL.md +++ b/BIN-INSTALL.md @@ -4,10 +4,10 @@ This describes the steps require to install the Cactus pre-compile binary, static linked distribution. ## Extracting -If you have not already extract the distribution: +If you have not already extract the distribution and cd into the cactus directory: ``` -tar -xzf "cactus-bin-${REL_TAG}.tar.gz" -cd "cactus-bin-${REL_TAG}" +tar -xzf cactus-bin-v2.6.7.tar.gz +cd cactus-bin-v2.6.7 ``` ## Setup