Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update GRIDSS 2.13.2 #46160

Draft
wants to merge 2 commits into
base: master
Choose a base branch
from
Draft

Update GRIDSS 2.13.2 #46160

wants to merge 2 commits into from

Conversation

scwatts
Copy link
Contributor

@scwatts scwatts commented Mar 5, 2024

  • VIRUSBreakend uses grep during execution
  • The BioContainers Docker image only provides BusyBox grep, which has poor performance
    • Increases runtime by up to ~1 hour from the single command above when compared to GNU grep
  • This PR includes GNU grep in the recipe to restore expected VIRUSBreakend performance

Please read the guidelines for Bioconda recipes before opening a pull request (PR).

General instructions

  • If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
  • New recipes not directly relevant to the biological sciences need to be submitted to the conda-forge channel instead of Bioconda.
  • PRs require reviews prior to being merged. Once your PR is passing tests and ready to be merged, please issue the @BiocondaBot please add label command.
  • Please post questions on Gitter or ping @bioconda/core in a comment.

Instructions for avoiding API, ABI, and CLI breakage issues

Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify run_exports (see here for the rationale and comprehensive explanation).
Add a run_exports section like this:

build:
  run_exports:
    - ...

with ... being one of:

Case run_exports statement
semantic versioning {{ pin_subpackage("myrecipe", max_pin="x") }}
semantic versioning (0.x.x) {{ pin_subpackage("myrecipe", max_pin="x.x") }}
known breakage in minor versions {{ pin_subpackage("myrecipe", max_pin="x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
known breakage in patch versions {{ pin_subpackage("myrecipe", max_pin="x.x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
calendar versioning {{ pin_subpackage("myrecipe", max_pin=None) }}

while replacing "myrecipe" with either name if a name|lower variable is defined in your recipe or with the lowercase name of the package in quotes.

Bot commands for PR management

Please use the following BiocondaBot commands:

Everyone has access to the following BiocondaBot commands, which can be given in a comment:

@BiocondaBot please update Merge the master branch into a PR.
@BiocondaBot please add label Add the please review & merge label.
@BiocondaBot please fetch artifacts Post links to CI-built packages/containers.
You can use this to test packages locally.

Note that the @BiocondaBot please merge command is now depreciated. Please just squash and merge instead.

Also, the bot watches for comments from non-members that include @bioconda/<team> and will automatically re-post them to notify the addressed <team>.

@scwatts
Copy link
Contributor Author

scwatts commented Mar 5, 2024

Both linux_test job attempts failed from exceeding available disk space on the VM:

.02:34:18 BIOCONDA INFO (ERR) [Mar  5 02:34:18] SERR [Mar  5 02:34:18] ERRO Task processing failed: API error (500): {"message":"write /usr/local/share/RepeatMasker/Libraries/taxonomy.dat: no space left on device"}

I've confirmed that the recipe builds locally with conda-build and bioconda-utils build. This recipe was also previously building okay.

Any help resolving this would be appreciated!

@scwatts
Copy link
Contributor Author

scwatts commented Aug 12, 2024

@BiocondaBot please fetch artifacts

@scwatts
Copy link
Contributor Author

scwatts commented Aug 12, 2024

Please do not merge until I add the please review & merge label!

@BiocondaBot
Copy link
Collaborator

Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
linux-64 gridss-2.13.2-h50ea8bc_4.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>

Docker image(s) built:

Package Tag CI Install with docker
gridss 2.13.2--h50ea8bc_4 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/gridss:2.13.2--h50ea8bc_4.tar.gz | docker load

@scwatts
Copy link
Contributor Author

scwatts commented Aug 12, 2024

The Docker image is missing the Dfam database:

$ docker run quay.io/biocontainers/gridss:2.13.2--h50ea8bc_4 cat /usr/local/share/RepeatMasker/Libraries/Dfam.h5
Placeholder file, should be replaced on Conda package installation.

Absence of the Dfham database causes an error when running the VIRUSBreakend tool. Presumably it is missing because of this check in the RepeatMaskter post-link.sh:

if [ -f /.dockerenv ]; then
cat >> "$PREFIX/.messages.txt" <<EOF
To install the databases needed by RepeatMasker, execute:
wget -O Dfam_curatedonly.h5.gz https://www.dfam.org/releases/Dfam_3.7/families/Dfam_curatedonly.h5.gz
gunzip -c Dfam_curatedonly.h5.gz > ${PREFIX}/share/RepeatMasker/Libraries/Dfam.h5
rm Dfam_curatedonly.h5.gz
EOF

The current GRIDSS Docker image available through Bioconda/BioContainers is also broken for the same reason, and will likely remain broken until the work in the below PR is complete:

@martin-g martin-g marked this pull request as draft August 12, 2024 09:03
@martin-g
Copy link
Contributor

Please do not merge until I add the please review & merge label!

I've set the PR to Draft.
Some people set the label, others - don't ...
Setting the PR to Draft disables the merge button!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants