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.

Sign up for GitHub

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

Jump to bottom

use TMPDIR for lumpy #6129

Open
wants to merge 2 commits into
base: main
Choose a base branch
from
Open

use TMPDIR for lumpy #6129

wants to merge 2 commits into from

Conversation

bgruening
Copy link
Member

FOR CONTRIBUTOR:

  • I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • License permits unrestricted use (educational + commercial)
  • This PR adds a new tool or tool collection
  • This PR updates an existing tool or tool collection
  • This PR does something else (explain below)

mvdbeek
mvdbeek reviewed Jul 7, 2024
View reviewed changes
tools/lumpy_sv/lumpy_preprocessing.xml
@@ -9,13 +9,13 @@
<command detect_errors="exit_code"><![CDATA[
set -o pipefail;

samtools collate -O --output-fmt sam '$bam_in' | samblaster $dup_handling --addMateTags | samtools view -bS - > blasted.bam &&
samtools collate -O --output-fmt sam -T "\${TMPDIR:-.}" -@ \${GALAXY_SLOTS:-1} '$bam_in' | samblaster $dup_handling --addMateTags | samtools view -bS - > blasted.bam &&
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The container is built with samtools 1.10, where collate doesn't know the -T argument

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I created a new container, but something still writes to /tmp.

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I think it writes to $TMPDIR, as the path is /tmp/tmp3s6znz26/tmp.0000.bam. Something else seems to be going wrong there, could be something has changed on the github worker. Does the test pass locally if you use --biocontainers ?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@mvdbeek mvdbeek mvdbeek left review comments

At least 1 approving review is required to merge this pull request.

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@bgruening @mvdbeek