Biocontainer images

Use biocontainers images for:

• bedtools
• bedgraphtobigwig
• cutadapt
• kallisto
• samtools
• star
• salmon
• gffread

Fixes #149 (closed)

The only issue that I observe is that the biocontainer images give the following WARNING when they are executed:

WARNING: Skipping mount /opt/conda/envs/zarp/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container

It does not affect the result though.

added 1 commit

• 398b0dd9 - Replace docker://bash:5.0.16 with docker://ubuntu:focal-20210416

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added Blocked label

added 1 commit

• 3925d4f5 - Update versions for docker biocontainers for star, gffread, salmon, kallisto, cutadapt and samtools

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OK, so the WARNING is gone now. I had to update some of the tool's versions. What is still missing for the public images is:

• fastqc
• ALFA

added 2 commits

• 7b8a922d - Use fastqc biocontainers image
• f2d51e34 - Merge branch 'feature/public-bioconda-images' of...

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added 1 commit

• cc8fb580 - Use biocontainers image for ALFA

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removed Blocked label

We now use biocontainers for the public tools. Fixes #149 (closed)

@kanitz Can you please review this?

approved this merge request

Looks great to me :)

Why does it say partially fixes #149 (closed)? Looks to me like all boxes are checked.

And out of curiosity: why the change from the Bash image to Ubuntu Focal?

Thanks a lot!

In the initial commit, I added only a few containers. Now it's a proper fix with all public containers (updated the comment above).

Regarding Ubuntu, I found a container that would not cause (hopefully) the docker rate limit issue. The bash container we were using was under zavolab.

Oh, and @gypas, please remember to squash to commits when you merge

changed the description

merged

mentioned in issue #149 (closed)