new rsat version 20240507, tested in local Docker

[eead-csic-compbio]

This PR adds a new version of the Docker BioContainer with the RSAT software, which now ships wit the code corresponding to tag 20240507 in source repo (https://github.com/rsa-tools/rsat-code). Accordingly, the Dockerfile now contains LABEL software.version="20240507".

The two main updates are:

• The container can now be run non-interactively, it has been tested in local Docker.
  • install-organisms has been updated to support again the installation of genomes from the NCBI. It was tested by @jvanheld was tested by installing bacterial genomes on the Bacterial RSAT server.

Example non-interactive calls would be:

docker run -v $PWD:/home/rsat_user -v $PWD/out:/home/rsat_user/out rsat:20240507 peak-motifs -i test.fa -outdir out -prefix test

docker run -v $PWD:/home/rsat_user -v $PWD/out:/home/rsat_user/out rsat:20240507 peak-motifs -i test.fa -outdir out -prefix test -motif_db footDB transfac /packages/rsat/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf

Note the examples require binding two folders:

1. The current folder from where the container is called ($PWD). This allows processing any FASTA file in the current directory.
2. The folder to save the results (out/). This should point to an existing local folder where anybody can write (chmod 777).

@medinaale @morganeTC @najlaksouri

[eead-csic-compbio]

Hi @ievarau, please use this PR to add any comments you might have during your tests

[ievarau]

• Tested building. Success. Important to build using Docker (Podman won't do).
• Tested running container non-interactively with two example calls provided above. Works as expected.
• Tested within Snakemake pipeline. Works as expected as well.

All in all, peak-motifs with this container version works as expected.

[biocontainers-bot]

No test-cmds.txt (test file) present, skipping tests

[eead-csic-compbio]

This PR is read y to be reviewed by somebody from BioContainers, thanks

[eead-csic-compbio]

Hi @mboudet , please let us know if there's anything you need from us

[mboudet]

Sorry for the delay, last week was mostly bank holidays here.

One quick question: any reason for installing git in a separate apt-get install step? (Ie line 91 instead of 43) (This is not blocking, just for curiosity).

[eead-csic-compbio]

Sorry for the delay, last week was mostly bank holidays here.

One quick question: any reason for installing git in a separate apt-get install step? (Ie line 91 instead of 43) (This is not blocking, just for curiosity).

I guess it was to make it clear that the installation of RSAT would be done using git

[mboudet]

Alright. Thank you for your contribution.