add mount of licensed tools#16
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mberacochea merged 3 commits intofeature/some-fixesfrom Apr 27, 2025
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SignalP 4.1 works with this changes. It's not possible to check if the licensed folder exists in the containers options becuse the folder seems to be staged later in the execution. I've noticed this while debugging with this lines in the container options ```groovy println file(licensedSoftwarePath) println file(licensedSoftwarePath).exists() println file(licensedSoftwarePath).listFiles() ``` Got: ```/Users/mbc/projects/ebi-metagenomics-assembly-analysis-pipeline/work/4f/2773cbbdb8434e2d06e182e6bcf75b/interproscan_db/licensed false null ``` This comit also has an override of a path otherwise signalp doesn't work because of a missing perl library. I've also adjusted the --appls options.. we should check with the IPS folks as the documentation is not clear IMO about which names should we use there, i.e. PfamA or just PFAM (uppercase), SignalP or SignalP_GRAM_POSITIVE...
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We need to add licensed tools to IPS.
documentation https://interproscan-docs.readthedocs.io/en/v5/ActivatingLicensedAnalyses.html. I have downloaded all tools locally (I can share those as archive).
I put some on CODON already
/hps/nobackup/rdf/metagenomics/service-team/ref-dbs/ips/5.73-104.0/licensedDocker file uses mounts https://github.com/EBI-Metagenomics/containers/blob/master/interproscan/5.73-104.0/Dockerfile#L38
My idea was to have
dataandlicensedfolders and mount them into nextflow module separately. But it doesn't work...