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CCBR / Dockers

A collection of Dockerfiles to facilitate reproducibility across computing environments.
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Install phantompeakqualtools instead of copying scripts? #5

Closed kelly-sovacool closed 1 year ago

kelly-sovacool commented 1 year ago

Is there a better way to support phantompeakqualtools than have the scripts copied in the container (https://github.com/CCBR/Dockers/tree/14c7a3a84c0bdd81ad207d7724a57a61013f6f56/chipseq/ccbr_spp_1.14)? It is available on bioconda: https://bioconda.github.io/recipes/phantompeakqualtools/README.html#package-phantompeakqualtools, perhaps the docker could install it mamba.

kelly-sovacool commented 1 year ago

There's actually a docker container available used by the nf-core chip-seq pipeline. We could just use that instead of duplicating our efforts. https://github.com/nf-core/chipseq/blob/51eba00b32885c4d0bec60db3cb0a45eb61e34c5/modules/nf-core/modules/phantompeakqualtools/main.nf

@kopardev I'm using the container used by nf-core (quay.io/biocontainers/phantompeakqualtools:1.2.2--hdfd78af_1), so no need to update this container unless you just want to.

kopardev commented 1 year ago

@kelly-sovacool, Sure go ahead and use the biocontainers docker ... but make sure to isolate the process as /opt2 /data2 will not be available and other tools may be different from the versions inccbr_base`... Ok?

kelly-sovacool commented 1 year ago

@kopardev do you have an example of what you mean by isolating the process as /opt2? Does this involve setting the --isolate flag?