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AmpliconSuite / AmpliconSuite-pipeline

A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
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Update install.sh #46

Closed auberginekenobi closed 7 months ago

auberginekenobi commented 7 months ago

Not sure if it breaks your logic but it seems to me that install.sh --finalize_only shouldn't require bwa, samtools and R. The use case here is that these are preinstalled in the containers so I shouldn't need to install them in my base environment.

jluebeck commented 7 months ago

These tests are essentially pre-flight checks designed to prevent users from creating an installation of the tool where those key dependencies are missing from the system path. Would it be possible, before running install.sh --finalize_only, to satisfy the installation of bwa, samtools and R in your container in such a way that they appear on the system path?

auberginekenobi commented 7 months ago

Hm, I guess I disagree in principle with the pre-flight checks being performed at all with the --finalize_only flag set. The recommended workflow for docker/singularity runs this code, and I think the main reason to use docker/singularity in the first place is to avoid the headache of having to install the dependencies, no?

Edit: currently trying to deploy the dockerized AS-pipeline to DNANexus. My current strategy has me configuring environment variables, data_repo, mosek etc. by hand since DNANexus is real specific about the input and output formats it accepts. Installing these dependencies to system could get expensive and slow since it would have to happen every time the app is run. Code at https://github.com/chavez-lab/ampliconsuite-dnanexus-applet if you're interested.

jluebeck commented 7 months ago

Thanks for the explanation, I see the issue you are referring to now where these checks are not necessary & cumbersome for the docker/singularity case. I am going to move them so they do not happen with --finalize_only. There should be an update to AmpliconSuite-pipeline with some other changes, in the next couple of weeks and this issue will be fixed then.

Sounds very useful regarding DNANexus. Please keep me posted as you deploy and I would be happy to give it a test/take a look when completed.