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AlexsLemonade / alsf-scpca

Management and analysis tools for ALSF Single-cell Pediatric Cancer Atlas data.
BSD 3-Clause "New" or "Revised" License
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Update Cellranger for mkfastq #89

Closed jashapiro closed 3 years ago

jashapiro commented 3 years ago

This PR updates the cellranger Dockerfile to also build bcl2fastq so that cellranger mkfastq can be run.

In order to build this, you now need to download bcl2fastq from Illumina as well as Cellranger, but I have not yet updated the documentation to reflect this fact, hence the draft status.

jashapiro commented 3 years ago

I have now updated the README, but part of me wonders if we should switch this image from ubuntu to centos, so that we can use the illumina provided RPM file, which should make building much faster (compiling bcl2fastq is not fast) and should also result in a smaller image.

Probably a future problem.

jashapiro commented 3 years ago

I think we definitely could have just left this as is, but your comment about using Centos had me curious and I wanted to test it out. So I gave it a try and using the rpm file and with Centos as a base image I was able to build it all within the Dockerfile wihout needing a separate install script and it was fairly fast taking only a few minutes. I checked and when you go into the image, the software is there. Either option could work, but maybe simpler to use the rpm file?

Let's do it! This takes way too long to build and I should have just switched rather than fighting with dependencies! Which centos did you use? (I think 7 is probably what we will want, because of some centos support changes that we don't need to get too far into now)

allyhawkins commented 3 years ago

Which centos did you use? (I think 7 is probably what we will want, because of some centos support changes that we don't need to get too far into now)

I originally used centos:8 as the base image but I just did centos:7 and it also worked fine so we should be good to go.

jashapiro commented 3 years ago

Realized that this has been hanging out for a bit. I revised it to use the rpm file, but left the build script for posterity. Requesting rereview...