Add dockerfile for bcl2fastq and cellranger #5
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| FROM dceoy/bcl2fastq | |||
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Thanks @thanhleviet 👍 Maybe we can just copy the instructions here instead so I can tag the container based on the version of bcl2fastq?
https://hub.docker.com/r/dceoy/bcl2fastq/dockerfile
The container is tagged to latest there so it could change.
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Did you mean copying the Dockerfile instruction? If so, no, because the download link to bcl2fastq has been closed.
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Ok. So lets just download and use that image then. No point adding a Docker image for that on nf-core. Are there any other containers on Dockerhub that are tagged with the version of bcf2fastq? Its better to be explicit about this in the pipeline if possible.
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| #Modified from http://github.com/TomKellyGenetics/cellranger_clean | |||
| FROM ubuntu:18.04 | |||
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Have you tested this container locally?
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yes, docker built it successfully but the image size is 6.2GB
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Please note that this is a work-in-progress. The container builds but calling cellranger is still being tested. I have it working locally but the remote versions are still being updated. Specifically:
- dependencies on a new version of jinja2 are required for SUMMARZE.REPORTS
- an updated version of tsne is required to run TSNE
- the scripts to create a cloupe file are closed source, as a workaround I have replaced it with a bash script that checks compatible inputs and returns a text file
The proprietary scripts from 10x Genomics are required to generate a working Cloupe file, they are not supported by this container. Please see the updated repo for details: https://github.com/TomKellyGenetics/cellranger_clean
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I'm okay with this container being used but please bear in mind that it is not supported by 10x Genomics (I have no affiliation with them). It is experimental for testing cellranger version 3. I don't have plans to maintain or support updated versions of cellranger it at this stage.
Cloupe files will not be supported by this version. Please note that they are subject to the 10x Genomics End User License Agreement.
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| #Modified from http://github.com/TomKellyGenetics/cellranger_clean | |||
| FROM ubuntu:18.04 | |||
There was a problem hiding this comment.
Please note that this is a work-in-progress. The container builds but calling cellranger is still being tested. I have it working locally but the remote versions are still being updated. Specifically:
- dependencies on a new version of jinja2 are required for SUMMARZE.REPORTS
- an updated version of tsne is required to run TSNE
- the scripts to create a cloupe file are closed source, as a workaround I have replaced it with a bash script that checks compatible inputs and returns a text file
The proprietary scripts from 10x Genomics are required to generate a working Cloupe file, they are not supported by this container. Please see the updated repo for details: https://github.com/TomKellyGenetics/cellranger_clean
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