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Illumina / hap.py

Haplotype VCF comparison tools
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Request for rtgtools tag on Docker Hub #16

Closed GodloveD closed 7 years ago

GodloveD commented 7 years ago

Thanks for providing this in an image on Docker Hub. Would it be possible to create another build with the --with-rtgtools option and tag it with :rtgtools or some such?

pkrusche commented 7 years ago

The build on Docker hub is slightly outdated (v0.3.6). From v0.3.7, the Docker image will include rtgtools by default -- I will build and upload an updated image.

GodloveD commented 7 years ago

Great. Looking forward to it.

pkrusche commented 7 years ago

I have pushed the 0.3.7 tag to https://hub.docker.com/r/pkrusche/hap.py/tags/ -- this should include rtgtools. The version is slightly ahead of 0.3.7 because some changes to the Dockerfile were necessary. Apart from the dependencies and compile process, the version is the same as 0.3.7.

pkrusche commented 7 years ago

Hope this fixes it. Please reopen if there are issues with the image.

GodloveD commented 7 years ago

Thanks very much. I used this image to install hap.py in a Singularity container on the NIH Biowulf cluster. Looks like it is working as far as I can tell from running the tests in your README.md.

The one thing I will suggest is that you may want to consider restructuring your Dockerfile in future builds. I think that docker creates a new layer for every RUN command, so many people cram multiple commands into a single RUN so that they don't make a million layers.

Thanks again. I appreciate it.

pkrusche commented 7 years ago

Thanks for the feedback! Improving the Dockerfile is on my backlog (in particular the process that downloads the reference is suboptimal also currently -- I think in the future I'll provide a lightweight image which doesn't include a reference Fasta file).

A slightly more streamlined Dockerfile based on Centos 6 is already included here: https://github.com/Illumina/hap.py/blob/dev/Dockerfile.centos6 ; I'll post an image once it is finished building.