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Bioconductor / bioc_docker

[DEPRECATED] Docker containers for Bioconductor
https://github.com/bioconductor/bioconductor_docker
Artistic License 2.0
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Online and offline parent containers #29

Closed lgatto closed 7 years ago

lgatto commented 7 years ago

The latest mscore built successfully, and proteomics is currently being re-built - fingers crossed. I haven't managed to do a good job at testing my changes locally because proteomics depends on mscore that is fetched from the docker hub. Here is a description

  1. I identify that I need to add libx11-dev to the failing container for an R package to build. Adding this new apt-get dependency to proteomics allows me to build the container locally.
  2. But I would prefer that dependency to be added to the parent container mscore. I make the change there and build it successfully locally.
  3. How can I test proteomics so that it uses the locally built mscore (step 2) rather then fetch bioconductor/proteomics from docker hub.

Without being able to test step 3, I need to wait that the containers get updated remotely before being sure that the child container effectively builds/works.

@lshep @sneumann - Any idea how to address my question in step 3?

lshep commented 7 years ago

I'm pretty sure if you build your docker locally calling it the parent name i.e docker build -t bioconductor/devel_mscore2 that when you go to build proteomics it will use the local copy and not fetch a new version...

You could also run the container docker run -t -i bioconductor/devel_mscore2 /bin/bash and add whatever additional dependencies manually first and start R to see if the install of packages from the proteomics install script works... not ideal since its all manually but serves its purpose.

lgatto commented 7 years ago

Thank you @lshep - I thought I tried setting the tag but didn't seem to work. I'll know soon enough, when the the proteomics2 build status comes up.