A number of fixes and best-practice tweaks.#83
A number of fixes and best-practice tweaks.#83davebx wants to merge 2 commits intogalaxyproject:masterfrom
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davebx
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Jun 23, 2016
davebx
commented
- Clean up the local environment file.
- Install R and BiocInstaller.
- Install BioConductor R packages Rgraphviz and motifbreakR.
- Use get_url for file downloads instead of curl or wget.
- Use the known working method for enabling supervisord on boot.
- Some post-playbook cleanup.
- Rearrange some apt actions, consolidate others.
- Clean up the local environment file. - Install R and BiocInstaller. - Install BioConductor R packages Rgraphviz and motifbreakR. - Use get_url for file downloads instead of curl or wget. - Use the known working method for enabling supervisord on boot. - Some post-playbook cleanup. - Rearrange some apt actions, consolidate others.
| if [[ -z $PYTHONPATH ]] ; then | ||
| export PYTHONPATH={{ dev_user_home }}/miniconda2/lib/python2.7 | ||
| else | ||
| export PYTHONPATH={{ dev_user_home }}/miniconda2/lib/python2.7:$PYTHONPATH |
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So that it doesn't stomp previously defined PYTHONPATH additions.
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I don't get why we are doing anything with the Python path at all I mean. Also you are putting conda ahead of system Python on the path - this breaks things. I'd just stick with adding conda to the path, but at the end and not touch Python path (unless there is a documented reason).
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I am fine with changes (to my low understanding of packer and ansible) but I would rather not have them in the image that we will link out to conference attendees in one hour. We have no time to test. Can we just add the requested R packages as a separate PR and build the image or are there actual bugs with the machine that this is fixing @davebx ? |
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👍 This looks great! |
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@martenson I have created pull request #84 based on master + these R additions. |
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