Actually, for recent Galaxy, I'd recommend making a conda recipe for UMI-tools and contributing it to bioconda:
Then your tool can just depend on this and the conda dependency resolver (default in Galaxy since 16.01) can find it. Others can comment on the recent work on conda/toolshed integration.
Peter
On 5 July 2016 at 08:56, Matthias De Smet Matthias.DeSmet@ugent.be wrote:
Hi
I’m trying to put together a tool + dependency package to use umi-tools (
https://github.com/CGATOxford/UMI-tools) from Galaxy.
I’m at a loss on how I should organise this.
The package is available from either github or pip. Which one is
preferable to use? How do I make sure the package dependencies are installed? I’ve found the <action type="download_by_url”> and <action type=“create_virtualenv”> actions, but I’m not really sure that’s the way to go. I havent found any real resources on how to build package dependencies either.
Any help? Now, approaching it by downloading the package from github
with <action type="download_by_url”> and installing it with <action type="shell_command">python setup.py install</action>. This, however, tries to install the package to /usr/bin/ which isn’t desirable (obviously).
Thanks a lot! M
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