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.
On 5 July 2016 at 08:56, Matthias De Smet <matthias.des...@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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