Actually, for recent Galaxy, I'd recommend making a conda recipe for UMI-tools and contributing it to bioconda:
https://bioconda.github.io/ 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.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 > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
