The script generated to call Galaxy is here: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/metadata.py#L838
The job template stuff that setups of the environment the job runs in is here: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh#L17 This second file changes in a large way with 16.01 which ditches eggs for virtual environments and wheels. We don't explicitly support running different versions of Python on the worker and handler it seems - but I have seen it work before. You could probably hack up DEFAULT_JOB_FILE_TEMPLATE.sh to point at a different instance of Galaxy for your version. I'd hope there was something easier though. On Mon, Jan 25, 2016 at 3:05 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock <p.j.a.c...@googlemail.com> > wrote: >> Hello all, >> >> We're currently looking at changing our Galaxy setup to link user accounts >> with Linux user accounts for better cluster integration (running jobs as the >> actual user on SGE). As part of this, we've tried setting up a fresh >> installation on a new VM which has thrown up some issues. >> >> [snip] > > The next problem on my list was jobs successfully submitting to SGE > and running, then failing with a Python exception: > > galaxy.eggs.EggNotFetchable > > These emails from Donald Shrum and Jingchao Zhang (BCC'd) look > very similar, although I don't see they ever had a reply/resolution: > > https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-October/020719.html > https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-January/018034.html > > We eventually realised that the new Galaxy VM server was running > Python 2.7 (default under CentOS 7), but the cluster nodes were > running Python 2.6 (default under CentOS 6). > > (Our current Galaxy server is also still running CentOS 6, which is > likely why I never hit this before.) > > Replacing the VM with CentOS 6 we were able to get this to > work - but was that necessary? How exactly do the cluster jobs > invoke Python (especially when run as the associated Linux > user account rather than under the Galaxy Linux account)? > > Sadly the cluster documentation does not mention Python at all: > > https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster/ > > This seems to be an oversight, > > Regards, > > Peter > ___________________________________________________________ > 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/
