Looks like I’m hitting this issue:
https://github.com/galaxyproject/galaxy/issues/2797
Steve
—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy
> On 29 Aug 2016, at 11:09 AM, Steve Cassidy wrote:
>
> Thanks Marius,
> I tried a build based on the image you
Thanks Marius,
I tried a build based on the image you mentioned and get the following error:
/export/galaxy-central/database/job_working_directory/000/1/tool_script.sh:
line 9: /tool_deps/_conda/bin/activate: No such file or directory
/export/galaxy-central/database/job_working_directory/000/1
Hi Steve,
Looks like you're running an older version of galaxy in the docker
container, since newer galaxy will build the metadata environment in a
separate environment called 'conda-metadata-env',
and we have also changed the way that the handlers receive their Python
environment (that's why sql
Ok, probing further trying to understand this. It looks like the job runner is
trying to call set_meta() from galaxy_ext/metadata/set_metadata.py. In there
there’s a line that tries to set up the PATH:
# insert *this* galaxy before all others on sys.path
sys.path.insert( 1, os.path.abspath( os.
Nah, definitely baby steps…
so, in the repo you point to there seems to be an error in the Dockerfile, the
ENV line should use the var=value syntax to have more than one setting on one
line (maybe that’s changed recently in docker).
with this I built a new docker image, when I run my first tool
Hi Steve,
you call this baby-steps? I think this is huge! :)
All what you are missing is to enable conda in Galaxy.
Look at Gregs new flavour which is entirely Conda/Galaxy based.
You need to enable these env vars to make Galaxy conda enabled:
https://github.com/gregvonkuster/docker-galaxy-csg/
