Hi all,
I’m making baby steps towards having a repeatable installation for my tools.
But I’m now stuck, so help would be appreciated.
I have a tool that works and is in the test toolshed (alveoimport in Data
Sources).
It depends on my python package which is now part of bioconda (pyalveo, ve
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/
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
On Thu, Aug 25, 2016 at 2:25 PM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:
> Hi Peter,
> No actually I meant in what file is the table job_parameter getting filled
> during execution?
> Katherine
>
> On Fri, Aug 5, 2016 at 3:00 PM, Peter van Heusden wrote:
>
>> You mean the stu
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.
