The docker version is 1.1.2.
I'm not entirely sure how to get the galaxy version, but hg sum resulted in
parent: 14955:c25df9f3d31e tip
Update tag latest_2014.10.06 for changeset ff6e36d7a238
branch: stable
So docker may be a bit too old. To get some more control over my OS, I did
a fresh Ubuntu i
Based on the screenshot you are calling the program correctly.
Can you tell me what version of Docker you are running and Galaxy you
are running? There have been a number of fixes in both programs over
the last six months to a year. Docker is known to consume a lot of
space in /var - it probably d
Our sysadmin just notified me docker was taking up large amounts of space
in
/var/lib/docker/devicemapper/devicemapper/data
and
/var/lib/docker/devicemapper/devicemapper/metadata
I noticed the following DEBUG message in paster.log:
galaxy.jobs.runners.local DEBUG 2015-01-23 13:30:19,503 (12) exec
See attached for screenshot!
Thanks for the links.
On Mon, Jan 26, 2015 at 11:37 AM, John Chilton wrote:
> Can you send me a screenshot of the Tool form right before you hit
> submit. It is odd that two commands are executed barely differing at
> all. There were some recent UI changes and I w
Can you send me a screenshot of the Tool form right before you hit
submit. It is odd that two commands are executed barely differing at
all. There were some recent UI changes and I want to make sure that
you are passing two inputs once and not submitting one input twice in
the newly named "batch mo
I'm still trying to debug this.
How do I change the working directory? I can't seem to find out how all
those directory mounts get passed to docker - the catDocker.xml appears to
generate a 'cat' command that I assume ends up in
()/job_working_directory/000/12/container.sh
but I can't find where t
I tried the second solution (setting everything to rw) and while I can
confirm that the command is changed accordingly, the results are the same:
Two empty output files and the same error message.
Command from paster.log:
docker run -e "GALAXY_SLOTS=$GALAXY_SLOTS" -v
/inside/home/jeltje/exp/varsca
My first thought is the bug mentioned here -
https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-November/020892.html
along with potential work arounds. Are you able to confirm that this
is or is not the problem at all?
-John
On Fri, Jan 23, 2015 at 2:37 PM, Jeltje van Baren
wrote:
> Hi,
>
Hi,
I'm following instructions at
https://github.com/apetkau/galaxy-hackathon-2014.
When I try to run the concatenate-datasets on two input files, two odd
things happen. First, TWO nearly identical commands are generated in the
History panel, only differing in their output filename. In paster.log
