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
<jeltje.van.baren@gmail.com> wrote:
> 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, only
> the second one shows up. Second, the program fails, with this info in the
> History:
>
> An error occurred with this dataset:
> Galaxy slots passed through contain as 1
> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/10/container.sh:
> line 2: can't create
> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/files/000/dataset_14.dat
>
> This happens for both commands in the History panel, only the output
> filename in the other error is dataset_15.dat
>
> Oddly, the dataset_14.dat and dataset_15.dat are both created during this
> command, they just end up empty.
>
> Paster.log:
>
> galaxy.jobs.runners DEBUG 2015-01-23 11:08:35,973 (10) command is: docker
> inspect busybox:ubuntu-14.04 > /dev/null 2>&1
> [ $? -ne 0 ] && docker pull busybox:ubuntu-14.04 > /dev/null 2>&1
>
> docker run -e "GALAXY_SLOTS=$GALAXY_SLOTS" -v
> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist:/inside/home/jeltje/exp/varscan2/programs/galaxy-dist:ro
> -v
> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/tools/docker:/inside/home/jeltje/exp/varscan2/programs/galaxy-dist/tools/docker:ro
> -v
> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/10:/inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/10:rw
> -v
> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/files:/inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/files:rw
> -w
> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/10
> --net none busybox:ubuntu-14.04
> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/10/container.sh;
> return_code=$?; if [ -f
> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/10/working_file
> ] ; then cp
> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/10/working_file
> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/files/000/dataset_15.dat
> ; fi; sh -c "exit $return_code"
> galaxy.jobs.runners.local DEBUG 2015-01-23 11:08:36,040 (10) executing job
> script:
> /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/10/galaxy_10.sh
> galaxy.jobs DEBUG 2015-01-23 11:08:36,091 (10) Persisting job destination
> (destination id: docker_local)
>
>
> What could be happening here, and how do I fix it?
>
> Thanks,
>
> -Jeltje
>
>
>

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