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.ba...@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 > > > > ___________________________________________________________ > 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/
