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=$GALAXY_SLOTS" -v /inside/home/jeltje/exp/varscan2/programs/galaxy-dist:/inside/home/jeltje/exp/varscan2/programs/galaxy-dist:rw -v /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/tools/docker:/inside/home/jeltje/exp/varscan2/programs/galaxy-dist/tools/docker:rw -v /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/12:/inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/12:rw -v /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/files:/inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/files:rw -w /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/12 --net none busybox:ubuntu-14.04 /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/12/container.sh; return_code=$?; if [ -f /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/12/working_file ] ; then cp /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/job_working_directory/000/12/working_file /inside/home/jeltje/exp/varscan2/programs/galaxy-dist/database/files/000/dataset_19.dat ; fi; sh -c "exit $return_code" -Jeltje On Fri, Jan 23, 2015 at 12:24 PM, John Chilton <jmchil...@gmail.com> wrote: > 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/ >
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