See attached for screenshot! Thanks for the links.
On Mon, Jan 26, 2015 at 11:37 AM, John Chilton <jmchil...@gmail.com> 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 want to make sure that > you are passing two inputs once and not submitting one input twice in > the newly named "batch mode"? > > container.sh is generated in command_factory.py using containers.py - > here are some relevant links. > > > https://bitbucket.org/galaxy/galaxy-central/src/tip/lib/galaxy/jobs/command_factory.py?at=default > > https://bitbucket.org/galaxy/galaxy-central/src/tip/lib/galaxy/tools/deps/containers.py?at=default > > https://bitbucket.org/galaxy/galaxy-central/src/tip/lib/galaxy/tools/deps/docker_util.py?at=default > > -John > > > On Mon, Jan 26, 2015 at 2:17 PM, Jeltje van Baren > <jeltje.van.ba...@gmail.com> wrote: > > 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 that's happening - container.sh isn't listed in > any > > file under galaxy-dist. > > job_conf.xml lists the directories that get passed as variables - again, > > when and where are those defined? > > > > Thanks, > > > > -Jeltje > > > > > > On Fri, Jan 23, 2015 at 1:35 PM, Jeltje van Baren > > <jeltje.van.ba...@gmail.com> wrote: > >> > >> 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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