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