On 07/31/2013 11:24 AM, Perez, Ricardo wrote:
Dear all,
When trying to run velvet optimizer in galaxy, all the files we get return the following:
"No peek"
When looking at the output of galaxy, we get the following:
galaxy.jobs.runners.local DEBUG 2013-07-31 09:31:46,829 execution finished: perl /usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/simon-gladman/velvet_optimiser/43c89d82a7d3/velvet_optimiser/velvet_optimiser_wrapper_vlsci.pl '19' '23' '2' '0' 'short' 'False' '<galaxy.datatypes.sequence.FastqSanger object at 0x6e664d0>' '/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2067.dat''not_shortMP''other:''no_amos''not_verbose' '/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2665.dat''/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2666.dat' '/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2667.dat''/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2663.dat' '/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2668.dat' > /usr/local/galaxy/galaxy-dist/database/files/002/dataset_2664.dat
galaxy.jobs.runners DEBUG 2013-07-31 09:31:47,027 executing external set_meta script for job 1983: /usr/local/galaxy/galaxy-dist/set_metadata.sh ./database/files /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983 . /usr/local/galaxy/galaxy-dist/universe_wsgi.ini /usr/local/galaxy/galaxy-dist/database/tmp/tmp3460Jz /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/galaxy.json /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3117_enOT5T,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3117_vy3tDq,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3117_IFmVK8,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3117_0j3kza,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3117_zwMKHf /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3116_YppZ1L,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3116_Sniis0,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3116_l9RPFx,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3116_It8rUk,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3116_AwvXlS /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3115_TOhpBs,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3115_wUomyo,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3115_nsUrJl,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3115_DAmGEt,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3115_hFGdc0 /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3114_59uEii,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3114_UcezIt,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3114_YmOlHD,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3114_owVBfP,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3114_O3UH82 /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3113_vMrQrs,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3113_YhwIGZ,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3113_pAG6wP,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3113_9ImAZ6,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3113_uI5cbM /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3112_NwB9j6,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3112_LK2cWo,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3112__FDnXW,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3112_mZQULN,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3112_k3SWCq
However when running velvet optimizer from the command line (the first command from above) we get the correct output just fine. We have re-installed the tools and velvet. It seems like galaxy is passing the command just fine, but we are getting nothing back to galaxy. Anyone has ideas on how to fix this problem?
Thank you very much for your time and support, --Ricardo Perez
Dear all,
We were able to find the root of this problem. It turns out that if you start galaxy as a service using the /.hg/store/data/contrib/galaxy.debian-init.i then some tools will fail later on in the installation. In our case it was velvet optimizer, velvetg, FastX-tool kit, and others. For people who may encounter this problem in the future, the way we got things running again is by running galaxy as:
sh run.sh --reload (or --daemon)
Thank you for your help, --Ricardo Perez