I'm having an issue installing the latest version of quast on my 17.09 galaxy cluster.
in the history I get:
/mnt/galaxy/tmp/job_working_directory/004/4494/tool_script.sh: line 9: quast: command not found WARNING:galaxy.model:Datatype class not found for extension 'tex' WARNING:galaxy.model:Datatype class not found for extension 'tex' WARNING:galaxy.model:Datat
in the galaxy log I get this: There are no tarballs to remove galaxy.jobs.runners DEBUG 2018-03-07 10:36:39,731 (4494) command is: rm -rf working; mkdir -p working; cd working; /mnt/galaxy/tmp/job_working_directory/004/4494/tool_script.sh; return_code=$?; if [ -f /mnt/galaxy/tmp/job_working_directory/004/4494/working/Quast_report.html ] ; then cp /mnt/galaxy/tmp/job_working_directory/004/4494/working/Quast_report.html /mnt/galaxy/files/006/dataset_6911.dat ; fi; if [ -f /mnt/galaxy/tmp/job_working_directory/004/4494/working/Icarus.html ] ; then cp /mnt/galaxy/tmp/job_working_directory/004/4494/working/Icarus.html /mnt/galaxy/files/006/dataset_6910.dat ; fi; if [ -f /mnt/galaxy/tmp/job_working_directory/004/4494/working/Quast_report.tex ] ; then cp /mnt/galaxy/tmp/job_working_directory/004/4494/working/Quast_report.tex /mnt/galaxy/files/006/dataset_6909.dat ; fi; if [ -f /mnt/galaxy/tmp/job_working_directory/004/4494/working/Quast_report.tsv ] ; then cp /mnt/galaxy/tmp/job_working_directory/004/4494/working/Quast_report.tsv /mnt/galaxy/files/006/dataset_6908.dat ; fi; if [ -f /mnt/galaxy/tmp/job_working_directory/004/4494/working/Quast_report.txt ] ; then cp /mnt/galaxy/tmp/job_working_directory/004/4494/working/Quast_report.txt /mnt/galaxy/files/006/dataset_6907.dat ; fi; cd '/mnt/galaxy/tmp/job_working_directory/004/4494'; [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True export PATH=$PATH:'/mnt/galaxy/tmp/job_working_directory/004/4494/conda-metadata-env/bin' ; export PATH=$PATH:'/mnt/galaxy/tmp/job_working_directory/004/4494/conda-metadata-env/bin' ; python "/mnt/galaxy/tmp/job_working_directory/004/4494/set_metadata_3O3qt7.py" "/mnt/galaxy/tmp/job_working_directory/004/4494/registry.xml" "/mnt/galaxy/tmp/job_working_directory/004/4494/working/galaxy.json" "/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_in_HistoryDatasetAssociation_7406_ZUHZjP,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_kwds_HistoryDatasetAssociation_7406_au3YsP,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_out_HistoryDatasetAssociation_7406_90hBZV,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_results_HistoryDatasetAssociation_7406_pyrWKf,/mnt/galaxy/files/006/dataset_6911.dat,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_override_HistoryDatasetAssociation_7406_1YlVhK" "/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_in_HistoryDatasetAssociation_7405_h6fLVd,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_kwds_HistoryDatasetAssociation_7405_PCqd0v,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_out_HistoryDatasetAssociation_7405_Bx_Rdc,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_results_HistoryDatasetAssociation_7405_W4ZIYk,/mnt/galaxy/files/006/dataset_6910.dat,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_override_HistoryDatasetAssociation_7405_o6sns_" "/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_in_HistoryDatasetAssociation_7404_m8wiuK,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_kwds_HistoryDatasetAssociation_7404_jWjin3,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_out_HistoryDatasetAssociation_7404_9bqn8_,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_results_HistoryDatasetAssociation_7404_Q42KjP,/mnt/galaxy/files/006/dataset_6909.dat,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_override_HistoryDatasetAssociation_7404_c86kkS" "/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_in_HistoryDatasetAssociation_7403_t63wrE,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_kwds_HistoryDatasetAssociation_7403_fHtYRc,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_out_HistoryDatasetAssociation_7403_tP_1Eu,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_results_HistoryDatasetAssociation_7403_ZeTa3h,/mnt/galaxy/files/006/dataset_6908.dat,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_override_HistoryDatasetAssociation_7403_uPAzCg" "/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_in_HistoryDatasetAssociation_7402_6kmMJj,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_kwds_HistoryDatasetAssociation_7402_kBMOGa,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_out_HistoryDatasetAssociation_7402_T6zLw4,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_results_HistoryDatasetAssociation_7402_12pG8C,/mnt/galaxy/files/006/dataset_6907.dat,/mnt/galaxy/tmp/job_working_directory/004/4494/metadata_override_HistoryDatasetAssociation_7402_ywEslH" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.drmaa DEBUG 2018-03-07 10:36:39,764 (4494) submitting file /mnt/galaxy/tmp/job_working_directory/004/4494/galaxy_4494.sh
any ideas: I did get some tool errors in the admin panel but I installed bgzip to bam and it seemed to get rid of these. Do you have any idea what might be going wrong?
