Question: Quast not installing correctly
0
gravatar for d.hand
3 months ago by
d.hand0
d.hand0 wrote:

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?

ADD COMMENTlink modified 3 months ago • written 3 months ago by d.hand0
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

As far as I know, the datatype tex is not supported in Galaxy, or at least not in the core distribution and it shouldn't be needed when using the most current tool version.

There are two versions/authors for this tool in the Main Tool Shed (http://usegalaxy.org/toolshed). Try installing the IUC version if that is not what you are using now: https://toolshed.g2.bx.psu.edu/view/iuc/quast/0834c823d4b9

If that is the version in use and installation is a problem, this can be reported to the IUC at either their Gitter channel https://gitter.im/galaxy-iuc/iuc or by opening an issue ticket at the development repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast. Be sure to reference the tool version/source and your Galaxy version/config to help with troubleshooting.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k
0
gravatar for d.hand
3 months ago by
d.hand0
d.hand0 wrote:

Thanks it is iuc quast.

ADD COMMENTlink written 3 months ago by d.hand0

Thanks for confirming the version. I see that you have reached out to the IUC group here https://gitter.im/galaxy-iuc/iuc?at=5aa162cfe4ff28713a0bfeb7 and I also asked one of the tool authors about your install problems last night (on an internal chat). They will get back to you at one of these sites with more help.

ADD REPLYlink modified 3 months ago • written 3 months ago by Jennifer Hillman Jackson25k
0
gravatar for d.hand
3 months ago by
d.hand0
d.hand0 wrote:

Actually I have found out all tools I have installed recently have command not found errors. Is this indicative of anything? how do I check them manually? I resized my galaxy partition recently so I'm not sure if this has anything to with it.

ADD COMMENTlink modified 3 months ago • written 3 months ago by d.hand0

Admin: Conversation now at the Galaxy gitter channel this morning about dependency configuration updates: https://gitter.im/galaxyproject/Lobby?at=5aaa2ef0e4ff28713a34c1dd

ADD REPLYlink modified 3 months ago • written 3 months ago by Jennifer Hillman Jackson25k
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