Question: Uploading mgf files throws error (Galaxy-P workflow)
0
gravatar for thomas.mohr
9 months ago by
thomas.mohr0 wrote:

Dear group,

uploading an mgf formatted file results in the error below and the file is not uploaded. The mgf is valid since upload to Galaxy-P works. The installation is linux, newest version of galaxy, no tools installed. What am I doing wrong ? Thanks a lot ! Thomas

galaxy.jobs.handler DEBUG 2018-01-24 15:18:00,030 (2) Dispatching to local runner galaxy.jobs DEBUG 2018-01-24 15:18:00,050 (2) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2018-01-24 15:18:00,135 Job [2] queued (105.209 ms) galaxy.jobs.handler INFO 2018-01-24 15:18:00,145 (2) Job dispatched galaxy.jobs.command_factory INFO 2018-01-24 15:18:00,283 Built script [/srv/opt/galaxy/database/jobs_directory/000/2/tool_script.sh] for tool command [python /srv/opt/galaxy/tools/data_source/upload.py /srv/opt/galaxy /srv/opt/galaxy/database/jobs_directory/000/2/registry.xml /srv/opt/galaxy/database/tmp/tmpdnGkds 2:/srv/opt/galaxy/database/jobs_directory/000/2/dataset_2_files:/srv/opt/galaxy/database/files/000/dataset_2.dat] galaxy.jobs.runners DEBUG 2018-01-24 15:18:00,408 (2) command is: rm -rf working; mkdir -p working; cd working; /srv/opt/galaxy/database/jobs_directory/000/2/tool_script.sh; return_code=$?; cd '/srv/opt/galaxy/database/jobs_directory/000/2'; [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True python "/srv/opt/galaxy/database/jobs_directory/000/2/set_metadata_0UIi6Q.py" "/srv/opt/galaxy/database/jobs_directory/000/2/registry.xml" "/srv/opt/galaxy/database/jobs_directory/000/2/working/galaxy.json" "/srv/opt/galaxy/database/jobs_directory/000/2/metadata_in_HistoryDatasetAssociation_2_R5mxyR,/srv/opt/galaxy/database/jobs_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_Gm1ovZ,/srv/opt/galaxy/database/jobs_directory/000/2/metadata_out_HistoryDatasetAssociation_2_ZPd892,/srv/opt/galaxy/database/jobs_directory/000/2/metadata_results_HistoryDatasetAssociation_2_hcdHfJ,/srv/opt/galaxy/database/files/000/dataset_2.dat,/srv/opt/galaxy/database/jobs_directory/000/2/metadata_override_HistoryDatasetAssociation_2_erpNf2" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2018-01-24 15:18:00,421 (2) executing job script: /srv/opt/galaxy/database/jobs_directory/000/2/galaxy_2.sh galaxy.jobs DEBUG 2018-01-24 15:18:00,432 (2) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local DEBUG 2018-01-24 15:18:02,932 execution finished: /srv/opt/galaxy/database/jobs_directory/000/2/galaxy_2.sh galaxy.jobs.output_checker DEBUG 2018-01-24 15:18:02,936 Tool produced standard error failing job - [Traceback (most recent call last): File "/srv/opt/galaxy/tools/data_source/upload.py", line 431, in <module> __main__() File "/srv/opt/galaxy/tools/data_source/upload.py", line 419, in __main__ add_file(dataset, registry, json_file, outpu] galaxy.jobs DEBUG 2018-01-24 15:18:02,959 (2) setting dataset 2 state to ERROR galaxy.jobs INFO 2018-01-24 15:18:03,168 Collecting metrics for Job 2 galaxy.jobs DEBUG 2018-01-24 15:18:03,233 job 2 ended (finish() executed in (300.111 ms)) 77.119.242.227 - - [24/Jan/2018:15:18:03 +0200] "GET /galaxy/api/histories/f2db41e1fa331b3e/contents?details=f2db41e1fa331b3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-01-24T14%3A17%3A59.000Z&qv=False&qv=False HTTP/1.1" 200 - "https://server1.mohrkeg.co.at/galaxy/" "Mozilla/5.0 (X11; Linux x86_64; rv:58.0) Gecko/20100101 Firefox/58.0" galaxy.tools.error_reports DEBUG 2018-01-24 15:18:03,253 Bug report plugin <galaxy.tools.error_reports.plugins.sentry.sentryplugin object="" at="" 0x7f4fa59ca190=""> generated response None galaxy.model.metadata DEBUG 2018-01-24 15:18:03,253 Cleaning up external metadata files 77.119.242.227 - - [24/Jan/2018:15:18:03 +0200] "GET /galaxy/api/histories/f2db41e1fa331b3e?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "https://server1.mohrkeg.co.at/galaxy/" "Mozilla/5.0 (X11; Linux x86_64; rv:58.0) Gecko/20100101 Firefox/58.0" 77.119.242.227 - - [24/Jan/2018:15:18:09 +0200] "PUT /galaxy/api/histories/f2db41e1fa331b3e/contents/datasets/f597429621d6eb2b HTTP/1.1" 200 - "https://server1.mohrkeg.co.at/galaxy/" "Mozilla/5.0 (X11; Linux x86_64; rv:58.0) Gecko/20100101 Firefox/58.0"

admin mgf datatype local galaxyp • 333 views
ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson25k • written 9 months ago by thomas.mohr0
0
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Some extra configuration will be needed. This datatype is not included in the primary Galaxy distribution. The public Galaxy-P server https://usegalaxyp.org/ has had some custom configuration to handle this datatype and other domain-specific tools/resources.

Try contacting the authors of these tools or review their website/forum/support help for admin config and tool install guidelines: https://galaxyproject.org/public-galaxy-servers/galaxy-p/

Some from that group do review questions at this forum, so you might get another answer, but I wouldn't wait for that. Contact them directly for the quickest resolution. Once resolved, if you want to post back the solution here, that would be great (but is optional!).

Thanks! Jen, Galaxy

ADD COMMENTlink written 9 months ago by Jennifer Hillman Jackson25k
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