Hi everyone,
I am trying to set up a local instance of Galaxy, including the Visulization using Trackster, on my Mac.
I followed the Introduction provieded at https://wiki.galaxyproject.org/VisualizationSetup and made sure that BEDtools and the necessary KentUtils are in Galaxys PATH (all can be run in Terminal).
However, when I try to load a local BAM file into Trackster I get an error:
Trackster Error
/Users/galaxy/galaxy/database/job_working_directory/000/9/galaxy_9.sh: line 21: bedGraphToBigWig: command not found
At the same time the console shows:
galaxy.tools.actions INFO 2016-02-19 13:23:17,187 Handled output (97.939 ms)
galaxy.tools.actions INFO 2016-02-19 13:23:18,069 Verified access to datasets (13.058 ms)
127.0.0.1 - - [19/Feb/2016:13:23:16 +0200] "GET /api/datasets/5969b1f7201f12ae?hda_ldda=hda&data_type=converted_datasets_state&chrom=chr2L&retry=true HTTP/1.1" 200 - "http://localhost:8080/visualization/trackster?dataset_id=5969b1f7201f12ae&dbkey=dm3&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:34.0) Gecko/20100101 Firefox/34.0"
galaxy.jobs DEBUG 2016-02-19 13:23:18,754 (10) Working directory for job is: /Users/galaxy/galaxy/database/job_working_directory/000/10
galaxy.jobs.handler DEBUG 2016-02-19 13:23:18,769 (10) Dispatching to local runner
galaxy.jobs DEBUG 2016-02-19 13:23:18,943 (10) Persisting job destination (destination id: local:///)
galaxy.jobs.runners DEBUG 2016-02-19 13:23:18,952 Job [10] queued (183.039 ms)
galaxy.jobs.handler INFO 2016-02-19 13:23:19,016 (10) Job dispatched
galaxy.tools.deps DEBUG 2016-02-19 13:23:19,374 Building dependency shell command for dependency 'ucsc_tools'
galaxy.tools.deps WARNING 2016-02-19 13:23:19,375 Failed to resolve dependency on 'ucsc_tools', ignoring
galaxy.tools.deps DEBUG 2016-02-19 13:23:19,375 Building dependency shell command for dependency 'bedtools'
galaxy.tools.deps WARNING 2016-02-19 13:23:19,375 Failed to resolve dependency on 'bedtools', ignoring
galaxy.jobs.runners DEBUG 2016-02-19 13:23:19,536 (10) command is: bedtools genomecov -bg -split -ibam /Users/galaxy/galaxy/database/files/000/dataset_7.dat -g /Users/galaxy/galaxy/tool-data/shared/ucsc/chrom/dm3.len > temp.bg ; bedGraphToBigWig temp.bg /Users/galaxy/galaxy/tool-data/shared/ucsc/chrom/dm3.len /Users/galaxy/galaxy/database/files/000/dataset_9.dat; return_code=$?; python "/Users/galaxy/galaxy/database/job_working_directory/000/10/set_metadata_RPeMM_.py" "/Users/galaxy/galaxy/database/tmp/tmpOkiVNP" "/Users/galaxy/galaxy/database/job_working_directory/000/10/galaxy.json" "/Users/galaxy/galaxy/database/job_working_directory/000/10/metadata_in_HistoryDatasetAssociation_9_MEy_sZ,/Users/galaxy/galaxy/database/job_working_directory/000/10/metadata_kwds_HistoryDatasetAssociation_9_39sIDu,/Users/galaxy/galaxy/database/job_working_directory/000/10/metadata_out_HistoryDatasetAssociation_9_uYWiC6,/Users/galaxy/galaxy/database/job_working_directory/000/10/metadata_results_HistoryDatasetAssociation_9_pgn41m,/Users/galaxy/galaxy/database/files/000/dataset_9.dat,/Users/galaxy/galaxy/database/job_working_directory/000/10/metadata_override_HistoryDatasetAssociation_9_ZbcftM" 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.local DEBUG 2016-02-19 13:23:19,604 (10) executing job script: /Users/galaxy/galaxy/database/job_working_directory/000/10/galaxy_10.sh
galaxy.jobs DEBUG 2016-02-19 13:23:19,677 (10) Persisting job destination (destination id: local:///)
127.0.0.1 - - [19/Feb/2016:13:23:23 +0200] "GET /api/datasets/5969b1f7201f12ae?hda_ldda=hda&data_type=converted_datasets_state&chrom=chr2L HTTP/1.1" 200 - "http://localhost:8080/visualization/trackster?dataset_id=5969b1f7201f12ae&dbkey=dm3&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:34.0) Gecko/20100101 Firefox/34.0"
127.0.0.1 - - [19/Feb/2016:13:23:28 +0200] "GET /api/datasets/5969b1f7201f12ae?hda_ldda=hda&data_type=converted_datasets_state&chrom=chr2L HTTP/1.1" 200 - "http://localhost:8080/visualization/trackster?dataset_id=5969b1f7201f12ae&dbkey=dm3&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:34.0) Gecko/20100101 Firefox/34.0"
127.0.0.1 - - [19/Feb/2016:13:23:33 +0200] "GET /api/datasets/5969b1f7201f12ae?hda_ldda=hda&data_type=converted_datasets_state&chrom=chr2L HTTP/1.1" 200 - "http://localhost:8080/visualization/trackster?dataset_id=5969b1f7201f12ae&dbkey=dm3&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:34.0) Gecko/20100101 Firefox/34.0"
galaxy.jobs.runners.local DEBUG 2016-02-19 13:23:35,406 execution finished: /Users/galaxy/galaxy/database/job_working_directory/000/10/galaxy_10.sh
galaxy.jobs DEBUG 2016-02-19 13:23:35,511 setting dataset state to ERROR
galaxy.jobs INFO 2016-02-19 13:23:35,845 Collecting metrics for Job 10
galaxy.jobs DEBUG 2016-02-19 13:23:35,868 job 10 ended (finish() executed in (462.226 ms))
galaxy.datatypes.metadata DEBUG 2016-02-19 13:23:35,868 Cleaning up external metadata files
127.0.0.1 - - [19/Feb/2016:13:23:38 +0200] "GET /api/datasets/5969b1f7201f12ae?hda_ldda=hda&data_type=converted_datasets_state&chrom=chr2L HTTP/1.1" 200 - "http://localhost:8080/visualization/trackster?dataset_id=5969b1f7201f12ae&dbkey=dm3&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:34.0) Gecko/20100101 Firefox/34.0"
Can someone give me a hint what is going worng? I tried installing BEDtools/UCSC tools from the toolshed, as well as trying to find a reason as to why the dependency on those tools cannot be resolved.
Thank you for your help!
