Question: Issues with setting up Trackster/Visulization on local Galaxy
0
gravatar for robertstreeck
2.3 years ago by
robertstreeck0 wrote:

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!

software error galaxy • 1.0k views
ADD COMMENTlink modified 2.2 years ago by matthias.desmet150 • written 2.3 years ago by robertstreeck0
1
gravatar for matthias.desmet
2.2 years ago by
Belgium
matthias.desmet150 wrote:

Hi,

the bedGraphToBigWig executables (and all others) need to be available in the $PATH variable of the user running Galaxy.
For example, if you download the executables and copy the to /usr/bin, they should typically be available in PATH.

You can test this by doing "which bedGraphToBigWig", which should then return the full path where the executable is installed.

M

 

ADD COMMENTlink written 2.2 years ago by matthias.desmet150

If you are sure the executables are available in you path, then you shoud check your job configuration, could be an issue with the env of your job runner.

M

ADD REPLYlink written 2.2 years ago by matthias.desmet150
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