Hello all Galaxy devs,

I’ve come across (what seems to be) a Galaxy bug (or rather, tool-shed bug) when I run the data manager data_manager_gatk_picard_index_builder (rev. a15709ad26ea) from the Galaxy main tool shed repo on a clean Galaxy install.

Installation goes fine - when I install this data manager, all dependencies are correctly installed: package_picard_1_56_0 (rev. 99a28567c3a3) and package_samtools_0_1_18 (rev. 171cd8bc208d).

After installation, I go to Admin -> Manage local data (beta) -> Run Data Manager Tools, click “Generate GATK-sorted Picard indexes” and the data manager form is displayed. I select the reference genome (either hg19 or hg38 - installed with data_manager_fetch_genome_dbkeys_all_fasta from the main tool shed, rev. bca4c608408c - working fine with other tools including bowtie2 and trackster), enter “hg19” both “Name of sequence” and “ID for sequence” fields, and click “Execute”.

The indexing job is added to the queue, but when I go to view data manager jobs for this data manager, I see it stopped with the following error:

Traceback (most recent call last):
  File "/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_gatk_picard_index_builder/a15709ad26ea/data_manager_gatk_picard_index_builder/data_manager/data_manager_gatk_picard_index_builder.py", line 179, in <module>
    if __name__ == "__main__": main()
  File "/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_gatk_picard_index_builder/a15709ad26ea/data_manager_gatk_picard_index_builder/data_manager/data_manager_gatk_picard_index_builder.py", line 162, in main
    raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) )
Exception: "None" is not a valid dbkey. You must specify a valid dbkey.

Inspecting galaxy.log doesn’t reveal anything relevant (at least for me - which is why I need your help!):

galaxy.jobs DEBUG 2015-04-17 11:13:23,031 (63) Working directory for job is: /home/galaxy/galaxy-dist/database/job_working_directory/000/63
galaxy.jobs.handler DEBUG 2015-04-17 11:13:23,044 (63) Dispatching to local runner
192.168.2.74 - - [17/Apr/2015:11:13:22 +0100] "POST /api/tools HTTP/1.1" 200 - "http://192.168.2.221:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_gatk_picard_index_builder%2Fgatk_picard_index_builder%2F0.0.1" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_2) AppleWebKit/600.4.10 (KHTML, like Gecko) Version/8.0.4 Safari/600.4.10"
galaxy.jobs DEBUG 2015-04-17 11:13:23,168 (63) Persisting job destination (destination id: local)
galaxy.jobs.handler INFO 2015-04-17 11:13:23,212 (63) Job dispatched
galaxy.tools.deps DEBUG 2015-04-17 11:13:23,393 Building dependency shell command for dependency 'samtools'
galaxy.tools.deps DEBUG 2015-04-17 11:13:23,395 Building dependency shell command for dependency 'picard'
galaxy.jobs.runners DEBUG 2015-04-17 11:13:23,475 (63) command is: PACKAGE_BASE=/home/galaxy/tool-deps/samtools/0.1.18/devteam/data_manager_gatk_picard_index_builder/a15709ad26ea; export PACKAGE_BASE; . /home/galaxy/tool-deps/samtools/0.1.18/devteam/data_manager_gatk_picard_index_builder/a15709ad26ea/env.sh; PACKAGE_BASE=/home/galaxy/tool-deps/picard/1.56.0/devteam/data_manager_gatk_picard_index_builder/a15709ad26ea; export PACKAGE_BASE; . /home/galaxy/tool-deps/picard/1.56.0/devteam/data_manager_gatk_picard_index_builder/a15709ad26ea/env.sh; python /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_gatk_picard_index_builder/a15709ad26ea/data_manager_gatk_picard_index_builder/data_manager/data_manager_gatk_picard_index_builder.py "/home/galaxy/galaxy-dist/database/files/000/dataset_70.dat" \ --jar "$JAVA_JAR_PATH/CreateSequenceDictionary.jar" \ --fasta_filename "/home/galaxy/galaxy-dist/tool-data/hg19/seq/hg19.fa" \ --fasta_dbkey "hg19" \ --fasta_description "Human, Feb. 2009, GRCh37/hg19" \ --data_table_name "gatk_picard_indexes"; return_code=$?; python /home/galaxy/galaxy-dist/database/job_working_directory/000/63/set_metadata_Ts4xSd.py /home/galaxy/galaxy-dist/database/tmp/tmpfomc7m /home/galaxy/galaxy-dist/database/job_working_directory/000/63/galaxy.json /home/galaxy/galaxy-dist/database/job_working_directory/000/63/metadata_in_HistoryDatasetAssociation_70_Lkhynl,/home/galaxy/galaxy-dist/database/job_working_directory/000/63/metadata_kwds_HistoryDatasetAssociation_70_IuPBQs,/home/galaxy/galaxy-dist/database/job_working_directory/000/63/metadata_out_HistoryDatasetAssociation_70_uuRnIn,/home/galaxy/galaxy-dist/database/job_working_directory/000/63/metadata_results_HistoryDatasetAssociation_70_aVp4XH,/home/galaxy/galaxy-dist/database/files/000/dataset_70.dat,/home/galaxy/galaxy-dist/database/job_working_directory/000/63/metadata_override_HistoryDatasetAssociation_70_hXaBQB; sh -c "exit $return_code"
galaxy.jobs.runners.local DEBUG 2015-04-17 11:13:23,476 (63) executing job script: /home/galaxy/galaxy-dist/database/job_working_directory/000/63/galaxy_63.sh
galaxy.jobs DEBUG 2015-04-17 11:13:23,526 (63) Persisting job destination (destination id: local)
galaxy.jobs.runners.local DEBUG 2015-04-17 11:13:24,976 execution finished: /home/galaxy/galaxy-dist/database/job_working_directory/000/63/galaxy_63.sh
galaxy.jobs DEBUG 2015-04-17 11:13:25,054 setting dataset state to ERROR
galaxy.jobs DEBUG 2015-04-17 11:13:25,122 job 63 ended
galaxy.datatypes.metadata DEBUG 2015-04-17 11:13:25,123 Cleaning up external metadata files


Some more system details:

Galaxy version: latest_15.03, running on Ubuntu 14.04.2 LTS
Java: 1.8.0_45-b14 from the webupd8 Ubuntu repo.
Using Postresql locally, everything else local too. Cloned from the Bitbucket repo (in case this matters).


Can anyone shed some light on this? In the traceback log above it seems options.fasta_dbkey is being set to “None” rather than “hg19” but I am not sure how to solve this, or if this is indeed the problem.


Thank you in advance!

All the best,
-- Paulo


____________________________________________________________

Paulo Filipe Silva | PhD, Biology | MSc, Bioinformatics
Bioinformatician @ CGPP - Centre for Predictive and Preventive Genetics

IBMC - Institute for Molecular and Cell Biology
Rua do Campo Alegre, 823
4150-180 Porto, Portugal
Telephone: +351 22 607 49 42 ext 2811
Fax: +351 22 600 29 23