Hello,
A Data Manager for this function exists in the Tool Shed. Perhaps it will help with troubleshooting?
https://toolshed.g2.bx.psu.edu/view/devteam/data_manager_picard_index_builde...
Best,
Jen
-- Jennifer Hillman-Jackson Galaxy Application Support http://usegalaxy.org http://galaxyproject.org http://biostar.usegalaxy.org
On Fri, Apr 29, 2016 at 2:09 PM, Beginner TI ruiwang.sz@gmail.com wrote:
Hi All,
I wrote a very simple wrapper for one picard function. Here is the xml file:
<tool name="CreateSequenceDictionary" id="picard_CreateSequenceDictionary" version="1.126.0"> <description>Create Sequence Dictionary</description>
<requirements> <requirement type="package" version="1.126.0">picard</requirement> </requirements>
<macros> <import>picard_macros.xml</import> </macros>
<command> @java_options@ java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary R="${ref_file}" O="${dict_file}" </command> <inputs> <param format="fa" name="ref_file" type="data" label="Using reference genome" help="-R,--reference_sequence" /> </inputs> <outputs> <data format="txt" name="dict_file" /> </outputs> <help> **Purpose** Create Sequence Dictionary from fa file </help> </tool>
It's ugly, I know. :-( Just want to finish a quick test...however when I tried to run a test, it always says something like:
Exception in thread "main" picard.PicardException: /media/4tb-ext/galaxy-data-store/database/files/008/dataset_8757.dat already exists. Delete this file and try again, or specify a different output file
When I looked at that file, it has a size 0, but even I remove that file, I'll still see the same thing.
Galaxy terminal executes:
galaxy.jobs.runners.local DEBUG 2016-04-29 13:55:51,423 (3189) executing: GALAXY_SLOTS="1"; export GALAXY_SLOTS; _JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} && export _JAVA_OPTIONS && java -jar $JAVA_JAR_PATH/picard.jar CreateSequenceDictionary R="/media/mybook/GATK_galaxyWrapper/hg38.fa" O="/media/4tb-ext/galaxy-data-store/database/files/008/dataset_8757.dat"
Seems it did the right thing, but why that set_meta set state to ERROR? Oh there was indeed a warning:
WARNING:galaxy.datatypes.registry:Overriding conflicting datatype with extension 'eset', using datatype from /media/4tb-ext/galaxy-data-store/database/tmp/tmp_Uuw5Y.
Have anyone seen this before? I'm quite confused since the same commandline runs smoothly in the terminal.
Thanks,
Rui
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