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_builder/00491eabe22b 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...@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 > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >
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