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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