Hi All,

I wrote a very simple wrapper for one picard function. Here is the xml file:

<description>Create Sequence Dictionary</description>

<requirement type="package" version="1.126.0">picard</requirement>

</requirements>

<import>picard_macros.xml</import>

</macros>

@java_options@

java -jar \$JAVA_JAR_PATH/picard.jar

CreateSequenceDictionary

R="${ref_file}"

O="${dict_file}"

</command>

</inputs>

</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