Question: getting parameter names served incorrectly
gravatar for anders.dannesboe
3.6 years ago by
anders.dannesboe0 wrote:


I was trying to use the and it kept on reporting an error.

Here is the Job Commandline:

python /data/galaxy/shed_tools/ "/data/galaxy/galaxy-dist/database/files/000/dataset_86.dat" \ --jar "$JAVA_JAR_PATH/CreateSequenceDictionary.jar" \ --fasta_filename "/data/galaxy/galaxy-dist/tool-data/sacCer2/seq/sacCer2.fa" \ --fasta_dbkey "sacCer2" \ --fasta_description "S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2)" \ --data_table_name "gatk_picard_indexes"


Each parameter name gets a " " append to it, so pythons optparse.OptParser will get " --jar" " --fast_dbkey" etc. served, and won't be able to parse its arguments.

Kind regards


ADD COMMENTlink modified 3.6 years ago by Daniel Blankenberg ♦♦ 1.7k • written 3.6 years ago by anders.dannesboe0

Hello, We are reviewing and will get back to you shortly. This may be a known issue that we have an in-progress solution for, but thank you for reporting it! Feedback is always great! Jen, Galaxy team

ADD REPLYlink written 3.6 years ago by Jennifer Hillman Jackson25k
gravatar for Daniel Blankenberg
3.6 years ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:

Hi Anders,

A fix for this issue has been pushed to the ToolShed. You can update the repository through the admin panel in your Galaxy instance. Let us know if you encounter additional issues.

ADD COMMENTlink written 3.6 years ago by Daniel Blankenberg ♦♦ 1.7k
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