Hi
I was trying to use the data_manager_gatk_picard_index_builder.py and it kept on reporting an error.
Here is the Job Commandline:
python /data/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_gatk_picard_index_builder/a15709ad26ea/data_manager_gatk_picard_index_builder/data_manager/data_manager_gatk_picard_index_builder.py "/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
Anders
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