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gvlproject / gvl.ansible.playbook

Playbook for building the Genomics Virtual Laboratory
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Extract genomic DNA issue #92

Open igormakunin opened 7 years ago

igormakunin commented 7 years ago

Extract genomic DNA tool needs 2bit fasta. It uses /mnt/galaxyIndices/alignseq.loc data_manager_twobit_builder does not write to this file. It writes to the same file in the data manager folder, but the tool does not see it. I fix it by copying alignseq.loc from data_manager_twobit_builder directory to /mnt/galaxyIndices/alignseq.loc

nuwang commented 7 years ago

From Jess: It's a bit of a hack, but the loc file one can be fixed by editing the tool xml

edit /mnt/galaxy/galaxy-app/tools/extract/extract_genomic_dna.xml line 19 from

to -g /mnt/galaxyIndices/tool-data/dm/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/9946bc39c834/