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gvlproject / gvl.ansible.playbook

Playbook for building the Genomics Virtual Laboratory
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Extract Genomic DNA error #51

Closed igormakunin closed 7 years ago

igormakunin commented 8 years ago

Fetch Sequences > "Extract Genomic DNA using coordinates from assembled/unassembled genomes" does not work with available genomes (tested on hg19).

The tool: /mnt/galaxy/galaxy-app/tools/extract/extract_genomic_dna.py

igormakunin commented 8 years ago

Galaxy-qld users have errors with the tool, so I've tried to fix it. It needs 2bit fasta. GVL-4.1.0 does not provide 2bit. I've installed data_manager_twobit_builder and created 2bit fasta on a test GVL-4.1.0 instance. Galaxy was restarted, but the tool failed: No sequences are available for 'hg19', request them by reporting this error. The fix: .loc files alignseq.loc, lastz_seqs.loc and twobit.loc were copied from /mnt/galaxyIndices/tool-data/dm/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/74b09c8e5f6e/ to /mnt/galaxyIndices/. Derek says the tool is 'native' to Galaxy, so it does not see path to loc file created for toolshed tools. Is it a proper way to fix the error? Can we add 2bit to indices? This will enable Extract Genomic DNA and lastz tools, with proper .loc files.

nuwang commented 7 years ago

Adding 2bit ref data to indices will make the archive size very big. Therefore, it's probably best to let the users who need this install the ref data themselves through the data manager.