How to access a genome fasta index (FAI) build with data_manager_sam_fasta_index_builder (qustion also on biostars)

[chrausch]

I am modifying a galaxy tool (in testtoolshed: falco) that should have access to samtools fasta indices of reference genomes.

Currently, in the tool's xml file: REF_FILE="${genomeSource.indices.fields.path}" is called.

But this links to /home/galaxy/galaxy/tool-data/hg19/seq in case hg19 is selected. I rather want it to look in: /home/galaxy/galaxy/tool-data/hg19/sam_indexes/hg19

What are the galaxy-internal variables to build up the path to this location?

Thanks, Christian

[shiltemann]

Hiya Christian :)

Your tool is configured to use the all_fasta data table to find the paths to the reference genomes, but the fastas created by that data manager are in the fasta_indexes data table, so I think if you edit the following line your tool xml file: <options from_data_table="all_fasta"> and change all_fasta to fasta_indexes it should work?

[chrausch]

Thanks Saskia, for this tip.
Indeed, the tool's xml file needed to be changed as indicated above. Furthermore, tool_data_table_conf.xml.sample needed to be changed accordingly (replace all all_fasta to fasta_indexes). Finally, a fasta_indexes.loc.sample file needed to be placed in the tool's tool-data directory. I copied the file with this name from /home/galaxy/galaxy/tool-data.