galaxyproject / galaxyproject/tools-devteam

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

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Description

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

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