Dear galaxy developers,
I'm curently working on my local galaxy and I encountered some difficulties to add new genomes. I'm working with the "bowtie mapping" and "sam_to_bam tools" and the problem was that my galaxy was not able to automatically set the genome of the output in my history. I was forced to change it by hand before I could launch "sam_to_bam" on my data. For this reason, my workflow including these two steps would fail.
I finally figure out the problem: my dbkey (i.e: reference in build.txt) for my genome wasn't identical to the name of my ebwt file (i.e: my local indexe files for bowtie). Changing the name so that they are identical (case sensitive!) solved the problem.
This wasn't mentioned anywhere, neither in the bowtie_indices.loc.sample file, not in the builds.txt.sample one. I've spent a couple of hour to figure out what the problem was. It would be great if you could write something about that in both files or at least in bowtie_indices.loc.sample
Ismael