Galaxy Error: Could not find Bowtie 2 index files

[caa5042]

Hi Guys

Im trying to run tophat for illumina in galaxy and I get this error

Error in tophat:

[2013-08-04 21:11:20] Beginning TopHat run (v2.0.9)
-----------------------------------------------
[2013-08-04 21:11:20] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-08-04 21:11:20] Checking for Samtools
Samtools version: 0.1.18.0
[2013-08-04 21:11:20] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (/db/galaxydb/dm3/bowtie_index/dm3.*.bt2)


what do i do?

[fubar]

A source download of Galaxy doesn't include many third party dependencies, genomes or indices and requires a fair bit of additional installation and tweaking to get everything working - eg see http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

Without knowing a lot more, it looks like you need to download and index the dm3 genome with bowtie2-build as described on the Galaxy wiki, in the directory where bowtie is looking for it as indicated in your error message:

Error: Could not find Bowtie 2 index files (/db/galaxydb/dm3/bowtie_index/dm3.*.bt2)