Thanks, adding the genome did work!
But I still don't understand why bowtie2 is looking at the
bowtie_indices.loc file instead of the bowtie2_indices.loc file?
Could that be a bug somewhere?
Here's why I think I'm using bowtie 2:
[2013-02-20 16:31:10] Beginning TopHat run (v2.0.6)
Hi guys,
I'm getting this error when running tophat for Illumina:
Error in tophat:
[2013-02-20 16:43:50] Beginning TopHat run (v2.0.6)
---
[2013-02-20 16:43:50] Checking for Bowtie
Bowtie version: 2.0.2.0
[2013-02-20 16:43:50] Checking for Samtools
Just for fun, I updated galaxy-dist/tool-data/bowtie_indices.loc to be:
mm10mm10mm10
/usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index
And ran it again.
Now it's looking at the correct directory (Bowtie2Index) but still says:
Error: Could not find Bowtie 2 index
But this is what's in my galaxy-dist/tool-data/bowtie2_indices.loc file:
mm10mm10mm10
/usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index
You need:
/usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome
J.
Why isn't it looking in that
