Just for fun, I updated galaxy-dist/tool-data/bowtie_indices.loc to be: mm10 mm10 mm10 /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 files (/usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index.*.bt2) But I do have files there: >ls -l /usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index total 4904587 -rwxrwxr-x 1 gg scicomp 886713321 May 23 2012 genome.1.bt2 -rwxrwxr-x 1 gg scicomp 661884440 May 23 2012 genome.2.bt2 -rwxrwxr-x 1 gg scicomp 4715 May 23 2012 genome.3.bt2 -rwxrwxr-x 1 gg scicomp 661884433 May 23 2012 genome.4.bt2 lrwxrwxrwx 1 gg scicomp 29 Feb 20 16:19 genome.fa -> ../WholeGenomeFasta/genome.fa -rwxrwxr-x 1 gg scicomp 886713321 May 23 2012 genome.rev.1.bt2 -rwxrwxr-x 1 gg scicomp 661884440 May 23 2012 genome.rev.2.bt2 Why am I getting that error? -Greg On Wed, Feb 20, 2013 at 4:53 PM, greg <[email protected]> wrote: > 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 > [2013-02-20 16:43:50] samtools_path: None > [2013-02-20 16:43:50] samtools_path after prog_path: > /usr/local/galaxy/installs/bin/samtools-0.1.18/samtools > Samtools version: 0.1.18.0 > [2013-02-20 16:43:50] Checking for Bowtie index files > Error: Could not find Bowtie 2 index files > (/usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/BowtieIndex.*.bt2) > > But this is what's in my galaxy-dist/tool-data/bowtie2_indices.loc file: > > mm10 mm10 mm10 > /usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index > > > Why isn't it looking in that directory for the bowtie2 files? It's > almost as if it's reading my bowtie_indices.loc file instead? > > Thanks, > > Greg ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
