Re: [galaxy-dev] tophat for illumina looking in wrong directory for bowtie2 indexes?
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) --- [2013-02-20 16:31:10] Checking for Bowtie Bowtie version: 2.0.2.0 -Greg On Wed, Feb 20, 2013 at 5:44 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote: 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 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/ ___ 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/
[galaxy-dev] tophat for illumina looking in wrong directory for bowtie2 indexes?
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: mm10mm10mm10 /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/
Re: [galaxy-dev] tophat for illumina looking in wrong directory for bowtie2 indexes?
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 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 scicomp29 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 margeem...@gmail.com 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: mm10mm10mm10 /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/
Re: [galaxy-dev] tophat for illumina looking in wrong directory for bowtie2 indexes?
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 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/ ___ 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/
