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/
