Hi,
We're loving Galaxy. This is an excellent interface and set of tools.
The issue we're having is running SAM to BAM. We've been following the "Illumina Mapping: Single Reads" screencast, with the only significant difference (I think) being that we're using our own uploaded reference genomes instead of a pre-built index for the Bowtie alignment.
When we get to the SAM to BAM step, we have two options for "Choose the source for the reference list": 1. Locally Cached, 2. History.
1. If we try to use "Locally Cached", we get the following error before the job is even added to the queue: "Unspecified genome build, click the pencil icon in the history item to set the genome build". We've tried to follow those directions, but don't see the reference genome we want in the list.
2. If we try to use "History" and specify the SAM file and then the FASTA file we used to do the bowtie alignment, we get the following error:
An error occurred running this job: Samtools Version: 0.1.12 (r862) Error creating indexes from reference (/galaxy/home/g2main/galaxy_main/database/files/001/894/dataset_1894598.dat), [fai_build_core] different line length in sequence 'gi|118467340|ref|NC_008596.1|'. Segmentation fault
Any guidance would be wonderful.
My user name is: dar78@pitt.edu
Thanks for your help, Dan Russell University of Pittsburgh