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

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
[fai_build_core] different line length in sequence
Segmentation fault

Any guidance would be wonderful.

My user name is: da...@pitt.edu

Thanks for your help,
Dan Russell
University of Pittsburgh

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