Here is an explanation I sent out a couple months ago. I'll be adding
this to the wiki soon. If you already have loc files in place, the
last paragraph may be most relevant to you.
The Bowtie and BWA tools are two of our tools that rely on an external
list of something--in this case, of the indices of reference genomes
required by Bowtie and BWA. We do not release these indices with
Galaxy and instead you create them yourself (or you can download them
in the case of Bowtie). These lists are stored in "loc" files. If
these files are not present, the tool cannot be loaded into the
browser. The loc files contain the name of each reference index and
the location of it on your system.
The loc files are stored in the tool-data directory. The Bowtie loc
file should be called "bowtie_indices.loc". There are actually two for
BWA, one for color indices and one for base indices. These need to be
called "sequence_index_color.loc" and "sequence_index_base.loc".
are sample loc files for Bowtie and BWA which give more information
about the format of the file. The sample files have the same names
with ".sample" appended and are also in the tool-data directory.
Bowtie offers numerous pre-built indices, which can be found at
. If you want to build indices not available pre-built, you can use
Bowtie's bowtie-build command to do it. The BWA indices all need to be
built individually, which can be done using the index command. See the
Bowtie and BWA documentation for details on how to use these commands.
Note that we did find that it is best to build the index on the same
system where the tool would be running.
Please let us know if you need anything else.
On Nov 30, 2009, at 11:06 AM, Dean Snyder wrote:
The "Select a reference genome" popup in the NGS mapping
empty for the Bowtie and BWA tools on my local Galaxy install (latest
release). How can I populate it?
Dean A. Snyder
Center for Inherited Disease Research (CIDR)
Johns Hopkins School of Medicine
Bayview Research Campus
333 Cassell Dr, Triad Bldg, Suite 2000
Baltimore, MD 21224
cell:717 668-3048 office:410-550-4629
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