Hi Mark,

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". There 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 http://bowtie-bio.sourceforge.net/index.shtml . 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.

Kelly Galaxy team

On Oct 1, 2009, at 4:26 PM, Mark Garner wrote:

Hello,

we're in the process of installing bowtie and bwa to get them working with Galaxy and have a question. Looking at left hand menu item "NGS: Mapping" on the home page of Galaxy that we have just installed we see:

NGS: Mapping Megablast compare short reads against nt and wgs databases Parse blast XML output

Digging in tools_config.xml we see:

<section name="NGS: Mapping" id="solexa_tools"> <!-- <tool file="sr_mapping/lastz_wrapper.xml" /> --> <tool file="metag_tools/megablast_wrapper.xml" /> <tool file="metag_tools/megablast_xml_parser.xml" /> <tool file="sr_mapping/bowtie_wrapper.xml" /> <tool file="sr_mapping/bwa_wrapper.xml" /> </section>

Looking in .../tools/sr_mapping we see both:

bowtie_wrapper.xml bwa_wrapper.xml

And checking say bowtie_wrapper.xml we see

<tool id="bowtie_wrapper" name="Bowtie" version="1.0.0"> <description> fast alignment of reads against reference sequence </ description >

Everything looks good so why do we not see sub-menu items for bowtie and bwa? All we see under NGS: Mapping are the two items I listed initially, "Megablast compare short reads against nt and wgs databases" and "Parse blast XML output".

Thanks for your help. Mark. _______________________________________________ galaxy-dev mailing list galaxy-dev@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev