Hi folks,

I am trying to setup a local copy of Galaxy and I am running into a few issues 
with which I would greatly appreciate some help.

1.       I am trying to setup my "built-in" indices for bowtie mapping and I 
have been following the instructions given at 
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup very closely. My 
'bowtie_indices.loc' file, located in the $GALAXY_DIST/tool-data/ directory has 
only one entry that is uncommented:
#buildname        filepath
where the blank spaces are tabs. These instructions differ from those given as 
comments in the 'bowtie_indices.loc' file, requiring 4 entries. I  any case, 
neither of these formats seem to be working. My file path should be correct:

cmd->ls /bioinformatics/bio_db/silva_SSURef_108_tax_silva_trunc/bowtie/*.ebwt

I have re-started my Galaxy server and cleared the cache on my browser and 
still no success. Should I be modifying any builds.txt file?  Any suggestions 
or am I missing something?

2.       Is there planned Galaxy support for bowtie2?

3.       I was very impressed by the JGI setup of Galaxy 
(https://galaxy.jgi-psf.org/) , particularly the NFS file import.
How can I implement this on my local copy?
Does using this option bypass the 2GB file upload limit of using the GUI? Does 
the data still go through the browser's POST method?

4.       Is there a way to specify the input files for a workflow when running 
the workflow through the command line? I've only seen methods for monitoring 
the contents of a folder, not for specifying a pair of input reads (ie: forward 
/ reverse reads from same Lib).

Thanks for the advice people!

Daniel Brami
Synthetic Genomics, Inc.
Senior Research Associate, Bioinformatics
11149 North Torrey Pines Road
La Jolla, California  92037
Phone: 858.433.2230
Fax: 858.754.2988

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