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:
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:
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!
Synthetic Genomics, Inc.
Senior Research Associate, Bioinformatics
11149 North Torrey Pines Road
La Jolla, California 92037
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at: