Hi
L-A,
Thank
you for the reply. Another kind member (thanks Dan Dorset!)
also took the time to explain me these over the phone this
morning.
The
missing piece of information, which you have included in
your instructions, and which was omitted in the
documentation, is the link between the bowtie_indices.loc
and the builds.txt file, which is never mentioned anywhere
as far as I know.
As
for the file size limit, it’s more of a question regarding
the understanding of how Galaxy works.
In
my local copy of Galaxy running on Unix, given an input file
using the complete path, does Galaxy need to copy the input
data through the browser to the ‘tmp’ and output directories
or does it use a system call. Can this be made into a link
to save space and time?
I
really do appreciate the help – thanks!
Daniel
Hello Daniel,
I had similar issues when setting up our own. The POST size
limit is not set by Galaxy. If I remember correctly it's in
your Apache config, though I don't remember exactly where it
was.
For the .loc files, here is an example:
dm3-bt dm3 D.melanogaster 3
/path/to/indexes/bowtie/d_melanogaster_fb5_22
The items are as follows:
- dm3-bt is a unique ID for this index. It can be whatever you
want but it needs to be unique in this file.
- dm3 is the build ID that you set in the
tool-data/shared/ucsc/builds.txt file. It's the first item
there. It's there to tell what genome build your index was
generated from. Make sure that the two of them correspond.
- D.melanogaster 3 is the display name that you want to have
in the widgets (can have spaces but no tabs)
- /path/to/indexes/bowtie/d_melanogaster_fb5_22 is the full
path of the index files without the final suffixes (the first
part before the first dot)
Each line's items must be separated by an actual tab
character. Depending on your editor, you might want to make
sure the tab key doesn't print like 4 spaces instead of \t.
Hope that helps
Best,
L-A
Le 23/02/2012 19:47, Brami, Daniel a écrit :
I have been
struggling with setting up my local Galaxy instance for the
past two days.
Can anyone post a copy of their
universe_wsgi.ini file , with the sensitive info commented /
removed?
I need an instance that can handle local
files greater than 2 GB (ie: does not go through POST method
of browser to get data) and has permissions to use pre-built
bowtie indices.
Also, a FUNCTIONNAL copy of the
‘bowtie_indices.loc’ would be very helpful. (none of my
prebuilt databases are appearing in drop down menu).
Please assist.
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
DBrami@SyntheticGenomics.com
www.SyntheticGenomics.com
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