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

From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Louise-Amélie Schmitt
Sent: Friday, February 24, 2012 12:23 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] universe_wsgi.ini

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
dbr...@syntheticgenomics.com<mailto:dbr...@syntheticgenomics.com>
www.SyntheticGenomics.com<http://www.syntheticgenomics.com/>






___________________________________________________________

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:



  http://lists.bx.psu.edu/

___________________________________________________________
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:

  http://lists.bx.psu.edu/

Reply via email to