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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