Hi Daniel,

I have to admit it took me some time and a lot of trial and error to figure out how the .loc files work :) I'm glad it works for you now.

I'm not fully sure about what exactly you want to do but here is what I think could be of help: If your Galaxy runs on the same machine your files are stored in, or if the place they are stored is mounted on your Galaxy's machine, don't bother with the upload tool in the analysis panel nor the Shared Data section, use the Admin section > "Manage data libraries" so you can load files from giving Galaxy a filesystem path. This way you can ask it to load the data without moving/copying it. (it's also superfast)

Hope that helps, L-A

Le 24/02/2012 19:25, Brami, Daniel a écrit :

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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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 DBrami@SyntheticGenomics.com mailto:DBrami@SyntheticGenomics.com www.SyntheticGenomics.com http://www.syntheticgenomics.com/

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