Hello David,

To clarify, the locally cached data files in the tool-data directory of the Galaxy distribution ( e.g., alignseq.loc, binned_scores.loc, etc ) contain "pointers" to the location of locally stored files that you've indexed.  These ".loc" files are used by certain tools for validation or to dynamically generate a select list.  For example, the alignseq.loc file is referenced the the blat_wrapper tool  ( see the ~/tools/metag_tools/blat_wrapper.py code ) to retrieve sequences for a specified build.

The "Database / build:" select list on the Edit Metadata Attributes page ( reached by clicking the pencil icon ) is a SelectParameter metadata element of the Data class ( see ~/lib/galaxy/datatypes/data.py ) whose options are retrieved from util.dbnames ( see ~/lib/galaxy/util/__init__.py ). 

These are 2 different categories of files, serving 2 different purposes. 

To have additional values displayed in the "Database/build:" select list, you can add values to the ~/tool-data/shared/ucsc/builds.txt file ( or some other file if you reconfigure dbnames in ~/util/__init__.py ), but the indexed files for those new values should be pointed to by your tool-data/faseq.loc file, which is referenced by a tool using it.

Please let me know if this was not clear.

Greg Von Kuster
Galaxy Development Team

David Goodstein wrote:

We identified our local sequence file in tool-data/faseq.loc.  However, that file never shows up as an option under the "database/build" pulldown
(when we "pencil" edit a dataset). What additional configuration is necessary to have our local files show up in the database/build pulldowns?

David Goodstein
UCB Center for Integrative Genomics

On 24 Jun 2008, at 16:47, Rochak Neupane wrote:

---------- Forwarded message ----------
From: Greg Von Kuster <ghv2@psu.edu>
Date: Wed, Jun 18, 2008 at 1:06 PM
Subject: Re: [galaxy-user] local sequence storage
To: Rochak Neupane <rneupane@berkeley.edu>
Cc: galaxy-user@bx.psu.edu

Hello Rochak,

Yes, this is certainly possible.  The Galaxy distribution is
configured to look in the ~/tool-data directory for files which point
to your locally cached sequences.  See the "tool_data_path" setting in
the Galaxy config ( universe_wsgi.ini ).  This directory contains
sample ".loc.sample" files that are included in the distribution to
provide information about how to point the ".loc" versions of the same
files to your own locally cached sequences.  The comments at the
beginning of each of these files provides this information.

Greg Von Kuster
Galaxy Development Team

Rochak Neupane wrote:


I recently started using galaxy. I installed a local copy of galaxy,  and am wondering how I can add our own sequences so that galaxy  understands them when fetching. So instead of fetching from PSU it'll  look at a local source. Is this doable? If so, how can I configure this?

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