PeptideAtlas software
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| $SBEAMS below refers to /net/dblocal/www/html/[devXX/]sbeams (as of June 16, 2009). | $SBEAMS below refers to /net/dblocal/www/html/[devXX/]sbeams (as of June 16, 2009). | ||
| - | ==Creating a PeptideAtlas build== | + | $PIPELINE refers to /net/db/projects/PeptideAtlas/pipeline. |
| + | ==Creating ("building" a PeptideAtlas build== | ||
| A collection of csh, bash, and perl scripts, plus various text, XML, and csv files, all outlined in [[Building Peptide Atlas]]. | A collection of csh, bash, and perl scripts, plus various text, XML, and csv files, all outlined in [[Building Peptide Atlas]]. | ||
| - | Many of these are in /net/db/projects/PeptideAtlas/pipeline/bin. | + | Many of these are in $PIPELINE: |
| + | * $PIPELINE/recipes -- notes on how to create and load a build; not executable | ||
| + | * $PIPELINE/run_scripts -- shell scripts for running the build pipeline | ||
| + | * $PIPELINE/bin -- mostly perl scripts, called directly or indirectly from the scripts in $PIPELINE/run_scripts | ||
| Some are in $SBEAMS. | Some are in $SBEAMS. | ||
Revision as of 21:38, 18 June 2009
The core data in PeptideAtlas is a large set of peptides organized into individual builds according to organism and sample type (for example, Yeast, Human Plasma, or Human Glycocapture). A peptide may belong to multiple builds.
$SBEAMS below refers to /net/dblocal/www/html/[devXX/]sbeams (as of June 16, 2009). $PIPELINE refers to /net/db/projects/PeptideAtlas/pipeline.
Creating ("building" a PeptideAtlas build
A collection of csh, bash, and perl scripts, plus various text, XML, and csv files, all outlined in Building Peptide Atlas.
Many of these are in $PIPELINE:
- $PIPELINE/recipes -- notes on how to create and load a build; not executable
- $PIPELINE/run_scripts -- shell scripts for running the build pipeline
- $PIPELINE/bin -- mostly perl scripts, called directly or indirectly from the scripts in $PIPELINE/run_scripts
Some are in $SBEAMS.
I am not sure why there are two locations.
Loading a PeptideAtlas build
A collection of perl scripts, all or most of which execute SQL queries on the SBEAMS database.
These are all in $SBEAMS:
- $SBEAMS/lib/scripts/PeptideAtlas
- $SBEAMS/lib/perl/SBEAMS/ -- general SBEAMS perl modules
- $SBEAMS/lib/perl/SBEAMS/PeptideAtlas -- perl modules for PeptideAtlas
Displaying PeptideAtlas via web interface
Perl scripts, mostly in $SBEAMS/cgi/PeptideAtlas.
