diff deseq-hts_1.0/README @ 9:e27b4f7811c2 draft

Updated DESeq version 1.12

--- a/deseq-hts_1.0/README	Wed Jun 27 15:38:39 2012 -0400
+++ b/deseq-hts_1.0/README	Tue Oct 08 08:09:28 2013 -0400
@@ -1,48 +1,52 @@
----------------------------------------------------
-DESeq-hts: A Galaxy wrapper for DESeq version 1.6.1
----------------------------------------------------
+----------------------------------------------------
+DESeq: A Galaxy wrapper for DESeq version 1.12.1
+----------------------------------------------------
 
 Description:
+------------
     DESeq can be used as a web service embedded in a Galaxy instance. 
     We call it as DESeq-hts. 
 
-Requirements: 
+Requirements:
+-------------
     MATLAB/OCTAVE and Python :- Preprocessing of sequencing reads and GFF files
-    R, Bio-conductor package :- Required for DESEQ 
+    R, Bio-conductor package :- Required for DESeq 
     SCIPY, NUMPY :- for python  
-    SAMTOOLS :- Read processing 
+    SAMTOOLS :- Sequencing read processing 
 
 Contents:
-    [src]
+---------
+    ./src
     All relevant scripts for DESeq-hts are located in the subdirectory
-    src. src/deseq.sh is the main script to start DESeq-hts. The 
-    preprocessing of BAM and GFF file start before the R DESEQ script. 
+    src. src/deseq-hts.sh is the main script to start DESeq-hts. The 
+    preprocessing of BAM and GFF file start before the R DESeq script. 
 	Please follow the shell script to understand the details. 
     
-    [galaxy]
+    ./galaxy
     Galaxy tool configuration file can be found galaxy folder. Please 
     make necessary editing for .xml file and remaining .sh files and 
     perform few tests. 
 
-    [setup_deseq-hts.sh]
+    ./setup_deseq-hts.sh
     Setup script for DESeq-hts.
 
-    [mex]
+    ./mex
     matlab executable files.
 
-    [bin]
+    ./bin
     Contains deseq_config.sh file which is used for the configuration of 
     DESeq-hts. According to your platform, the default file will be changed.
 
-    [test_data]
-    This subsirectory contains all data for running a functional test in
+    ./test_data
+    This sub-directory contains all data for running a functional test in
     Galaxy framework. You may need to move these test files into the test-data
     directory.
 
-    [tools]
+    ./tools
     A python based GFF parsing program. Also contains small utils programs.
 
 Getting started:
+----------------
     Check for all requirements first, then
 
     a) Run ./setup_deseq-hts.sh and setup paths and configuration options for DESeq-hts.
@@ -57,6 +61,7 @@
     c) Edit the Galaxy tool configuration file to adjust the path if necessary. 
 
 Licenses:
+---------
     If **DESeq** is used to obtain results for scientific publications it should be cited as [1].
 
     This wrapper program (DESeq-hts) is free software; you can redistribute it and/or modify it 
@@ -65,11 +70,21 @@
 
     Written (W) 2009-2012 Jonas Behr, Regina Bohnert, Andre Kahles, Gunnar Raetsch, Vipin T. Sreedharan
     Copyright (C) 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany and 
-                  2012 cBio Memorial Sloan Kettering Cancer Center, New York City, USA.
+                  2013 cBio Memorial Sloan Kettering Cancer Center, New York City, USA.
 
 References:
+-----------
     [1] Anders, S and Huber, W (2010): `Differential expression analysis for sequence count data`. 
 
+Contributions:
+--------------
+    15 Aug. 2013 
+    Philippe Moncuquet
+    Bioinformatics Analyst, Bioinformatics Core, CSIRO Mathematics, Informatics and Statistics
+    
+    Extended the DESeq result.
+
 Contact:
-    [e-mail] 
+--------
+    support [at] oqtans.org