Mercurial > repos > vipints > deseq_hts

comparison deseq-hts_2.0/README @ 10:2fe512c7bfdf draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
DESeq2 version 1.0.19 added to the repo
author vipints <vipin@cbio.mskcc.org>
date Tue, 08 Oct 2013 08:15:34 -0400
parents
children
comparison
equal deleted inserted replaced
9:e27b4f7811c2 10:2fe512c7bfdf
1 ------------------------------------------------------
2 DESeq2-hts: A Galaxy wrapper for DESeq2 version 1.0.19
3 ------------------------------------------------------
4
5 Description:
6 ------------
7 DESeq2 can be used as a web service embedded in a Galaxy instance.
8 We call it as DESeq2-hts.
9
10 Requirements:
11 -------------
12 MATLAB/OCTAVE and Python :- Preprocessing of sequencing reads and GFF files
13 R, Bio-conductor package :- Required for DESeq2
14 SCIPY, NUMPY :- for python
15 SAMTOOLS :- Sequencing read processing
16
17 Contents:
18 ---------
19 ./src
20 All relevant scripts for DESeq-hts are located in the subdirectory
21 src. src/deseq2-hts.sh is the main script to start DESeq2-hts. The
22 preprocessing of BAM and GFF file start before the R DESeq2 script.
23 Please follow the shell script to understand the details.
24
25 ./galaxy
26 Galaxy tool configuration file can be found galaxy folder. Please
27 make necessary editing for .xml file and remaining .sh files and
28 perform few tests.
29
30 ./setup.sh
31 Setup script for DESeq2-hts.
32
33 ./mex
34 matlab executable files.
35
36 ./bin
37 Contains deseq2_config.sh file which is used for the configuration of
38 DESeq2-hts. According to your platform, the default file will be changed.
39
40 ./test_data
41 This sub-directory contains all data for running a functional test in
42 Galaxy framework. You may need to move these test files into the test-data
43 directory.
44
45 ./tools
46 A python based GFF parsing program. Also contains small utils programs.
47
48 Getting started:
49 ----------------
50 Check for all requirements first, then
51
52 a) Run ./setup.sh and setup paths and configuration options for DESeq2-hts.
53
54 b) Inside the mex folder execute the make file to create platform dependent .mex files
55 cd mex/Makefile
56 make [interpreter]
57 make octave for octave
58 make matlab for matlab
59 make all for octave and matlab
60
61 c) Edit the Galaxy tool configuration file to adjust the path if necessary.
62
63 Licenses:
64 ---------
65 If **DESeq2** is used to obtain results for scientific publications it should be cited as [1].
66
67 This wrapper program (DESeq2-hts) is free software; you can redistribute it and/or modify it
68 under the terms of the GNU General Public License as published by the Free Software Foundation;
69 either version 3 of the License, or (at your option) any later version.
70
71 Written (W) 2009-2012 Jonas Behr, Regina Bohnert, Andre Kahles, Gunnar Raetsch, Vipin T. Sreedharan
72 Copyright (C) 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany and
73 2013 cBio Memorial Sloan Kettering Cancer Center, New York City, USA.
74
75 References:
76 -----------
77 [1] Anders, S and Huber, W (2010): `Differential expression analysis for sequence count data`.
78
79 Contact:
80 --------
81 vipin [at] cbio.mskcc.org
82