annotate rDiff/INSTALL @ 3:29a698dc5c7e default tip

Merge multiple heads.
author Dave Bouvier <dave@bx.psu.edu>
date Mon, 27 Jan 2014 14:15:36 -0500
parents 0f80a5141704
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
1 To setup rDiff, please follow these steps:
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
2
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
3 1) Download the SAMTools (version 0.1.7) from http://samtools.sourceforge.net/
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
4 and install it. You need to add the flag -fPIC in the SAMTools Makefile for compilation.
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
5
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
6 2) Change to directory that contains rDiff and configure rDiff by typing:
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
7
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
8 ./configure
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
9
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
10 this etects and stores paths of dependencies necessary to compile and run rDiff.
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
11 You can also set these variables manually using the interactive configuration:
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
12
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
13 ./configure -i
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
14
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
15 3) To compile rDiff, type:
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
16
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
17 make
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
18
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
19 4) When successfully completed, rDiff is usable. Check out the <Examples>:
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
20
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
21 make example
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
22
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
23 This will download an example dataset and run the rDiff.parametric on it.
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
24 You can also run rDiff.parametric, rDiff.nonparametric or rDiff.poisson by typing:
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
25
0f80a5141704 version 0.3 uploaded
vipints
parents:
diff changeset
26 make more_examples