-
Notifications
You must be signed in to change notification settings - Fork 16
/
INSTALL
50 lines (34 loc) · 2.1 KB
/
INSTALL
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
================
RiboDiff INSTALL
================
Before install RiboDiff, make sure the required packages are already installed on your
computer. Please refer to README.md file for details regarding which packages are required.
This document shows how to install RiboDiff on your computer. You can either install
it globally such that every user can use it, or you can install it to your own directory.
For a global install (you need root permissions to do so), go to the package directory and
execute the following commands:
python setup.py build
python setup.py test (optional step)
python setup.py install
Alternatively, for a local install, execute the following commands instead:
python setup.py build
python setup.py test (optional step)
python setup.py install --user
This will install RiboDiff to a default location in your home directory. This location
can vary for different operating systems. You can also install it to other location by
executing:
python setup.py install --prefix=/PATH/PREFIX
Please replace /PATH/PREFIX with your prefered path where RiboDiff will be installed.
Make sure this path exists in your PATHONPATH environment variable. If not, you
can edit PATHONPATH in your ~/.bashrc if you are using Linux or ~/.bash_profile if
Mac OS X by adding the folowing line:
export PYTHONPATH=/PATH/PREFIX/lib/python2.7/site-packages/:$PYTHONPATH
To run RiboDiff, all you need is to execute the TE.py in ./scripts directory:
python ./scripts/TE.py -e <exp_outline.txt> -c <cnt_table.txt> -o <result.txt>
Probably, you may wish to have a test run on the toy data provided within this package
after the installation. To do so, simplily excute this command:
python ./scripts/TE.py -e ./tests/experimental_design.csv -c ./tests/gene_count_table.tab -o ./tests/toy.res.tab -d 0 -r 1 -p 1
You can find the result files with prefix name as toy.res in ./tests directory.
Please use the same TE.py script to run your own data. You can run it from anywhere on your
computer by giving the complete path to it. Please find details on how to prepare input data
for RiboDiff in MANUAL file in this package.