Setup - orenlivne/ober GitHub Wiki

The PRIMAL code is meant to run on any Unix-like system (Unix, Linux and Cygwin with certain caveats. We do not fully support Cygwin at this time due to path issues, although most programs will work).

1. Checkout the code tree under this github project's primal directory into a directory, which will be assumed to be /home/oren/ober hereafter.

svn co https://github.com/orenlivne/ober/primal/src /home/oren/ober

Or download the tarball from the primal/release and open it. On some cluster machines, a proxy server may need to be set up for svn to work over https.

2. Make a dedicated directory for applications (/home/oren/apps in this example).

3. Add the following to your ~/.bash_profile:

export OBER="/home/oren/ober"
export APPS="/home/oren/apps"
source /home/oren/ober/system/dots/bash_profile

4. Run your new ~/.bash_profile.

5. Install third-part programs under $APPS:

• PLINK - Download
• Tabix - Download

6. In a new terminal, run provision-python $APPS/virtualenv ober. This will create a virtual environment with the necessary packages. It will use $APPS/virtualenv as a working directory to store python packages. Warning: on some system additional manual package installations may be required. See the documentation inside the ${OBER}/system/bin/provision-python script.

7. Open a new terminal so that ~/.bash_profile can run. It will automatically enable the ober virtualenv.

8. (Optional) run the test suite and see that it passes:

python -m unittest tests.SuiteImpute
....................... OK

Next topic: how to run the PRIMAL code.