--------------------
      Overview     
--------------------

This document explains how to install other tools that are required for the pipeline

These instructions have been tailored to Hyperion, that is tools that are installed for everyone are not given much attention here.

For everything else, tools will be installed in the individual user directory, instructions should work for the environment on Hyperion.



---------------------
    Install Pysam    
---------------------


First, get the pysam v0.8.0 source code - on Hyperion you can just copy the file from Logan's directory:

cp ~ljeveret/Tools/pysam-0.8.0.tar.gz .

Or, if this file goes missing, download v0.8.0 here: https://pypi.python.org/pypi/pysam/0.8.0

NOTE: Yes, this is an older version of pysam, but newer versions are not compatible with HTSeq or certain scripts in the pipeline, so get THIS version

On Hyperion, navigate to the wherever you put the pysam-0.8.0.tar.gz file, and then run the following commands (Make sure to check the output of each command for errors before proceeding!):

tar -xzf pysam-0.8.0.tar.gz
cd pysam-0.8.0
python setup.py build
python setup.py install --user

Now test if pysam is installed by running the following command to open a python session:

/usr/bin/python

Then in the python session, run this command:

import pysam

You should not get any error message when running this command.  This next command will check the pysam version:

print pysam.__version__

This should tell you the version is 0.8.0
(Hit Ctrl+D to exit out of Python session)



---------------------
    Install HTSeq    
---------------------

Download HTSeq-0.6.1p1.tar.gz from this page: https://pypi.python.org/pypi/HTSeq

Upload the HTSeq-0.6.1p1.tar.gz file to your user directory and then run the following commands:

tar -xzf HTSeq-0.6.1p1.tar.gz
cd HTSeq-0.6.1p1
python setup.py install --user

After install, you should see a program called "htseq-count" in your ~/.local/bin/ directory.

Also make sure the following line is somewhere in your .bash_profile file:

PATH=$PATH:$HOME/.local/bin



---------------------
    Install STAR    
---------------------

The easiest way is to create a soft-link to the installation in Logan's directory, by running the following commands:

cd ~/.local/bin
ln -s ~ljeveret/Tools/STAR-STAR_2.4.0f1/bin/Linux_x86_64_static/STAR

As noted above, this requires the following line (just once) somewhere in your .bash_profile file:

PATH=$PATH:$HOME/.local/bin



---------------------
      Install R      
---------------------

Again, easiest thing to do is just link to my installation of R, which has all required packages installed already.  

Just add the following to your .bash_profile file:

PATH=~ljeveret/Tools/R-3.1.1/bin:$PATH
