Software_Installation

Linux Software Installation – Exercises 2

Part 1. Install PYTHON software with PIP

1.1 Check the version of python and pip

On BioHPC computers, the "python" command points to "python2.7.5", with "pip" command linked to this default python. The "python3" command points to "python3.6.7", with "pip3" command linked to this default python3.

Before you install any python modules, it is always a good idea to ask these three questions.

Which copy of Python installation you will be running?
What is the version of the Python?
Whether the pip command you are running is associated with the Python you will be running?

Use the following commands to address these questions:

which python3 
ls -l /usr/local/bin/python3
python3 -V
which pip3
head -n1 /usr/local/bin/pip3

1.2 Install and use python module deepTools Install deepTools in the directory ~/.local/

pip3 install deepTools --user

Run deepTools installed in the directory ~/.local/

export PATH=$HOME/.local/bin:$PATH
which deeptools
export LC_ALL=en_US.utf-8
export LANG=en_US.utf-8
deeptools

The new deeptools requires Locale to be set as en_US.utf-8.

1.3 Check the version for deeptool and numpy python modules

python3
import deeptools
deeptools.__file__

import numpy
numpy.__file__
numpy.__version__

After you are done, press “Ctrl-D” to exit python prompt.

• Make sure that you type double-underline for the command “__version__” . • The "__file__" command checks the files from which the modules are loaded; • The deeptools module does not have the “__version__” property; • An old version of pysam could cause deeptools to fail, in that case you will need to update the pysam by “--upgrade” option;

1.4 (optional) Install a different version of deeptools in an alternative location

Install deepTools v3.3.2 in /workdir/$USER

pip3 install deepTools==3.3.2 --prefix /workdir/$USER --ignore-installed

Run deepTools in /workdir/$USER

export PATH=/workdir/$USER/bin:$PATH
export PYTHONPATH=/workdir/$USER/lib/python3.6/site-packages
which deeptools
export LC_ALL=en_US.utf-8
export LANG=en_US.utf-8
deeptools

Part 2. Install PERL software with CPAN

2.1 Configure CPAN

mkdir ~/perl
export PERL5LIB=~/perl/lib/perl5
cpan

At cpan pompt “cpan[1]>”, type the following commands:

o conf makepl_arg INSTALL_BASE=~/perl 
o conf mbuild_arg INSTALL_BASE=~/perl 
o conf prefs_dir ~/perl /prefs 
o conf commit

2.2 Install PERL modules with CPAN

install XML::Simple

This module is only accessible if you “export PERL5LIB=~/perl/lib/perl5”. Delete the whole directory /perl if installation goes wrong.

Part 3. Install C software

Normally, the software web site or the README (sometimes INSTALL) file in the source code directory provides step-by-step instructions. As a non-root user, quite often you need to modify the instructions, e.g. adding “--prefix=~/mydirectory” at the configuration step.

3.1 Download the source code

cd /workdir/$USER
wget http://catchenlab.life.illinois.edu/stacks/source/stacks-2.53.tar.gz
tar xvfz stacks-2.53.tar.gz

If the source code is available from github, use “git clone https://github.com/lh3/bwa.git” to get the latest source code.
If the source code you downloaded is a *tar.bz2 file, use “tar xvfj myfile.tar.bz2” command to decompress.

3.2 Configure

mkdir $HOME/stacks
cd /workdir/$USER/stacks-2.53
export LD_LIBRARY_PATH=/usr/local/gcc-7.3.0/lib64:/usr/local/gcc-7.3.0/lib
export PATH=/usr/local/gcc-7.3.0/bin:$PATH
./configure --prefix=$HOME/stacks

The default gcc compiler would not work with stacks v2. If you use the default gcc, you will get an error message complaining your gcc is too old. The two commands here “export LD_LIBRARY_PATH..” “export PATH…” switch the default gcc to v7.3.0.
The “--prefix=“ parameter instruct the software to be installed in "$HOME/stacks".
After this step, a new Makerfile is created with instructions how to compile and install the software. The Makerfile is a text file. If you want, you can use any text editor to examine the file, you will find lines like “prefix = /home/xxxxx/stacks”.

3.3 Compile

make
make install

·After this step, you will find binary executables and libraries in your installation directory: $HOME/stacks.

3.4 Run software

export LD_LIBRARY_PATH=/usr/local/gcc-7.3.0/lib64:/usr/local/gcc-7.3.0/lib
export PATH=$HOME/stacks/bin:$PATH
sstacks

Part 4. Install R package

First, start R by command “R”. If you want to use a different version of R, you need to modify PATH, e.g. “export PATH=/programs/R-3.4.2s/bin:$PATH”.

At R prompt “>”, type the following command to install R package “qtl”

install.packages("qtl")

You will be prompted for two questions. Answer "yes" and press "Enter" to both questions.

Would you like to use a personal library instead? (yes/No/cancel) yes Would you like to create a personal library? yes

Still at R prompt, load qtl package, get the version and physical path of the package

library(qtl)
packageVersion("qtl")
find.package("qtl")

The package is installed in $HOME/R. If something goes wrong, you can delete the whole directory and start from scratch.