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.
Use the following commands to address these questions:
1.2 Install and use python module deepTools Install deepTools in the directory ~/.local/
Run deepTools installed in the directory ~/.local/
1.3 Check the version for deeptool and numpy python modules
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/$USER
Run deepTools in /workdir/$USER
Part 2. Install PERL software with CPAN
2.1 Configure CPAN
At cpan pompt “cpan>”, type the following commands:
2.2 Install PERL modules with CPAN
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
·After this step, you will find binary executables and libraries in your installation directory: $HOME/stacks.
3.4 Run software
Part 4. Install R package
First, start R by command “R”. If you want to use a different version of R, you need to modify PATH, e.g. “export PATH=/programs/R-3.4.2s/bin:$PATH”.
At R prompt “>”, type the following command to install R package “qtl”
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
The package is installed in $HOME/R. If something goes wrong, you can delete the whole directory and start from scratch.