Language-specific software package installation

Certain programming languages require the use of multiple add-on packages to reach their full functionality. If we are missing a package you need, there are two options: either request it be installed email us at cac.help@queensu.ca or perform a local install. Both methods will give you a working copy of the software package

Perl

To install Perl modules to a local directory, use the following bash commands to create a localized install of whatever modules you may need. It's actually not as complicated as it looks.

# install local::lib
wget http://search.cpan.org/CPAN/authors/id/H/HA/HAARG/local-lib-2.000018.tar.gz
tar -xzf local-lib-2.000018.tar.gz
cd local-lib-2.000018
perl Makefile.PL --bootstrap
make test && make install

# setting up appropriate environment variables so that perl knows about our new ~/perl5/lib directory
cd ~                
echo 'eval "$(perl -I$HOME/perl5/lib/perl5 -Mlocal::lib)"' >> ~/.bashrc
source ~/.bashrc

# check that local::lib is indeed installing to the right directory, you should see a bunch of paths beginning with ~/perl5/lib/perl5/ get printed out
perl -e 'print "@INC"'

Installing Perl modules from CPAN will now allow you install whatever you need. For an example of using CPAN to install BioPerl, see below. This part requires a bit of baby-sitting, just hit enter whenever a prompt comes up.

cpan
install CJFIELDS/BioPerl-1.6.924.tar.gz
q

Python

We highly recommend using one of the two Anaconda installations on the SW cluster. These already have a large number of pre-installed packages and will serve you well. However, if they are missing something you need, you can make a local install using the following instructions:

use anaconda3 #or "use anaconda2" for python 2.7
pip install --user packageName

R

When using R, make sure to use the centralized install first with "use R". The system R version on the login node has a slightly different set of installed libraries from the versions of R found on the production nodes, which can result in dependency issues. Adding "use R" to your scripts will avoid this.

When installing R packages from CRAN, it's easiest to manually specify the CRAN mirror to download from with:

install.packages("packageName", repos="mirrorURL")

where mirrorURL is one of the repositories listed at [1]. It will tell you at some point that the directory is not writeable and ask you if you want to make a local library instead- select 'yes'. The package should install normally and be ready for use.

When installing packages from Bioconductor:

source("http://bioconductor.org/biocLite.R")
biocLite("packageName")

If you see an error about "URLs are not supported", simply change any "https" URL to "http" and it will work. Again, it will ask you to make a "personal library", select 'yes'.

Using your own software

It's very easy to use software that is not pre-installed on the systems. Simply specify the absolute or relative path to your software in a script and it will run. For example, if you had a program called "test" located in ~/bin/, you could easily invoke it with "~/bin/test" in your scripts.