Optional: Install SVDetect

We have installed SVdetect for you already as installation is a bit difficult (though still much easier than the alternatives listed in the introduction). You can verify it's location using which SVDetect in your $PATH under $BI/bin. One of the advantages (or disadvantages) of using the communal resource is that someone else can update all the necessary programs and packages for you. Alternatively, you can make a personal copy of the program yourself using the following commands. NOTE that this is presented mostly to underscore how spoiled we are with modules and the BioITeam.

Install SVDetect scripts

Navigate to the SVDetect project page

More information:

• SVDetect code repository
• SVDetect Paper

Download the code onto TACC.

wget https-N http://downloads.sourceforge.net/projectsproject/svdetect/filesSVDetect/latest/download0.80/SVDetect_r0.8b.tar.gz
tar -xvzf SVDetect_r*.tar.gz
cd SVDetect_r*

Move the Perl scripts and make them executable

cp bin/SVDetect $HOME/local/bin
chmod 775 scripts/BAM_preprocessingPairs.pl
cp scripts/BAM_preprocessingPairs.pl $HOME/local/bin

Install required Perl modules

SVdetect requires a few Perl modules to be installed. In the default TACC environment, you can use the cpan shell to install most well-behaved Perl modules (with the exception of some complicated ones that require other libraries to be installed or things to compile). Here's how:

This can not be done from an idev session
login1$ cpan
# choose yes to do as much automatically as possible and 'local::lib' for how you want to install modules as you don't have admin rights on TACC
...
cpan[4]> install Config::General
...
cpan[4]> install Tie::IxHash
...
cpan[4]> install Parallel::ForkManager
...
cpan[4]> quit
login1$