Install Testing

These are notes to the author for testing that a clean install by an external user will work, but also largely describes how an external user can install in a way most likely to succeed.

First, if not already done, install perlbrew and some version of Perl:

setenv PERLBREW_ROOT /visible_to_all_nodes/mygroup/perlbrew
mkdir /visible_to_all_nodes/mygroup/perlbrew
curl -kL http://install.perlbrew.pl | bash
perlbrew init
# follow instructions; to use permanently update your shell login script, for testing do not
# and also make sure that your PERL5LIB is nice and clean (probably empty)
perlbrew install perl-5.14.2
perlbrew switch perl-5.14.2

For subsequent testing, prepare a perlbrew shell (ignore this section if you have a permanent install, ie. you have the following first 2 lines in your shell login script):

setenv PERLBREW_ROOT /visible_to_all_nodes/mygroup/perlbrew
source /visible_to_all_nodes/mygroup/perlbrew/etc/cshrc
perlbrew switch perl-5.14.2
# which puts you in a new shell; so again we need to set the environment
setenv PERL5LIB ""
setenv PERL_INLINE_DIRECTORY ".Inline"
mkdir .Inline
setenv SAMTOOLS /path/to/samtools_source_with_Makefile_having-fPIC-m64
setenv PERLBREW_ROOT /visible_to_all_nodes/mygroup/perlbrew
source /visible_to_all_nodes/mygroup/perlbrew/etc/cshrc

Prepare CPAN:

cpan
cpan> o conf makepl_arg ''
cpan> o conf mbuildpl_arg ''
# if necessary, configure CPAN to follow prerequisites as well
cpan> o conf commit
cpan> install Bundle::CPAN

Install VRPipe:

cd ~/my/testing/area
git clone git://github.com/VertebrateResequencing/vr-pipe.git
cd vr-pipe
git checkout master
git pull
perl Build.PL
./Build installdeps
# you may encounter problems with the CPAN dependencies, most likely you will have to do:
cpan
cpan> force install Inline::Filters
cpan> install JJNAPIORK/MooseX-Types-Parameterizable-0.07.tar.gz
cpan> q
perl Build.PL
./Build test
./Build install