Installing Bio::DB::Sam perl module

Question

I am trying to install a perl module Bio::DB::Sam on my home directory on a remote server.

I downloaded the module, extracted the files, and ran:

per         


        

Answer 1

Here is a script that will fetch the SAMtools source and compile it, then fetch and compile the Perl bindings.

wget http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2
tar xjf samtools-0.1.18.tar.bz2 && cd samtools-0.1.18
make CFLAGS=-fPIC
export SAMTOOLS=`pwd`
cpanm Bio::DB::Sam

Part of the problem you were likely seeing is that the SAMtools project has recently undergone some major code reorganization (and this has naturally made it difficult to work with external language bindings).