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I am installing perl module Bio::DB::Sam.

Shortly, installer asks me to locate bam.h and libbam.a files:

--> Working on Bio::DB::Sam
Fetching http://www.cpan.org/authors/id/L/LD/LDS/Bio-SamTools-1.39.tar.gz ... OK
Configuring Bio-SamTools-1.39 ... Please enter the location of the bam.h and compiled libbam.a files:

I know where these files are beforehand and I would like to automatize the process. Something like:

echo "/Users/al/programs/samtools-0.1.19" | cpanm Bio::DB::Sam

or 

echo "/Users/alice/programs/samtools-0.1.19" | xargs cpanm Bio::DB::Sam

Basically, I want to install this module without any interaction with user. Thanks for suggestions. Everything I have tried so far still asks for location of these files.

Miller
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Perlnika
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1 Answers1

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It looks like you can use the SAMTOOLS environment variable to specify a location. See the Build.PL file that handles the module's installation.

tobyink
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  • Excellent! You made my day. I exported SAMTOOLS variable and installation went successfully without prompting. – Perlnika Aug 25 '14 at 14:11