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Id: 86069
Status: new
Priority: 0/
Queue: Bio-SamTools

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Owner: Nobody in particular
Requestors: rdhayes [...] lbl.gov
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Subject: Suggested patch for installation failure to find samtools headers in include/bam/ path
Date: Tue, 11 Jun 2013 15:39:26 -0700
To: bug-Bio-SamTools [...] rt.cpan.org
From: Richard Hayes <rdhayes [...] lbl.gov>
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Tested with Bio-SamTools v1.38 My perl is 5.16.0 $ uname -a Linux gpint07 2.6.32-5-amd64 #1 SMP Mon Feb 25 00:26:11 UTC 2013 x86_64 GNU/Linux Samtools does not have a full install process, so many times the library and header files are copied by hand to some location or another. I've noticed a lot a installations of samtool 0.1.18 and 0.1.19, at least in my environment, are following the install advice for Tophat and placing headers under <samtools basedir>/include/bam/ rather than <samtools Show quoted text
basedir>/include/. See here, for example:
http://tophat.cbcb.umd.edu/tutorial.shtml#samtools I've patched the Bio-SamTools Build.PL with this to get a working non-interactive install of Bio::DB::Sam for our webservers, without any intervention aside from setting the SAMTOOLS environment variable to the correct samtools install base path *** Build.PL.orig Tue Jun 11 14:38:16 2013 --- Build.PL Tue Jun 11 14:59:14 2013 *************** *** 75,80 **** --- 75,82 ---- if -e "$samtools/$HeaderFile"; $sam_include = "$samtools/include" if -e "$samtools/include/$HeaderFile"; + $sam_include = "$samtools/include/bam" + if -e "$samtools/include/bam/$HeaderFile"; $sam_lib = $samtools if -e "$samtools/$LibFile"; $sam_lib = "$samtools/lib" Best regards, -- Richard D. Hayes, Ph.D. Joint Genome Institute / Lawrence Berkeley National Lab http://www.phytozome.net


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