| 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> |
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