| Subject: | Re: Suggested patch for installation failure to find samtools headers in include/bam/ path |
| Date: | Tue, 24 Sep 2013 12:37:08 -0700 |
| To: | bug-Bio-SamTools [...] rt.cpan.org, Lincoln Stein <lincoln.stein [...] gmail.com> |
| From: | Richard Hayes <rdhayes [...] lbl.gov> |
Hi,
I noticed the recent v1.39 Bio-Samtools release on CPAN. I can continue to
work around this condition in the Build.PL, but getting this patch into the
next release tarball is also greatly appreciated.
Best regards,
Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net
On Tue, Jun 11, 2013 at 3:39 PM, Richard Hayes <rdhayes@lbl.gov> wrote:
Show quoted text
> 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
> 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
>