Build bowtie using gcc-4.7
Hi Ben,
as you know the Debian Med team has packaged bowtie for Debian. We
also do provide bowtie2 as a separate package because there is some
usecase for the old version. Everything I'm writing here applies to
bowtie 0.12.7 which was downloaded from:
http://sourceforge.net/projects/bowtie-bio/files/bowtie/
I noticed that there is a quite recent but empty download directory
versioned 0.12.8. It seems that the development is not completely
stalled and thus the following hints might be useful for you.
Recently we received a bug report that the package does not build when
using gcc 4.7 and we were able to find a patch. You can find it here:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/bowtie/trunk/debian/patches/gcc-4.7.patch?view=markup
Feel free to take it over into your next upstream version.
As an additional remark: bowtie comes with a private copy of an old
SeqAn version (1.1 - currently in Debian is version 1.3). We would like
to link against the Debian packaged library instead of a private copy.
Do you see any chance in implementing this?
Kind regards and thanks for providing bowtie as Free Software
Andreas.
--
http://fam-tille.de
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