diff options
| -rw-r--r-- | .SRCINFO | 26 | ||||
| -rw-r--r-- | PKGBUILD | 40 | ||||
| -rw-r--r-- | amos-3.1.0-gcc4.7.patch | 11 |
3 files changed, 77 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..8ed7120cc897 --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,26 @@ +pkgbase = amos + pkgdesc = A modular, open source whole-genome assembler + pkgver = 3.1.0 + pkgrel = 3 + url = http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS + arch = i686 + arch = x86_64 + license = Artistic + makedepends = boost + depends = python2 + depends = perl + depends = perl-xml-parser + depends = perl-dbi + depends = perl-statistics-descriptive + depends = qt4 + depends = xorg-server + optdepends = mummer: for AMOScmp, minimus2, amosvalidate + optdepends = blat: for minimus2-blat + options = !makeflags + source = http://downloads.sourceforge.net/project/amos/amos/3.1.0/amos-3.1.0.tar.gz + source = amos-3.1.0-gcc4.7.patch + md5sums = 51ebe835c93eef9acd39101738b2048c + md5sums = 1eafa4de5d5837b8761c8f49e40a20d4 + +pkgname = amos + diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..9a65c53de459 --- /dev/null +++ b/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Eric Biggers <ebiggers3@gmail.com> + +pkgname=amos +pkgver=3.1.0 +pkgrel=3 +pkgdesc='A modular, open source whole-genome assembler' +arch=('i686' 'x86_64') +url="http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS" +license=('Artistic') +options=(!makeflags) # Parallel build is broken in released version + +# qt4 and xorg-server required by "Hawkeye" program +depends=('python2' 'perl' 'perl-xml-parser' 'perl-dbi' + 'perl-statistics-descriptive' 'qt4' 'xorg-server') + +optdepends=('mummer: for AMOScmp, minimus2, amosvalidate' + 'blat: for minimus2-blat') + +makedepends=('boost') + +source=( +"http://downloads.sourceforge.net/project/${pkgname}/${pkgname}/${pkgver}/${pkgname}-${pkgver}.tar.gz" +"amos-3.1.0-gcc4.7.patch" +) + +build() { + cd ${pkgname}-${pkgver} + patch -p1 < ${srcdir}/amos-3.1.0-gcc4.7.patch + PYTHON=/usr/bin/python2 PERL=/usr/bin/perl \ + ./configure --prefix=/usr --with-qmake-qt4=/usr/bin/qmake-qt4 + make +} + +package() { + cd ${pkgname}-${pkgver} + make DESTDIR=${pkgdir} install + install -Dm644 COPYING ${pkgdir}/usr/share/licenses/amos/COPYING +} +md5sums=('51ebe835c93eef9acd39101738b2048c' + '1eafa4de5d5837b8761c8f49e40a20d4') diff --git a/amos-3.1.0-gcc4.7.patch b/amos-3.1.0-gcc4.7.patch new file mode 100644 index 000000000000..2c74e64be962 --- /dev/null +++ b/amos-3.1.0-gcc4.7.patch @@ -0,0 +1,11 @@ +diff -rup old/src/Align/find-tandem.cc new/src/Align/find-tandem.cc +--- old/src/Align/find-tandem.cc 2011-07-24 19:27:26.000000000 -0400 ++++ new/src/Align/find-tandem.cc 2012-06-22 22:21:23.925745100 -0400 +@@ -7,6 +7,7 @@ + #include <vector> + #include <ctime> + #include <sys/time.h> ++#include <unistd.h> + using namespace std; + + const int OFFSET_TABLE_SIZE = 100; |