commit: 8e3157e581a2503912b86bb5e48fb73e82c26cc9
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Mar 31 20:18:38 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Mar 31 20:18:38 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8e3157e5
sci-biology/amos: fix installation process and dependencies
Package-Manager: portage-2.2.18
sci-biology/amos/ChangeLog | 9 ++-
sci-biology/amos/amos-3.1.0-r2.ebuild | 66 ++++++++++++++++++++++
sci-biology/amos/amos-9999.ebuild | 27 ++++++++-
sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch | 15 +++++
...mos-3.1.0-goBambus2.py-indent-and-cleanup.patch | 25 ++++++++
5 files changed, 138 insertions(+), 4 deletions(-)
diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog
index 7d1df6d..9bdce77 100644
--- a/sci-biology/amos/ChangeLog
+++ b/sci-biology/amos/ChangeLog
@@ -1,7 +1,14 @@
# ChangeLog for sci-biology/amos
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*amos-3.1.0-r2 (31 Mar 2015)
+
+ 31 Mar 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz>
+ +amos-3.1.0-r2.ebuild, +files/amos-3.1.0-gcc-4.7.patch,
+ +files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch, amos-9999.ebuild:
+ sci-biology/amos: fix installation process and dependencies
+
29 Dec 2013; Justin Lecher <j...@gentoo.org> -amos-3.1.0-r1.ebuild,
amos-9999.ebuild, -files/amos-3.1.0-gcc-4.7.patch,
-files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch,
diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild
b/sci-biology/amos/amos-3.1.0-r2.ebuild
new file mode 100644
index 0000000..b814791
--- /dev/null
+++ b/sci-biology/amos/amos-3.1.0-r2.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/amos-3.1.0-r1.ebuild,v 1.1
2013/12/29 00:24:16 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit eutils python-r1
+
+DESCRIPTION="A Modular, Open-Source whole genome assembler"
+HOMEPAGE="http://amos.sourceforge.net/";
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="qt4"
+
+DEPEND="
+ dev-libs/boost
+ qt4? ( dev-qt/qtcore:4 )"
+RDEPEND="${DEPEND}
+ dev-lang/perl
+ dev-perl/DBI
+ dev-perl/Statistics-Descriptive
+ sci-biology/blat
+ sci-biology/mummer"
+
+MAKEOPTS+=" -j1"
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-gcc-4.7.patch \
+ "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch
+}
+
+# amos-3.1.0-r2/work/amos-3.1.0/src/Bambus/Untangler/DotLib.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/Bambus/Untangler/AsmLib.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAreader.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/AmosFoundation.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/Foundation.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/AmosLib.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTArecord.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/ParseFasta.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/xfig.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAwriter.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAgrammar.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAiterator.pm
+
+# --with-jellyfish location of Jellyfish headers
+
+src_install() {
+ default
+ python_replicate_script "${ED}"/usr/bin/goBambus2
+ # bambus needs TIGR::FASTAreader.pm and others
+ # configure --libdir sadly copies both *.a files and *.pm into
/usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it
+ mkdir -p "${D}"/usr/share/"${PN}"/perl/AMOS || die
+ mv "${D}"/usr/lib64/AMOS/*.pm "${D}"/usr/share/"${PN}"/perl/AMOS || die
+ mkdir -p "${D}"/usr/share/"${PN}"/perl/TIGR || die
+ mv "${D}"/usr/lib64/TIGR/*.pm "${D}"/usr/share/"${PN}"/perl/TIGR || die
+ echo "PERL5LIB=/usr/share/${PN}/perl" > "${S}/99${PN}"
+ doenvd "${S}/99${PN}" || die
+ # move also /usr/lib64/AMOS/AMOS.py to /usr/bin
+ mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die
+}
diff --git a/sci-biology/amos/amos-9999.ebuild
b/sci-biology/amos/amos-9999.ebuild
index baecc2f..610c3d6 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -16,11 +16,32 @@
EGIT_REPO_URI="git://amos.git.sourceforge.net/gitroot/amos/amos"
LICENSE="Artistic"
SLOT="0"
KEYWORDS=""
-IUSE=""
+IUSE="mpi qt4"
DEPEND="
+ mpi? ( virtual/mpi )
dev-libs/boost
- dev-qt/qtcore:4"
+ qt4? ( dev-qt/qtcore:4 )
+ sci-biology/blat
+ sci-biology/jellyfish"
RDEPEND="${DEPEND}
dev-perl/DBI
+ dev-perl/Statistics-Descriptive
sci-biology/mummer"
+
+# --with-jellyfish location of Jellyfish headers
+
+src_install() {
+ default
+ python_replicate_script "${ED}"/usr/bin/goBambus2
+ # bambus needs TIGR::FASTAreader.pm and others
+ # configure --libdir sadly copies both *.a files and *.pm into
/usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it
+ mkdir -p "${D}/usr/share/${PN}/perl/AMOS" || die
+ mv "${D}"/usr/lib64/AMOS/*.pm "${D}/usr/share/${PN}/perl/AMOS" || die
+ mkdir -p "${D}"/usr/share/"${PN}"/perl/TIGR || die
+ mv "${D}"/usr/lib64/TIGR/*.pm "${D}"/usr/share/"${PN}"/perl/TIGR || die
+ echo "PERL5LIB=/usr/share/${PN}/perl" > "${S}/99${PN}"
+ doenvd "${S}/99${PN}" || die
+ # move also /usr/lib64/AMOS/AMOS.py to /usr/bin
+ mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die
+}
diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
new file mode 100644
index 0000000..de2a411
--- /dev/null
+++ b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
@@ -0,0 +1,15 @@
+ src/Align/find-tandem.cc | 1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc
+index ddf1cab..a29e21e 100644
+--- a/src/Align/find-tandem.cc
++++ b/src/Align/find-tandem.cc
+@@ -7,6 +7,7 @@
+ #include <vector>
+ #include <ctime>
+ #include <sys/time.h>
++#include <unistd.h>
+ using namespace std;
+
+ const int OFFSET_TABLE_SIZE = 100;
diff --git
a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
new file mode 100644
index 0000000..97a8f59
--- /dev/null
+++ b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
@@ -0,0 +1,25 @@
+--- amos-3.1.0/src/Pipeline/goBambus2.py.orig 2013-09-11 01:05:29.850090457
+0200
++++ amos-3.1.0/src/Pipeline/goBambus2.py 2013-09-11 01:07:03.250090701
+0200
+@@ -1,7 +1,7 @@
+ #pipeline script for assembly + Bambus 2
+ #contributed by Todd J Treangen
+
+-import string, sys, os, subprocess#, spincursor
++import sys, os, subprocess#, spincursor
+
+ RED = "\033[0;31m"
+ GREEN = "\033[0;32m"
+@@ -360,7 +360,7 @@
+ print "\t\t%s...failed%s"%(RED,NONE)
+ sys.exit(1)
+
+- p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s
%s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE,
stdout=vtext, stderr=logfile)
++ p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s
%s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE,
stdout=vtext, stderr=logfile)
+
+ if xopt_dict["verbose"] == 1:
+ print "10) running OutputResults"
+@@ -388,4 +388,3 @@
+ else:
+ print "\t\t%s...failed%s"%(RED,NONE)
+ sys.exit(1)
+-)
