sci-biology/amos: fix installation process and dependencies

Package-Manager: portage-2.2.18

6 files changed, 139 insertions, 4 deletions

diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog
index 7d1df6d02..9bdce778d 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 <mmokrejs@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 <jlec@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/Manifest b/sci-biology/amos/Manifest
new file mode 100644
index 000000000..27ad50ff2
--- /dev/null
+++ b/sci-biology/amos/Manifest
@@ -0,0 +1 @@
+DIST amos-3.1.0.tar.gz 2094268 SHA256 2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491 WHIRLPOOL df9b547fcc0b7bf0149641fd8df9e4558f61bb6c17ded0facfeecde25d3a6307b40414e7cb8b2f021fa8cc192ee956672c26e0fc287981f4733a393739e80b61
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 000000000..b81479179
--- /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 baecc2f9e..610c3d64c 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 000000000..de2a41184
--- /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 000000000..97a8f59d0
--- /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)
+-)