sci-biology/amos: Fix python support

Package-Manager: portage-2.2.7/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 86 insertions, 6 deletions

diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog
index cc4a147a25d8..aa7d8279e95f 100644
--- a/sci-biology/amos/ChangeLog
+++ b/sci-biology/amos/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/amos
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/ChangeLog,v 1.18 2013/03/19 07:41:20 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/ChangeLog,v 1.19 2013/12/29 00:24:16 jlec Exp $
+
+*amos-3.1.0-r1 (29 Dec 2013)
+
+  29 Dec 2013; Justin Lecher <jlec@gentoo.org> +amos-3.1.0-r1.ebuild,
+  +files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch:
+  Fix python support
 
   19 Mar 2013; Justin Lecher <jlec@gentoo.org> amos-3.1.0.ebuild, metadata.xml:
   Change USE name from qt to qt4, #462218
diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest
index e7a65e564e5c..4b9c2dc4872f 100644
--- a/sci-biology/amos/Manifest
+++ b/sci-biology/amos/Manifest
@@ -2,14 +2,26 @@
 Hash: SHA512
 
 AUX amos-3.1.0-gcc-4.7.patch 400 SHA256 59be7e1fa3c4125f463e666f304f2194fc73026c71005ac16891e950e75b8af6 SHA512 3777885d5cd5edcb881abfbe1580092e073311797bd4776cd3ec9d27b634339718238be7f452f1ea1a0aea5fb9f6059d6b6f6a47bc2a0fb6d1811a2ec51a0835 WHIRLPOOL 5c446c940eed42a5d8b47c102e97a4fc3c9818aa40f6049ab6b4e78ee8cf445665afbc78b9c2742e3de3adccb087e8f61ba3ebe567140d2e26d2a6167fe13b65
+AUX amos-3.1.0-goBambus2.py-indent-and-cleanup.patch 1057 SHA256 6dba8f9c13ebabb5aa55c8b6ec71a015315662d00ee749df96e6715b9de45736 SHA512 5d2a0d4b222a23f30db560937b1c0e447f61dc786e097b259696fa41dca1e57a17a1e684bbd9fa9ddcee1334f7e6e3a91ccb7567d4fe079c3bdb3bb54034d11f WHIRLPOOL 3abec572fa4384f7b4d60aa6cb5d3da945e9e78ab462757945e55f7a64440023a229a08ab40b861d9823d7694e5f92683459381865757f9ef284c228ac3409a2
 DIST amos-3.1.0.tar.gz 2094268 SHA256 2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491 WHIRLPOOL df9b547fcc0b7bf0149641fd8df9e4558f61bb6c17ded0facfeecde25d3a6307b40414e7cb8b2f021fa8cc192ee956672c26e0fc287981f4733a393739e80b61
+EBUILD amos-3.1.0-r1.ebuild 843 SHA256 e6587afa883d08328df034ff0ec5ef8f430e4ef9cedd6dd05c9b73fec1941610 SHA512 371db720c33b538cced7aece8104484693f018368bd26ba59d401086a288d67be75a568de7ef170c9996ec683ff656cefbcfc294d7f3e6c32ecb3f5f96a5a521 WHIRLPOOL b378dcf9208bd4b2956003e074af4bf91ccd8bbcfd991b43027f95be77f26b7c5f565bcb3c88046bea8947e1d43a3b774671807dbd06aab10806916fda53c0e9
 EBUILD amos-3.1.0.ebuild 653 SHA256 2b497be87eef143697927bd2f06c149087cfedbb4027ca25c7e1e200cd9cc4c3 SHA512 25f206269a55131916670577a9cd7a4bfcd049fd289a2ef28841cd7edac9196c4c660ea83bcec6658635e7cc3ac6a2362ab059937bad80548fd38226f28d918d WHIRLPOOL 1c594fae25ad90eb8edd656dcdbfe12920d54c3543027c15cd8ae3484a7b3120294b795f17e35ebe72d9ee3d2e9856b3a49df4fb09b03b95819f3df396eeec4f
-MISC ChangeLog 2613 SHA256 f5b5d5058179d300b7a35f9c797f20f4c1baece0029f60cb8bf53c7904bdc392 SHA512 63bb662ebaaabf06c72b40b2aca525a156a9c30097a81e82c2f331cbf3d2d6fd53bb2eca4cee80609bc06eab43244eee9e6f1004c982b12a2306d0a37610a501 WHIRLPOOL 4bafacbedd0a501a531018e782e96c385f4e31e391d72950db117de5486c07d9bc124b0dbb63a5a7d88939981d9aa787235623bbd9160a8f1b0d62fa600c26b9
+MISC ChangeLog 2794 SHA256 4e743b62da20b61037c578cc5633f097fcf001ddd4abc5a6375a3d3843fdec5e SHA512 8f7f3500bd3ee48d9b9928cb92b2cab9001ff034e930e6f4af3ebc5aa3f468841d75b4075b8bcad74202aac07f7fa500d383457d89ab100fe7e6da1d57c3d808 WHIRLPOOL 766764fd2eb4a34098ea639919ac99613bbd2d03dd857e87052ef79e19d16363a1b5648aea2429ae26622c4802ad16fad1bb04057b7965d7b4e1f371973e9573
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/amos/amos-3.1.0-r1.ebuild b/sci-biology/amos/amos-3.1.0-r1.ebuild
new file mode 100644
index 000000000000..d26e5fa88161
--- /dev/null
+++ b/sci-biology/amos/amos-3.1.0-r1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2013 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="qt4? ( dev-qt/qtcore:4 )"
+RDEPEND="${DEPEND}
+	dev-perl/DBI
+	dev-perl/Statistics-Descriptive
+	sci-biology/mummer"
+
+MAKEOPTS+=" -j1"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-gcc-4.7.patch \
+		"${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch
+}
+
+src_install() {
+	default
+	python_replicate_script "${ED}"/usr/bin/goBambus2
+}
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 000000000000..97a8f59d0208
--- /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)
+-)