Bump to EAPI=5 and fix file collision, bug #422643; thanks Martin Mokrejs contacting upstream regarding this issue

Package-Manager: portage-2.2.20/cvs/Linux x86_64
Manifest-Sign-Key: 0xE9402A79B03529A2!

3 files changed, 41 insertions, 24 deletions

diff --git a/sci-biology/phrap/ChangeLog b/sci-biology/phrap/ChangeLog
index ab217fde3a9f..a9bc4e43e1ce 100644
--- a/sci-biology/phrap/ChangeLog
+++ b/sci-biology/phrap/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/phrap
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/phrap/ChangeLog,v 1.3 2013/03/11 16:36:19 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/phrap/ChangeLog,v 1.4 2015/06/16 08:34:28 jlec Exp $
+
+*phrap-1.080812-r1 (16 Jun 2015)
+
+  16 Jun 2015; Justin Lecher <jlec@gentoo.org> +phrap-1.080812-r1.ebuild,
+  -phrap-1.080812.ebuild:
+  Bump to EAPI=5 and fix file collision, bug #422643; thanks Martin Mokrejs
+  contacting upstream regarding this issue
 
   11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
@@ -15,4 +22,3 @@
   +phrap-1.080812.ebuild:
   Import from Science overlay, bug 114094. Thanks to Brady Catherman and Martin
   Mokrejs.
-
diff --git a/sci-biology/phrap/Manifest b/sci-biology/phrap/Manifest
index 8c4ef022649d..5ff8f3e0ba00 100644
--- a/sci-biology/phrap/Manifest
+++ b/sci-biology/phrap/Manifest
@@ -1,14 +1,26 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 DIST phrap-1.080812-distrib.tar.gz 317350 SHA256 7025f3cb30e5a3305a13d150f39a85580ade0bbf8169b25db65cbe396e201052
-EBUILD phrap-1.080812.ebuild 1239 SHA256 b68f50ce708a5a04b81a7eab43a8b0eeb4dc974b038947b62b236ba72eec6a2f SHA512 498c9f5a59dbbaede8815b386140075377995abd20422866db6e6477140f6d1e6a8330f83049b2a89e6a14eb3fda3512c9cf7b80ebf6cc1566a02428e077dc10 WHIRLPOOL c245966f7e3d5b3149ca90f408ec7a8eee5efe5d9750b58296cbf45876c89dc81921b40a9860313b25bc4f7b1d77172c785d3e06096764df79218906a497145c
-MISC ChangeLog 695 SHA256 a74fd8956aebf14e8add1179956307ffa7b92540830dcf08beb663e5d4bfad35 SHA512 4367e60e1ff6352d5e417bc3acc616c0bf6f9f13bfb9dc3b86b79dbf1e2197ba861d142b39d17ba09504508bd97aeb9ae0d397114e32cec68d593dea4c3cbde1 WHIRLPOOL a6df93f3ab84e2cf30cd652f6cc6f5a84f85e5d72e387a2621e1d2e5688393abb121cfebb12c34247554030d2e29d060fe4151901780e77951794a40d0480f1e
+EBUILD phrap-1.080812-r1.ebuild 1018 SHA256 32dc3d242a422c50c39f6a134719be4fe8ca2dc80e4c921125478a2bc55eebb7 SHA512 f8f4dd6d24b1523979d5e042f1379d516c9f82b797f2f6876555b4cb6d18a5bdfed26b8bcd3eaf9bd6cd7a7178e085cadf0bcaa0fbcfe70bbd4bd685e3904278 WHIRLPOOL 622014fff2d2a001a73c86cfc6016debbd62d49e336920e0e1bbcd2168b1c4d3103e2b0c7cc786f5d7315d5f1fa55775ce97104d7eb064d2cb4e2ff3082c3c5f
+MISC ChangeLog 948 SHA256 e18d1784109b55db14e7b9a4fb61e5d4b66813e114669c28420953cb014b6be5 SHA512 f23fd3cf92ef5071d962702da3bd3253b949a1982ea4a67d9ea09308c6bec3811753916b37a3853c02b199bcb56245549c8d84dc7bbb84eb2cf3dcd6ad158f6e WHIRLPOOL f44d52aa4612ccf877d37ad97102a4a8d565e406b68805e366e573f179beda0d2076268298d1905202c2958d23f69bcee8e5a018ad6874cb7308a858d9151176
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.19 (GNU/Linux)
+Version: GnuPG v2.0
 
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-fmkAnRUnTVrNk7wHPenV5dOtoQ4mSCtT
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diff --git a/sci-biology/phrap/phrap-1.080812.ebuild b/sci-biology/phrap/phrap-1.080812-r1.ebuild
index 666e423e2541..b4f9ba8c34fa 100644
--- a/sci-biology/phrap/phrap-1.080812.ebuild
+++ b/sci-biology/phrap/phrap-1.080812-r1.ebuild
@@ -1,8 +1,10 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/phrap/phrap-1.080812.ebuild,v 1.4 2013/02/17 10:28:37 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/phrap/phrap-1.080812-r1.ebuild,v 1.1 2015/06/16 08:34:28 jlec Exp $
 
-DESCRIPTION="Phrap, swat, cross_match: Shotgun assembly and alignment utilities"
+EAPI=5
+
+DESCRIPTION="Shotgun assembly and alignment utilities"
 HOMEPAGE="http://www.phrap.org/"
 SRC_URI="phrap-${PV}-distrib.tar.gz"
 
@@ -12,8 +14,9 @@ KEYWORDS="~amd64 ~x86"
 IUSE=""
 
 DEPEND=""
-RDEPEND="dev-lang/perl
-		dev-perl/perl-tk"
+RDEPEND="
+	dev-lang/perl
+	dev-perl/perl-tk"
 
 S="${WORKDIR}"
 
@@ -25,18 +28,14 @@ pkg_nofetch() {
 	einfo "and put it in ${DISTDIR}"
 }
 
-src_compile() {
-	sed -i 's/CFLAGS=/#CFLAGS=/' makefile
-	sed -i 's|#!/usr/local/bin/perl|#!/usr/bin/env perl|' phrapview
-	emake || die "emake failed"
-	# TODO: we need to extract staden sources because for compilation some of those
-	# files are needed: http://www.phrap.org/phredphrap/phrap.html
-	# (look for gcphrap and other gc* programs)
-	# emake gcphrap || die
+src_prepare() {
+	sed -i 's/CFLAGS=/#CFLAGS=/' makefile || die
+	sed -i 's|#!/usr/local/bin/perl|#!/usr/bin/env perl|' phrapview || die
 }
 
 src_install() {
-	dobin cluster cross_match loco phrap phrapview swat
+	dobin cross_match loco phrap phrapview swat
+	newbin cluster cluster_phrap
 	for i in {general,phrap,swat}.doc ; do
 		newdoc ${i} ${i}.txt
 	done