[gentoo-commits] proj/sci:master commit in: sci-biology/glimmer/

[gentoo-commits] proj/sci:master commit in: sci-biology/glimmer/

[Martin Mokrejs]

commit:     022254bc1a437ea1255b6fb5f89da3f74ad91b6e
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 25 20:57:58 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 25 20:57:58 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=022254bc

EAPI bump

Package-Manager: portage-2.2.18

 sci-biology/glimmer/ChangeLog              | 7 +++++--
 sci-biology/glimmer/glimmer-3.02-r3.ebuild | 2 +-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/sci-biology/glimmer/ChangeLog b/sci-biology/glimmer/ChangeLog
index c3d61e9..2871a0a 100644
--- a/sci-biology/glimmer/ChangeLog
+++ b/sci-biology/glimmer/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/glimmer
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.10 2013/03/11 15:17:43 jlec Exp $
 
+  25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  glimmer-3.02-r3.ebuild:
+  EAPI bump
+
   11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
 
@@ -44,4 +48,3 @@
   07 Sep 2008; weaver <weaver@gentoo.org> +metadata.xml,
   +glimmer-3.02.ebuild:
   Import from science overlay
-

diff --git a/sci-biology/glimmer/glimmer-3.02-r3.ebuild b/sci-biology/glimmer/glimmer-3.02-r3.ebuild
index c8a09d8..94a2fa0 100644
--- a/sci-biology/glimmer/glimmer-3.02-r3.ebuild
+++ b/sci-biology/glimmer/glimmer-3.02-r3.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/glimmer-3.02-r2.ebuild,v 1.3 2010/07/16 17:29:32 hwoarang Exp $
 
-EAPI="2"
+EAPI="5"
 
 inherit eutils
 

[gentoo-commits] proj/sci:master commit in: sci-biology/glimmer/

[Martin Mokrejs]

commit:     f0955bf1fe7c7f0658066773e57e4629b4ffb74c
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 25 22:13:57 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 25 22:13:57 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f0955bf1

added dependency on sci-biology/elph as in Fedora; also stole from Fedora few more sed(1) tricks to remove yet missed hardcoded paths

Package-Manager: portage-2.2.18

 sci-biology/glimmer/ChangeLog            | 5 +++++
 sci-biology/glimmer/glimmer-3.02b.ebuild | 8 ++++++--
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/sci-biology/glimmer/ChangeLog b/sci-biology/glimmer/ChangeLog
index c3157e4..f1aa5cd 100644
--- a/sci-biology/glimmer/ChangeLog
+++ b/sci-biology/glimmer/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.10 2013/03/11 15:17:43 jlec Exp $
 
+  25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  glimmer-3.02b.ebuild:
+  added dependency on sci-biology/elph as in Fedora; also stole from Fedora few
+  more sed(1) tricks to remove yet missed hardcoded paths
+
 *glimmer-3.02b (25 May 2015)
 
   25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

diff --git a/sci-biology/glimmer/glimmer-3.02b.ebuild b/sci-biology/glimmer/glimmer-3.02b.ebuild
index cc3411f..1f7db36e 100644
--- a/sci-biology/glimmer/glimmer-3.02b.ebuild
+++ b/sci-biology/glimmer/glimmer-3.02b.ebuild
@@ -19,8 +19,7 @@ KEYWORDS="~amd64 ~x86"
 
 DEPEND=""
 RDEPEND="app-shells/tcsh
-	!app-crypt/pkcrack
-	!media-libs/libextractor"
+	sci-biology/elph"
 
 #S="${WORKDIR}/${PN}${PV}"
 S="${WORKDIR}/${PN}3.02"
@@ -32,6 +31,11 @@ src_prepare() {
 	sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die
 	# GCC 4.3 include fix
 	sed -i 's/include  <string>/include  <string.h>/' src/Common/delcher.hh || die
+	#
+	sed -i "s+/fs/szgenefinding/Glimmer3/bin+%${D}/bin/glimmer3+" scripts/g3-* || die
+	sed -i "s+/fs/szgenefinding/Glimmer3/scripts+%${D}/share/glimmer/scripts+" scripts/g3-* || die
+	sed -i "s+/nfshomes/adelcher/bin/elph+%${D}/bin/elph+" scripts/g3-* || die
+	sed -i "s/@ if/if/" src/c_make.gen || die
 	# avoid file collision on /usr/bin/extract #247394
 	epatch "${FILESDIR}/${P}-jobserver-fix.patch"
 	epatch "${FILESDIR}/${P}-ldflags.patch"