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

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

[Martin Mokrejs]

commit:     7227ff362b255f8a88cadc725ad2b768aeb5e54b
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Feb 21 11:21:31 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Feb 21 11:21:31 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7227ff36

sci-biology/tgicl: make sure we call perl and not perl-5.15.2 directly

(Portage version: 2.1.9.28/git/Linux i686, unsigned Manifest commit)

---
 sci-biology/tgicl/tgicl-2.1.ebuild |    5 +++++
 1 files changed, 5 insertions(+), 0 deletions(-)

diff --git a/sci-biology/tgicl/tgicl-2.1.ebuild b/sci-biology/tgicl/tgicl-2.1.ebuild
index 087a38c..5871289 100644
--- a/sci-biology/tgicl/tgicl-2.1.ebuild
+++ b/sci-biology/tgicl/tgicl-2.1.ebuild
@@ -41,4 +41,9 @@ src_install(){
 	einfo "We have to use the mgblast binary provided by upstream because it cannot be compiled against newer ncbi-tools anymore"
 	einfo "We also keep pvmsx binary because the pvmsx package needs pvm3.h header which is probably the one from pvm bundle which is not in portage at all, contact sys-cluster herd"
 	for f in mdust psx sclust tclust nrcl zmsort cap3 formatdb cdbfasta cdbyank; do rm -f "${D}"/usr/bin/$f || die "Cannot delete ${D}"/usr/bin/"$f"; done
+
+	# fix first lines of teh script to use /usr/bin/perl instead of /usr/bin/perl-$version
+	for f in tgicl tgicl_asm.psx tgicl_asmpta.psx tgicl_cluster.psx; do
+		sed -i 's@^#!/usr/bin/perl-*@#! /usr/bin/perl@' "${D}"/usr/bin/$f || die "Failed to fix ${D}"/usr/bin/"$f";
+	done
 }

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

[Justin Lecher]

commit:     656cf7c805be62e456be33277c81c7c267e00706
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 24 06:36:24 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep 24 06:36:24 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=656cf7c8

sci-biology/tgicl: Bump to EAPI=5

Package-Manager: portage-2.2.13

---
 sci-biology/tgicl/ChangeLog        |  7 +++++++
 sci-biology/tgicl/metadata.xml     | 10 +++++-----
 sci-biology/tgicl/tgicl-2.1.ebuild | 26 ++++++++++++++------------
 3 files changed, 26 insertions(+), 17 deletions(-)

diff --git a/sci-biology/tgicl/ChangeLog b/sci-biology/tgicl/ChangeLog
new file mode 100644
index 0000000..683f68c
--- /dev/null
+++ b/sci-biology/tgicl/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-biology/tgicl
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  24 Sep 2014; Justin Lecher <jlec@gentoo.org> tgicl-2.1.ebuild, metadata.xml:
+  Bump to EAPI=5
+

diff --git a/sci-biology/tgicl/metadata.xml b/sci-biology/tgicl/metadata.xml
index 07b5255..2bc8930 100644
--- a/sci-biology/tgicl/metadata.xml
+++ b/sci-biology/tgicl/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
-	<maintainer>
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
 </pkgmetadata>

diff --git a/sci-biology/tgicl/tgicl-2.1.ebuild b/sci-biology/tgicl/tgicl-2.1.ebuild
index ed9d403..0c920ea 100644
--- a/sci-biology/tgicl/tgicl-2.1.ebuild
+++ b/sci-biology/tgicl/tgicl-2.1.ebuild
@@ -2,7 +2,8 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=3
+EAPI=5
+
 inherit perl-module
 
 DESCRIPTION="TIGR perl scripts for clustering large EST/mRNAs datasets and aceconv, mgblast and pvmsx binaries"
@@ -14,17 +15,18 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-DEPEND="virtual/perl-Module-Build
-		sci-biology/cap3-bin
-		sci-biology/ncbi-tools
-		sci-biology/cdbfasta
-		sci-biology/clview
-		sci-biology/nrcl
-		sci-biology/psx
-		sci-biology/sclust
-		sci-biology/seqclean
-		sci-biology/tclust
-		sci-biology/zmsort"
+DEPEND="
+	virtual/perl-Module-Build
+	sci-biology/cap3-bin
+	sci-biology/ncbi-tools
+	sci-biology/cdbfasta
+	sci-biology/clview
+	sci-biology/nrcl
+	sci-biology/psx
+	sci-biology/sclust
+	sci-biology/seqclean
+	sci-biology/tclust
+	sci-biology/zmsort"
 RDEPEND="${DEPEND}"
 
 S="${WORKDIR}"/TGICL-2.1

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

[Justin Lecher]

commit:     0c6a2f7ec0c5e1629c0b2a3ee9ba7b15defb6f8a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 15 07:23:08 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jun 15 07:23:08 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0c6a2f7e

sci-biology/tgicl: Fix dependency problems due to recent mask of perl-core packages

Package-Manager: portage-2.2.20

 sci-biology/tgicl/ChangeLog        | 7 +++++--
 sci-biology/tgicl/tgicl-2.1.ebuild | 4 ++--
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/sci-biology/tgicl/ChangeLog b/sci-biology/tgicl/ChangeLog
index 683f68c..76e6585 100644
--- a/sci-biology/tgicl/ChangeLog
+++ b/sci-biology/tgicl/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for sci-biology/tgicl
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  15 Jun 2015; Justin Lecher <jlec@gentoo.org> tgicl-2.1.ebuild:
+  sci-biology/tgicl: Fix dependency problems due to recent mask of perl-core
+  packages
+
   24 Sep 2014; Justin Lecher <jlec@gentoo.org> tgicl-2.1.ebuild, metadata.xml:
   Bump to EAPI=5
-

diff --git a/sci-biology/tgicl/tgicl-2.1.ebuild b/sci-biology/tgicl/tgicl-2.1.ebuild
index 0c920ea..67bb99d 100644
--- a/sci-biology/tgicl/tgicl-2.1.ebuild
+++ b/sci-biology/tgicl/tgicl-2.1.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: $
 
@@ -16,7 +16,7 @@ KEYWORDS="~amd64 ~x86"
 IUSE=""
 
 DEPEND="
-	virtual/perl-Module-Build
+	dev-perl/Module-Build
 	sci-biology/cap3-bin
 	sci-biology/ncbi-tools
 	sci-biology/cdbfasta