[gentoo-commits] proj/sci:master commit in: sci-biology/phusion2/

[gentoo-commits] proj/sci:master commit in: sci-biology/phusion2/

[Martin Mokrejs]

commit:     fdbb0df35cd149e408bb18fdcfa8debc839c6026
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Feb 16 18:00:57 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Feb 16 18:00:57 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fdbb0df3

sci-biology/phusion2: renamed a package; version bump; note that upstream sourceforge site contains additional components of the bundle

Package-Manager: portage-2.2.26

 sci-biology/phusion2/metadata.xml        | 12 ++++++++++
 sci-biology/phusion2/phusion2-3.0.ebuild | 40 ++++++++++++++++++++++++++++++++
 2 files changed, 52 insertions(+)

diff --git a/sci-biology/phusion2/metadata.xml b/sci-biology/phusion2/metadata.xml
new file mode 100644
index 0000000..1699e58
--- /dev/null
+++ b/sci-biology/phusion2/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+<maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>

diff --git a/sci-biology/phusion2/phusion2-3.0.ebuild b/sci-biology/phusion2/phusion2-3.0.ebuild
new file mode 100644
index 0000000..5f2d7ca
--- /dev/null
+++ b/sci-biology/phusion2/phusion2-3.0.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="Whole genome shotgun assembler using phrap (for Sanger-based reads)"
+HOMEPAGE="http://www.sanger.ac.uk/resources/software/phusion/"
+SRC_URI="http://downloads.sourceforge.net/project/${PN}/${P}.tar.gz"
+
+LICENSE="all-rights-reserved" # temporarily placed value
+# from http://genome.cshlp.org/content/13/1/81.full
+# Availability
+# Phusion is undergoing a rewrite of the code to make this a portable package. It will be made available free of charge to academic sites, but requires licensing for commercial use. For more information please contact the authors.
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="app-shells/tcsh
+	sys-cluster/openmpi"
+RDEPEND="${DEPEND}
+	sci-biology/phrap
+	dev-lang/perl"
+
+# contains bundled ssaha
+# file collision with sci-biology/shrimp on /usr/bin/fasta2fastq
+
+S="${WORKDIR}"
+
+src_prepare(){
+	rm -f phusion2 *.o
+	sed -e 's/^CFLAGS =/# CFLAGS =/' -i Makefile || die
+}
+
+src_install(){
+	dobin ctgreads.pl phusion2
+	dodoc how_to_make_mates
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/phusion2/

[Andrew Ammerlaan]

commit:     4b2335ef0355e2c8107af544fd7a63f3fc83ca3e
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Feb  3 04:36:50 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Feb  3 04:36:50 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4b2335ef

sci-biology/phusion2: EAPI bump, add keywords

Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/phusion2/phusion2-3.0.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sci-biology/phusion2/phusion2-3.0.ebuild b/sci-biology/phusion2/phusion2-3.0.ebuild
index aa27fffde..2ea281d41 100644
--- a/sci-biology/phusion2/phusion2-3.0.ebuild
+++ b/sci-biology/phusion2/phusion2-3.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -26,6 +26,7 @@ RDEPEND="${DEPEND}
 S="${WORKDIR}"
 
 src_prepare(){
+	default
 	rm -f phusion2 *.o
 	sed -e 's/^CFLAGS =/# CFLAGS =/' -i Makefile || die
 }

[gentoo-commits] proj/sci:master commit in: sci-biology/phusion2/

[Horea Christian]

commit:     ab79326f10b0ef555bac21b434fe965d4fb92fb2
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Jan 27 19:42:38 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Jan 27 19:42:44 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ab79326f

sci-biology/phusion2: masked, because:

dependency sci-biology/phrap removed from ::gentoo in f3cfb83adfc5dd1b85d0c9dce5ffbf166b25f4e4

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/phusion2/phusion2-3.0.ebuild | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/sci-biology/phusion2/phusion2-3.0.ebuild b/sci-biology/phusion2/phusion2-3.0.ebuild
index 2ea281d41..8c90b0a8f 100644
--- a/sci-biology/phusion2/phusion2-3.0.ebuild
+++ b/sci-biology/phusion2/phusion2-3.0.ebuild
@@ -12,7 +12,9 @@ LICENSE="all-rights-reserved" # temporarily placed value
 # Availability
 # Phusion is undergoing a rewrite of the code to make this a portable package. It will be made available free of charge to academic sites, but requires licensing for commercial use. For more information please contact the authors.
 SLOT="0"
-KEYWORDS="~amd64"
+#KEYWORDS="~amd64"
+# dependency sci-biology/phrap removed from ::gentoo in f3cfb83adfc5dd1b85d0c9dce5ffbf166b25f4e4
+KEYWORDS=""
 
 DEPEND="app-shells/tcsh
 	sys-cluster/openmpi"

[gentoo-commits] proj/sci:master commit in: sci-biology/phusion2/

[Andrew Ammerlaan]

commit:     0b262811124d42d89b7f8897a58cbedbd71591b4
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 10 13:53:36 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Feb 10 13:53:36 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0b262811

sci-biology/phusion2: treeclean, unavailable deps

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/phusion2/metadata.xml        | 15 ------------
 sci-biology/phusion2/phusion2-3.0.ebuild | 39 --------------------------------
 2 files changed, 54 deletions(-)

diff --git a/sci-biology/phusion2/metadata.xml b/sci-biology/phusion2/metadata.xml
deleted file mode 100644
index 0f267b755..000000000
--- a/sci-biology/phusion2/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
-	</upstream>
-</pkgmetadata>

diff --git a/sci-biology/phusion2/phusion2-3.0.ebuild b/sci-biology/phusion2/phusion2-3.0.ebuild
deleted file mode 100644
index 8c90b0a8f..000000000
--- a/sci-biology/phusion2/phusion2-3.0.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Whole genome shotgun assembler using phrap (for Sanger-based reads)"
-HOMEPAGE="https://sourceforge.net/projects/phusion2"
-SRC_URI="https://downloads.sourceforge.net/project/${PN}/${P}.tar.gz"
-
-LICENSE="all-rights-reserved" # temporarily placed value
-# from http://genome.cshlp.org/content/13/1/81.full
-# Availability
-# Phusion is undergoing a rewrite of the code to make this a portable package. It will be made available free of charge to academic sites, but requires licensing for commercial use. For more information please contact the authors.
-SLOT="0"
-#KEYWORDS="~amd64"
-# dependency sci-biology/phrap removed from ::gentoo in f3cfb83adfc5dd1b85d0c9dce5ffbf166b25f4e4
-KEYWORDS=""
-
-DEPEND="app-shells/tcsh
-	sys-cluster/openmpi"
-RDEPEND="${DEPEND}
-	sci-biology/phrap
-	dev-lang/perl"
-
-# contains bundled ssaha
-# file collision with sci-biology/shrimp on /usr/bin/fasta2fastq
-
-S="${WORKDIR}"
-
-src_prepare(){
-	default
-	rm -f phusion2 *.o
-	sed -e 's/^CFLAGS =/# CFLAGS =/' -i Makefile || die
-}
-
-src_install(){
-	dobin ctgreads.pl phusion2
-	dodoc how_to_make_mates
-}