subject:"\[gentoo\-commits\] proj\/sci\:master commit in\: sci\-biology\/oases\/files\/, sci\-biology\/oases\/"

[gentoo-commits] proj/sci:master commit in: sci-biology/oases/files/, sci-biology/oases/

2016-04-10 Thread Martin Mokrejs

commit: dc8f115ece85ad0ba1cae058febbb79ee40b89c1
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Sun Apr 10 21:04:10 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Apr 10 21:04:10 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=dc8f115e

sci-biology/oases: new package

Package-Manager: portage-2.2.28

 sci-biology/oases/files/Makefile.patch | 15 +
 sci-biology/oases/metadata.xml | 12 +++
 sci-biology/oases/oases-0.2.08.ebuild  | 34 +
 sci-biology/oases/oases-.ebuild| 39 ++
 4 files changed, 100 insertions(+)

diff --git a/sci-biology/oases/files/Makefile.patch 
b/sci-biology/oases/files/Makefile.patch
new file mode 100644
index 000..58652b0
--- /dev/null
+++ b/sci-biology/oases/files/Makefile.patch
@@ -0,0 +1,15 @@
+--- Makefile.ori   2016-04-10 22:34:31.976222662 +0200
 Makefile   2016-04-10 22:37:49.636225327 +0200
+@@ -1,8 +1,8 @@
+-CC = gcc
+-CFLAGS = -Wall
+-DEBUG = -g
++CC ?= gcc
++CFLAGS ?= -Wall
++DEBUG ?= -g
+ LIBS = -lm
+-OPT = -O3
++#OPT = -O3
+ export MAXKMERLENGTH = 64
+ export CATEGORIES = 2
+ DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)

diff --git a/sci-biology/oases/metadata.xml b/sci-biology/oases/metadata.xml
new file mode 100644
index 000..f68a1b6
--- /dev/null
+++ b/sci-biology/oases/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+  
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+  
+  
+sci-biol...@gentoo.org
+Gentoo Biology Project
+  
+

diff --git a/sci-biology/oases/oases-0.2.08.ebuild 
b/sci-biology/oases/oases-0.2.08.ebuild
new file mode 100644
index 000..eff7842
--- /dev/null
+++ b/sci-biology/oases/oases-0.2.08.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="De novo transcriptome assembler"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases";
+SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
+   http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+KEYWORDS=""
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+   >=sci-biology/velvet-1.2.08"
+
+S="${WORKDIR}"/oases_0.2.8
+
+src_prepare(){
+   epatch "${FILESDIR}"/Makefile.patch
+   sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die
+}
+
+src_install(){
+   dobin oases
+   dodoc README.md
+   dodoc "${DISTDIR}"/OasesManual.pdf
+}

diff --git a/sci-biology/oases/oases-.ebuild 
b/sci-biology/oases/oases-.ebuild
new file mode 100644
index 000..0c54394
--- /dev/null
+++ b/sci-biology/oases/oases-.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+[ "$PV" == "" ] && inherit git-r3
+
+inherit eutils
+
+DESCRIPTION="De novo transcriptome assembler"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases";
+if [ "$PV" == "" ]; then
+   EGIT_REPO_URI="git://github.com/dzerbino/oases.git"
+   SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+   KEYWORDS=""
+else
+   SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
+   http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+   KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+   >=sci-biology/velvet-1.2.08"
+
+src_prepare(){
+   epatch "${FILESDIR}"/Makefile.patch
+}
+
+src_install(){
+   dobin oases
+   dodoc README.md
+   dodoc "${DISTDIR}"/OasesManual.pdf
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/oases/files/, sci-biology/oases/

2016-04-10 Thread Martin Mokrejs

commit: dc8f115ece85ad0ba1cae058febbb79ee40b89c1
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Sun Apr 10 21:04:10 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Apr 10 21:04:10 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=dc8f115e

sci-biology/oases: new package

Package-Manager: portage-2.2.28

 sci-biology/oases/files/Makefile.patch | 15 +
 sci-biology/oases/metadata.xml | 12 +++
 sci-biology/oases/oases-0.2.08.ebuild  | 34 +
 sci-biology/oases/oases-.ebuild| 39 ++
 4 files changed, 100 insertions(+)

diff --git a/sci-biology/oases/files/Makefile.patch 
b/sci-biology/oases/files/Makefile.patch
new file mode 100644
index 000..58652b0
--- /dev/null
+++ b/sci-biology/oases/files/Makefile.patch
@@ -0,0 +1,15 @@
+--- Makefile.ori   2016-04-10 22:34:31.976222662 +0200
 Makefile   2016-04-10 22:37:49.636225327 +0200
+@@ -1,8 +1,8 @@
+-CC = gcc
+-CFLAGS = -Wall
+-DEBUG = -g
++CC ?= gcc
++CFLAGS ?= -Wall
++DEBUG ?= -g
+ LIBS = -lm
+-OPT = -O3
++#OPT = -O3
+ export MAXKMERLENGTH = 64
+ export CATEGORIES = 2
+ DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)

diff --git a/sci-biology/oases/metadata.xml b/sci-biology/oases/metadata.xml
new file mode 100644
index 000..f68a1b6
--- /dev/null
+++ b/sci-biology/oases/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+  
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+  
+  
+sci-biol...@gentoo.org
+Gentoo Biology Project
+  
+

diff --git a/sci-biology/oases/oases-0.2.08.ebuild 
b/sci-biology/oases/oases-0.2.08.ebuild
new file mode 100644
index 000..eff7842
--- /dev/null
+++ b/sci-biology/oases/oases-0.2.08.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="De novo transcriptome assembler"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases";
+SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
+   http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+KEYWORDS=""
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+   >=sci-biology/velvet-1.2.08"
+
+S="${WORKDIR}"/oases_0.2.8
+
+src_prepare(){
+   epatch "${FILESDIR}"/Makefile.patch
+   sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die
+}
+
+src_install(){
+   dobin oases
+   dodoc README.md
+   dodoc "${DISTDIR}"/OasesManual.pdf
+}

diff --git a/sci-biology/oases/oases-.ebuild 
b/sci-biology/oases/oases-.ebuild
new file mode 100644
index 000..0c54394
--- /dev/null
+++ b/sci-biology/oases/oases-.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+[ "$PV" == "" ] && inherit git-r3
+
+inherit eutils
+
+DESCRIPTION="De novo transcriptome assembler"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases";
+if [ "$PV" == "" ]; then
+   EGIT_REPO_URI="git://github.com/dzerbino/oases.git"
+   SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+   KEYWORDS=""
+else
+   SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
+   http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+   KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+   >=sci-biology/velvet-1.2.08"
+
+src_prepare(){
+   epatch "${FILESDIR}"/Makefile.patch
+}
+
+src_install(){
+   dobin oases
+   dodoc README.md
+   dodoc "${DISTDIR}"/OasesManual.pdf
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/oases/files/, sci-biology/oases/

2016-04-10 Thread Martin Mokrejs

commit: dc8f115ece85ad0ba1cae058febbb79ee40b89c1
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Sun Apr 10 21:04:10 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Apr 10 21:04:10 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=dc8f115e

sci-biology/oases: new package

Package-Manager: portage-2.2.28

 sci-biology/oases/files/Makefile.patch | 15 +
 sci-biology/oases/metadata.xml | 12 +++
 sci-biology/oases/oases-0.2.08.ebuild  | 34 +
 sci-biology/oases/oases-.ebuild| 39 ++
 4 files changed, 100 insertions(+)

diff --git a/sci-biology/oases/files/Makefile.patch 
b/sci-biology/oases/files/Makefile.patch
new file mode 100644
index 000..58652b0
--- /dev/null
+++ b/sci-biology/oases/files/Makefile.patch
@@ -0,0 +1,15 @@
+--- Makefile.ori   2016-04-10 22:34:31.976222662 +0200
 Makefile   2016-04-10 22:37:49.636225327 +0200
+@@ -1,8 +1,8 @@
+-CC = gcc
+-CFLAGS = -Wall
+-DEBUG = -g
++CC ?= gcc
++CFLAGS ?= -Wall
++DEBUG ?= -g
+ LIBS = -lm
+-OPT = -O3
++#OPT = -O3
+ export MAXKMERLENGTH = 64
+ export CATEGORIES = 2
+ DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)

diff --git a/sci-biology/oases/metadata.xml b/sci-biology/oases/metadata.xml
new file mode 100644
index 000..f68a1b6
--- /dev/null
+++ b/sci-biology/oases/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+  
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+  
+  
+sci-biol...@gentoo.org
+Gentoo Biology Project
+  
+

diff --git a/sci-biology/oases/oases-0.2.08.ebuild 
b/sci-biology/oases/oases-0.2.08.ebuild
new file mode 100644
index 000..eff7842
--- /dev/null
+++ b/sci-biology/oases/oases-0.2.08.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="De novo transcriptome assembler"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases";
+SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
+   http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+KEYWORDS=""
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+   >=sci-biology/velvet-1.2.08"
+
+S="${WORKDIR}"/oases_0.2.8
+
+src_prepare(){
+   epatch "${FILESDIR}"/Makefile.patch
+   sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die
+}
+
+src_install(){
+   dobin oases
+   dodoc README.md
+   dodoc "${DISTDIR}"/OasesManual.pdf
+}

diff --git a/sci-biology/oases/oases-.ebuild 
b/sci-biology/oases/oases-.ebuild
new file mode 100644
index 000..0c54394
--- /dev/null
+++ b/sci-biology/oases/oases-.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+[ "$PV" == "" ] && inherit git-r3
+
+inherit eutils
+
+DESCRIPTION="De novo transcriptome assembler"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases";
+if [ "$PV" == "" ]; then
+   EGIT_REPO_URI="git://github.com/dzerbino/oases.git"
+   SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+   KEYWORDS=""
+else
+   SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
+   http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+   KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+   >=sci-biology/velvet-1.2.08"
+
+src_prepare(){
+   epatch "${FILESDIR}"/Makefile.patch
+}
+
+src_install(){
+   dobin oases
+   dodoc README.md
+   dodoc "${DISTDIR}"/OasesManual.pdf
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/oases/files/, sci-biology/oases/

2016-04-10 Thread Martin Mokrejs

commit: dc8f115ece85ad0ba1cae058febbb79ee40b89c1
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Sun Apr 10 21:04:10 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Apr 10 21:04:10 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=dc8f115e

sci-biology/oases: new package

Package-Manager: portage-2.2.28

 sci-biology/oases/files/Makefile.patch | 15 +
 sci-biology/oases/metadata.xml | 12 +++
 sci-biology/oases/oases-0.2.08.ebuild  | 34 +
 sci-biology/oases/oases-.ebuild| 39 ++
 4 files changed, 100 insertions(+)

diff --git a/sci-biology/oases/files/Makefile.patch 
b/sci-biology/oases/files/Makefile.patch
new file mode 100644
index 000..58652b0
--- /dev/null
+++ b/sci-biology/oases/files/Makefile.patch
@@ -0,0 +1,15 @@
+--- Makefile.ori   2016-04-10 22:34:31.976222662 +0200
 Makefile   2016-04-10 22:37:49.636225327 +0200
+@@ -1,8 +1,8 @@
+-CC = gcc
+-CFLAGS = -Wall
+-DEBUG = -g
++CC ?= gcc
++CFLAGS ?= -Wall
++DEBUG ?= -g
+ LIBS = -lm
+-OPT = -O3
++#OPT = -O3
+ export MAXKMERLENGTH = 64
+ export CATEGORIES = 2
+ DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)

diff --git a/sci-biology/oases/metadata.xml b/sci-biology/oases/metadata.xml
new file mode 100644
index 000..f68a1b6
--- /dev/null
+++ b/sci-biology/oases/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+  
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+  
+  
+sci-biol...@gentoo.org
+Gentoo Biology Project
+  
+

diff --git a/sci-biology/oases/oases-0.2.08.ebuild 
b/sci-biology/oases/oases-0.2.08.ebuild
new file mode 100644
index 000..eff7842
--- /dev/null
+++ b/sci-biology/oases/oases-0.2.08.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="De novo transcriptome assembler"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases";
+SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
+   http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+KEYWORDS=""
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+   >=sci-biology/velvet-1.2.08"
+
+S="${WORKDIR}"/oases_0.2.8
+
+src_prepare(){
+   epatch "${FILESDIR}"/Makefile.patch
+   sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die
+}
+
+src_install(){
+   dobin oases
+   dodoc README.md
+   dodoc "${DISTDIR}"/OasesManual.pdf
+}

diff --git a/sci-biology/oases/oases-.ebuild 
b/sci-biology/oases/oases-.ebuild
new file mode 100644
index 000..0c54394
--- /dev/null
+++ b/sci-biology/oases/oases-.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+[ "$PV" == "" ] && inherit git-r3
+
+inherit eutils
+
+DESCRIPTION="De novo transcriptome assembler"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases";
+if [ "$PV" == "" ]; then
+   EGIT_REPO_URI="git://github.com/dzerbino/oases.git"
+   SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+   KEYWORDS=""
+else
+   SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
+   http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+   KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+   >=sci-biology/velvet-1.2.08"
+
+src_prepare(){
+   epatch "${FILESDIR}"/Makefile.patch
+}
+
+src_install(){
+   dobin oases
+   dodoc README.md
+   dodoc "${DISTDIR}"/OasesManual.pdf
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/oases/files/, sci-biology/oases/

2016-04-10 Thread Martin Mokrejs

commit: dc8f115ece85ad0ba1cae058febbb79ee40b89c1
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Sun Apr 10 21:04:10 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Apr 10 21:04:10 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=dc8f115e

sci-biology/oases: new package

Package-Manager: portage-2.2.28

 sci-biology/oases/files/Makefile.patch | 15 +
 sci-biology/oases/metadata.xml | 12 +++
 sci-biology/oases/oases-0.2.08.ebuild  | 34 +
 sci-biology/oases/oases-.ebuild| 39 ++
 4 files changed, 100 insertions(+)

diff --git a/sci-biology/oases/files/Makefile.patch 
b/sci-biology/oases/files/Makefile.patch
new file mode 100644
index 000..58652b0
--- /dev/null
+++ b/sci-biology/oases/files/Makefile.patch
@@ -0,0 +1,15 @@
+--- Makefile.ori   2016-04-10 22:34:31.976222662 +0200
 Makefile   2016-04-10 22:37:49.636225327 +0200
+@@ -1,8 +1,8 @@
+-CC = gcc
+-CFLAGS = -Wall
+-DEBUG = -g
++CC ?= gcc
++CFLAGS ?= -Wall
++DEBUG ?= -g
+ LIBS = -lm
+-OPT = -O3
++#OPT = -O3
+ export MAXKMERLENGTH = 64
+ export CATEGORIES = 2
+ DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)

diff --git a/sci-biology/oases/metadata.xml b/sci-biology/oases/metadata.xml
new file mode 100644
index 000..f68a1b6
--- /dev/null
+++ b/sci-biology/oases/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+  
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+  
+  
+sci-biol...@gentoo.org
+Gentoo Biology Project
+  
+

diff --git a/sci-biology/oases/oases-0.2.08.ebuild 
b/sci-biology/oases/oases-0.2.08.ebuild
new file mode 100644
index 000..eff7842
--- /dev/null
+++ b/sci-biology/oases/oases-0.2.08.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="De novo transcriptome assembler"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases";
+SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
+   http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+KEYWORDS=""
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+   >=sci-biology/velvet-1.2.08"
+
+S="${WORKDIR}"/oases_0.2.8
+
+src_prepare(){
+   epatch "${FILESDIR}"/Makefile.patch
+   sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die
+}
+
+src_install(){
+   dobin oases
+   dodoc README.md
+   dodoc "${DISTDIR}"/OasesManual.pdf
+}

diff --git a/sci-biology/oases/oases-.ebuild 
b/sci-biology/oases/oases-.ebuild
new file mode 100644
index 000..0c54394
--- /dev/null
+++ b/sci-biology/oases/oases-.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+[ "$PV" == "" ] && inherit git-r3
+
+inherit eutils
+
+DESCRIPTION="De novo transcriptome assembler"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases";
+if [ "$PV" == "" ]; then
+   EGIT_REPO_URI="git://github.com/dzerbino/oases.git"
+   SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+   KEYWORDS=""
+else
+   SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
+   http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+   KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+   >=sci-biology/velvet-1.2.08"
+
+src_prepare(){
+   epatch "${FILESDIR}"/Makefile.patch
+}
+
+src_install(){
+   dobin oases
+   dodoc README.md
+   dodoc "${DISTDIR}"/OasesManual.pdf
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/oases/files/, sci-biology/oases/

2016-04-10 Thread Martin Mokrejs

commit: dc8f115ece85ad0ba1cae058febbb79ee40b89c1
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Sun Apr 10 21:04:10 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Apr 10 21:04:10 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=dc8f115e

sci-biology/oases: new package

Package-Manager: portage-2.2.28

 sci-biology/oases/files/Makefile.patch | 15 +
 sci-biology/oases/metadata.xml | 12 +++
 sci-biology/oases/oases-0.2.08.ebuild  | 34 +
 sci-biology/oases/oases-.ebuild| 39 ++
 4 files changed, 100 insertions(+)

diff --git a/sci-biology/oases/files/Makefile.patch 
b/sci-biology/oases/files/Makefile.patch
new file mode 100644
index 000..58652b0
--- /dev/null
+++ b/sci-biology/oases/files/Makefile.patch
@@ -0,0 +1,15 @@
+--- Makefile.ori   2016-04-10 22:34:31.976222662 +0200
 Makefile   2016-04-10 22:37:49.636225327 +0200
+@@ -1,8 +1,8 @@
+-CC = gcc
+-CFLAGS = -Wall
+-DEBUG = -g
++CC ?= gcc
++CFLAGS ?= -Wall
++DEBUG ?= -g
+ LIBS = -lm
+-OPT = -O3
++#OPT = -O3
+ export MAXKMERLENGTH = 64
+ export CATEGORIES = 2
+ DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)

diff --git a/sci-biology/oases/metadata.xml b/sci-biology/oases/metadata.xml
new file mode 100644
index 000..f68a1b6
--- /dev/null
+++ b/sci-biology/oases/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+  
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+  
+  
+sci-biol...@gentoo.org
+Gentoo Biology Project
+  
+

diff --git a/sci-biology/oases/oases-0.2.08.ebuild 
b/sci-biology/oases/oases-0.2.08.ebuild
new file mode 100644
index 000..eff7842
--- /dev/null
+++ b/sci-biology/oases/oases-0.2.08.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="De novo transcriptome assembler"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases";
+SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
+   http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+KEYWORDS=""
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+   >=sci-biology/velvet-1.2.08"
+
+S="${WORKDIR}"/oases_0.2.8
+
+src_prepare(){
+   epatch "${FILESDIR}"/Makefile.patch
+   sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die
+}
+
+src_install(){
+   dobin oases
+   dodoc README.md
+   dodoc "${DISTDIR}"/OasesManual.pdf
+}

diff --git a/sci-biology/oases/oases-.ebuild 
b/sci-biology/oases/oases-.ebuild
new file mode 100644
index 000..0c54394
--- /dev/null
+++ b/sci-biology/oases/oases-.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+[ "$PV" == "" ] && inherit git-r3
+
+inherit eutils
+
+DESCRIPTION="De novo transcriptome assembler"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases";
+if [ "$PV" == "" ]; then
+   EGIT_REPO_URI="git://github.com/dzerbino/oases.git"
+   SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+   KEYWORDS=""
+else
+   SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
+   http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+   KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+   >=sci-biology/velvet-1.2.08"
+
+src_prepare(){
+   epatch "${FILESDIR}"/Makefile.patch
+}
+
+src_install(){
+   dobin oases
+   dodoc README.md
+   dodoc "${DISTDIR}"/OasesManual.pdf
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/oases/files/, sci-biology/oases/

2016-04-10 Thread Martin Mokrejs

commit: dc8f115ece85ad0ba1cae058febbb79ee40b89c1
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Sun Apr 10 21:04:10 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Apr 10 21:04:10 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=dc8f115e

sci-biology/oases: new package

Package-Manager: portage-2.2.28

 sci-biology/oases/files/Makefile.patch | 15 +
 sci-biology/oases/metadata.xml | 12 +++
 sci-biology/oases/oases-0.2.08.ebuild  | 34 +
 sci-biology/oases/oases-.ebuild| 39 ++
 4 files changed, 100 insertions(+)

diff --git a/sci-biology/oases/files/Makefile.patch 
b/sci-biology/oases/files/Makefile.patch
new file mode 100644
index 000..58652b0
--- /dev/null
+++ b/sci-biology/oases/files/Makefile.patch
@@ -0,0 +1,15 @@
+--- Makefile.ori   2016-04-10 22:34:31.976222662 +0200
 Makefile   2016-04-10 22:37:49.636225327 +0200
+@@ -1,8 +1,8 @@
+-CC = gcc
+-CFLAGS = -Wall
+-DEBUG = -g
++CC ?= gcc
++CFLAGS ?= -Wall
++DEBUG ?= -g
+ LIBS = -lm
+-OPT = -O3
++#OPT = -O3
+ export MAXKMERLENGTH = 64
+ export CATEGORIES = 2
+ DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)

diff --git a/sci-biology/oases/metadata.xml b/sci-biology/oases/metadata.xml
new file mode 100644
index 000..f68a1b6
--- /dev/null
+++ b/sci-biology/oases/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+  
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+  
+  
+sci-biol...@gentoo.org
+Gentoo Biology Project
+  
+

diff --git a/sci-biology/oases/oases-0.2.08.ebuild 
b/sci-biology/oases/oases-0.2.08.ebuild
new file mode 100644
index 000..eff7842
--- /dev/null
+++ b/sci-biology/oases/oases-0.2.08.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="De novo transcriptome assembler"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases";
+SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
+   http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+KEYWORDS=""
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+   >=sci-biology/velvet-1.2.08"
+
+S="${WORKDIR}"/oases_0.2.8
+
+src_prepare(){
+   epatch "${FILESDIR}"/Makefile.patch
+   sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die
+}
+
+src_install(){
+   dobin oases
+   dodoc README.md
+   dodoc "${DISTDIR}"/OasesManual.pdf
+}

diff --git a/sci-biology/oases/oases-.ebuild 
b/sci-biology/oases/oases-.ebuild
new file mode 100644
index 000..0c54394
--- /dev/null
+++ b/sci-biology/oases/oases-.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+[ "$PV" == "" ] && inherit git-r3
+
+inherit eutils
+
+DESCRIPTION="De novo transcriptome assembler"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases";
+if [ "$PV" == "" ]; then
+   EGIT_REPO_URI="git://github.com/dzerbino/oases.git"
+   SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+   KEYWORDS=""
+else
+   SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
+   http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+   KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+   >=sci-biology/velvet-1.2.08"
+
+src_prepare(){
+   epatch "${FILESDIR}"/Makefile.patch
+}
+
+src_install(){
+   dobin oases
+   dodoc README.md
+   dodoc "${DISTDIR}"/OasesManual.pdf
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/oases/files/, sci-biology/oases/

2016-04-10 Thread Martin Mokrejs

commit: dc8f115ece85ad0ba1cae058febbb79ee40b89c1
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Sun Apr 10 21:04:10 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Apr 10 21:04:10 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=dc8f115e

sci-biology/oases: new package

Package-Manager: portage-2.2.28

 sci-biology/oases/files/Makefile.patch | 15 +
 sci-biology/oases/metadata.xml | 12 +++
 sci-biology/oases/oases-0.2.08.ebuild  | 34 +
 sci-biology/oases/oases-.ebuild| 39 ++
 4 files changed, 100 insertions(+)

diff --git a/sci-biology/oases/files/Makefile.patch 
b/sci-biology/oases/files/Makefile.patch
new file mode 100644
index 000..58652b0
--- /dev/null
+++ b/sci-biology/oases/files/Makefile.patch
@@ -0,0 +1,15 @@
+--- Makefile.ori   2016-04-10 22:34:31.976222662 +0200
 Makefile   2016-04-10 22:37:49.636225327 +0200
+@@ -1,8 +1,8 @@
+-CC = gcc
+-CFLAGS = -Wall
+-DEBUG = -g
++CC ?= gcc
++CFLAGS ?= -Wall
++DEBUG ?= -g
+ LIBS = -lm
+-OPT = -O3
++#OPT = -O3
+ export MAXKMERLENGTH = 64
+ export CATEGORIES = 2
+ DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)

diff --git a/sci-biology/oases/metadata.xml b/sci-biology/oases/metadata.xml
new file mode 100644
index 000..f68a1b6
--- /dev/null
+++ b/sci-biology/oases/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+  
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+  
+  
+sci-biol...@gentoo.org
+Gentoo Biology Project
+  
+

diff --git a/sci-biology/oases/oases-0.2.08.ebuild 
b/sci-biology/oases/oases-0.2.08.ebuild
new file mode 100644
index 000..eff7842
--- /dev/null
+++ b/sci-biology/oases/oases-0.2.08.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="De novo transcriptome assembler"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases";
+SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
+   http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+KEYWORDS=""
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+   >=sci-biology/velvet-1.2.08"
+
+S="${WORKDIR}"/oases_0.2.8
+
+src_prepare(){
+   epatch "${FILESDIR}"/Makefile.patch
+   sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die
+}
+
+src_install(){
+   dobin oases
+   dodoc README.md
+   dodoc "${DISTDIR}"/OasesManual.pdf
+}

diff --git a/sci-biology/oases/oases-.ebuild 
b/sci-biology/oases/oases-.ebuild
new file mode 100644
index 000..0c54394
--- /dev/null
+++ b/sci-biology/oases/oases-.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+[ "$PV" == "" ] && inherit git-r3
+
+inherit eutils
+
+DESCRIPTION="De novo transcriptome assembler"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases";
+if [ "$PV" == "" ]; then
+   EGIT_REPO_URI="git://github.com/dzerbino/oases.git"
+   SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+   KEYWORDS=""
+else
+   SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
+   http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf";
+   KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+   >=sci-biology/velvet-1.2.08"
+
+src_prepare(){
+   epatch "${FILESDIR}"/Makefile.patch
+}
+
+src_install(){
+   dobin oases
+   dodoc README.md
+   dodoc "${DISTDIR}"/OasesManual.pdf
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/oases/files/, sci-biology/oases/

[gentoo-commits] proj/sci:master commit in: sci-biology/oases/files/, sci-biology/oases/

[gentoo-commits] proj/sci:master commit in: sci-biology/oases/files/, sci-biology/oases/

[gentoo-commits] proj/sci:master commit in: sci-biology/oases/files/, sci-biology/oases/

[gentoo-commits] proj/sci:master commit in: sci-biology/oases/files/, sci-biology/oases/

[gentoo-commits] proj/sci:master commit in: sci-biology/oases/files/, sci-biology/oases/

[gentoo-commits] proj/sci:master commit in: sci-biology/oases/files/, sci-biology/oases/

[gentoo-commits] proj/sci:master commit in: sci-biology/oases/files/, sci-biology/oases/

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