* [gentoo-commits] proj/sci:master commit in: sci-biology/velvet/
@ 2013-12-28 23:17 Justin Lecher
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher @ 2013-12-28 23:17 UTC (permalink / raw
To: gentoo-commits
commit: 48c8d6e83f00a3d7eb17c077fa4c13ab1f5c1ab6
Author: mahnmut <mahnmut411 <AT> gmail <DOT> com>
AuthorDate: Thu Dec 26 17:29:46 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Dec 26 17:29:46 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=48c8d6e8
Create velvet-1.2.1O.ebuild
---
sci-biology/velvet/velvet-1.2.1O.ebuild | 54 +++++++++++++++++++++++++++++++++
1 file changed, 54 insertions(+)
diff --git a/sci-biology/velvet/velvet-1.2.1O.ebuild b/sci-biology/velvet/velvet-1.2.1O.ebuild
new file mode 100644
index 0000000..9e0dd6e
--- /dev/null
+++ b/sci-biology/velvet/velvet-1.2.1O.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/velvet-1.2.1O.ebuild,v 1.5 2013/09/19 09:02:55 mahn Exp $
+# adapt from phajdan.jr ebuild
+
+EAPI=4
+
+inherit eutils toolchain-funcs flag-o-matic
+
+MY_P=${PN}_${PV}
+
+DESCRIPTION="A sequence assembler for very short reads"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/"
+SRC_URI="http://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="-doc"
+KEYWORDS="amd64 x86"
+
+RDEPEND="sys-libs/zlib"
+DEPEND="${RDEPEND}
+ doc? ( virtual/latex-base )"
+
+S="${WORKDIR}"/${MY_P}
+
+src_prepare() {
+ # necessary?
+ append-flags -O3 # as recommended by upstream
+ use doc || sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
+}
+
+src_compile() {
+ tc-export CC
+ MAKE_XOPTS=""
+ if [[ $VELVET_MAXKMERLENGTH != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS MAXKMERLENGTH=$VELVET_MAXKMERLENGTH"; fi
+ if [[ $VELVET_CATEGORIES != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS CATEGORIES=$VELVET_CATEGORIES"; fi
+ emake -j1 $MAKE_XOPTS || die
+ emake -j1 $MAKE_XOPTS color || die
+}
+
+src_install() {
+ dobin velvet{g,h,g_de,h_de} || die
+ insinto /usr/share/${PN}
+ doins -r contrib || die
+ dodoc Manual.pdf CREDITS.txt ChangeLog || die
+}
+
+pkg_postinst() {
+ elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual,"
+ elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your"
+ elog "environment or /etc/make.conf, then re-emerge the package. For example:"
+ elog " VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
+}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/velvet/
@ 2013-12-28 23:17 Justin Lecher
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher @ 2013-12-28 23:17 UTC (permalink / raw
To: gentoo-commits
commit: 900f13fe813b59aba02b9b8dbc5683a8634cfffc
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Dec 28 23:15:51 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Dec 28 23:15:51 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=900f13fe
sci-biology/velvet: Some improvements regarding die and optional enviromental variables; respect CC, CFLAGS
Package-Manager: portage-2.2.7
---
sci-biology/velvet/ChangeLog | 11 +++++
sci-biology/velvet/metadata.xml | 5 +++
sci-biology/velvet/velvet-1.2.10.ebuild | 73 +++++++++++++++++++++++++++++++++
sci-biology/velvet/velvet-1.2.1O.ebuild | 54 ------------------------
4 files changed, 89 insertions(+), 54 deletions(-)
diff --git a/sci-biology/velvet/ChangeLog b/sci-biology/velvet/ChangeLog
new file mode 100644
index 0000000..9efc41e
--- /dev/null
+++ b/sci-biology/velvet/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/velvet
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*velvet-1.2.10 (28 Dec 2013)
+
+ 28 Dec 2013; Justin Lecher <jlec@gentoo.org> -velvet-1.2.1O.ebuild,
+ +velvet-1.2.10.ebuild, +metadata.xml:
+ Some improvements regarding die and optional enviromental variables; respect
+ CC, CFLAGS
+
diff --git a/sci-biology/velvet/metadata.xml b/sci-biology/velvet/metadata.xml
new file mode 100644
index 0000000..f17a827
--- /dev/null
+++ b/sci-biology/velvet/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/velvet/velvet-1.2.10.ebuild b/sci-biology/velvet/velvet-1.2.10.ebuild
new file mode 100644
index 0000000..3ed797e
--- /dev/null
+++ b/sci-biology/velvet/velvet-1.2.10.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/velvet-1.2.1O.ebuild,v 1.5 2013/09/19 09:02:55 mahn Exp $
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+MY_P=${PN}_${PV}
+
+DESCRIPTION="A sequence assembler for very short reads"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/"
+SRC_URI="http://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc openmp"
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+ doc? ( virtual/latex-base )"
+
+S="${WORKDIR}"/${MY_P}
+
+src_prepare() {
+ if ! use doc; then
+ sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
+ fi
+ elog "Upstream recommendes using -O3 in CFLAGS"
+ echo
+ elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual,"
+ elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your"
+ elog "environment or /etc/make.conf, then re-emerge the package. For example:"
+ elog " VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
+ MAKEOPTS+=" -j1"
+
+ if [[ $(tc-getCC) =~ gcc ]]; then
+ local eopenmp=-fopenmp
+ elif [[ $(tc-getCC) =~ icc ]]; then
+ local eopenmp=-openmp
+ else
+ elog "Cannot detect compiler type so not setting openmp support"
+ fi
+ append-flags -fPIC ${eopenmp}
+ append-ldflags ${eopenmp}
+
+ tc-export CC
+
+ MAKE_XOPTS=(
+ CC=$(tc-getCC)
+ CFLAGS="${CFLAGS}"
+ OPT="${CFLAGS}"
+ )
+ if [[ ${VELVET_MAXKMERLENGTH} != "" ]]; then MAKE_XOPTS+=( MAXKMERLENGTH=${VELVET_MAXKMERLENGTH} ); fi
+ if [[ ${VELVET_CATEGORIES} != "" ]]; then MAKE_XOPTS+=( CATEGORIES=${VELVET_CATEGORIES} ); fi
+}
+
+src_compile() {
+ emake "${MAKE_XOPTS[@]}"
+ emake "${MAKE_XOPTS[@]}" color
+}
+
+src_test() {
+ emake "${MAKE_XOPTS[@]}" test
+}
+
+src_install() {
+ dobin velvet{g,h,g_de,h_de}
+ insinto /usr/share/${PN}
+ doins -r contrib
+ dodoc Manual.pdf CREDITS.txt ChangeLog
+}
diff --git a/sci-biology/velvet/velvet-1.2.1O.ebuild b/sci-biology/velvet/velvet-1.2.1O.ebuild
deleted file mode 100644
index 9e0dd6e..0000000
--- a/sci-biology/velvet/velvet-1.2.1O.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/velvet-1.2.1O.ebuild,v 1.5 2013/09/19 09:02:55 mahn Exp $
-# adapt from phajdan.jr ebuild
-
-EAPI=4
-
-inherit eutils toolchain-funcs flag-o-matic
-
-MY_P=${PN}_${PV}
-
-DESCRIPTION="A sequence assembler for very short reads"
-HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/"
-SRC_URI="http://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="-doc"
-KEYWORDS="amd64 x86"
-
-RDEPEND="sys-libs/zlib"
-DEPEND="${RDEPEND}
- doc? ( virtual/latex-base )"
-
-S="${WORKDIR}"/${MY_P}
-
-src_prepare() {
- # necessary?
- append-flags -O3 # as recommended by upstream
- use doc || sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
-}
-
-src_compile() {
- tc-export CC
- MAKE_XOPTS=""
- if [[ $VELVET_MAXKMERLENGTH != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS MAXKMERLENGTH=$VELVET_MAXKMERLENGTH"; fi
- if [[ $VELVET_CATEGORIES != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS CATEGORIES=$VELVET_CATEGORIES"; fi
- emake -j1 $MAKE_XOPTS || die
- emake -j1 $MAKE_XOPTS color || die
-}
-
-src_install() {
- dobin velvet{g,h,g_de,h_de} || die
- insinto /usr/share/${PN}
- doins -r contrib || die
- dodoc Manual.pdf CREDITS.txt ChangeLog || die
-}
-
-pkg_postinst() {
- elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual,"
- elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your"
- elog "environment or /etc/make.conf, then re-emerge the package. For example:"
- elog " VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
-}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/velvet/
@ 2013-12-28 23:40 Justin Lecher
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher @ 2013-12-28 23:40 UTC (permalink / raw
To: gentoo-commits
commit: 38b3a2d1841263f329ff7e682df93c6af78ecf07
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Dec 28 23:20:09 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Dec 28 23:20:09 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=38b3a2d1
merged into tree
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
---
sci-biology/velvet/ChangeLog | 11 -----
sci-biology/velvet/metadata.xml | 5 ---
sci-biology/velvet/velvet-1.2.10.ebuild | 73 ---------------------------------
3 files changed, 89 deletions(-)
diff --git a/sci-biology/velvet/ChangeLog b/sci-biology/velvet/ChangeLog
deleted file mode 100644
index 9efc41e..0000000
--- a/sci-biology/velvet/ChangeLog
+++ /dev/null
@@ -1,11 +0,0 @@
-# ChangeLog for sci-biology/velvet
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*velvet-1.2.10 (28 Dec 2013)
-
- 28 Dec 2013; Justin Lecher <jlec@gentoo.org> -velvet-1.2.1O.ebuild,
- +velvet-1.2.10.ebuild, +metadata.xml:
- Some improvements regarding die and optional enviromental variables; respect
- CC, CFLAGS
-
diff --git a/sci-biology/velvet/metadata.xml b/sci-biology/velvet/metadata.xml
deleted file mode 100644
index f17a827..0000000
--- a/sci-biology/velvet/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-biology</herd>
-</pkgmetadata>
diff --git a/sci-biology/velvet/velvet-1.2.10.ebuild b/sci-biology/velvet/velvet-1.2.10.ebuild
deleted file mode 100644
index 3ed797e..0000000
--- a/sci-biology/velvet/velvet-1.2.10.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/velvet-1.2.1O.ebuild,v 1.5 2013/09/19 09:02:55 mahn Exp $
-
-EAPI=5
-
-inherit eutils flag-o-matic toolchain-funcs
-
-MY_P=${PN}_${PV}
-
-DESCRIPTION="A sequence assembler for very short reads"
-HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/"
-SRC_URI="http://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc openmp"
-
-RDEPEND=""
-DEPEND="${RDEPEND}
- doc? ( virtual/latex-base )"
-
-S="${WORKDIR}"/${MY_P}
-
-src_prepare() {
- if ! use doc; then
- sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
- fi
- elog "Upstream recommendes using -O3 in CFLAGS"
- echo
- elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual,"
- elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your"
- elog "environment or /etc/make.conf, then re-emerge the package. For example:"
- elog " VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
- MAKEOPTS+=" -j1"
-
- if [[ $(tc-getCC) =~ gcc ]]; then
- local eopenmp=-fopenmp
- elif [[ $(tc-getCC) =~ icc ]]; then
- local eopenmp=-openmp
- else
- elog "Cannot detect compiler type so not setting openmp support"
- fi
- append-flags -fPIC ${eopenmp}
- append-ldflags ${eopenmp}
-
- tc-export CC
-
- MAKE_XOPTS=(
- CC=$(tc-getCC)
- CFLAGS="${CFLAGS}"
- OPT="${CFLAGS}"
- )
- if [[ ${VELVET_MAXKMERLENGTH} != "" ]]; then MAKE_XOPTS+=( MAXKMERLENGTH=${VELVET_MAXKMERLENGTH} ); fi
- if [[ ${VELVET_CATEGORIES} != "" ]]; then MAKE_XOPTS+=( CATEGORIES=${VELVET_CATEGORIES} ); fi
-}
-
-src_compile() {
- emake "${MAKE_XOPTS[@]}"
- emake "${MAKE_XOPTS[@]}" color
-}
-
-src_test() {
- emake "${MAKE_XOPTS[@]}" test
-}
-
-src_install() {
- dobin velvet{g,h,g_de,h_de}
- insinto /usr/share/${PN}
- doins -r contrib
- dodoc Manual.pdf CREDITS.txt ChangeLog
-}
^ permalink raw reply related [flat|nested] 3+ messages in thread
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