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

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

commit:     e60260d0cfac4c0834f36777c589e87f43d08c62
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 15 19:42:12 2012 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 15 19:42:12 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e60260d0

sci-biology/mosaik: version bump for 2.1.33 and GIT HEAD, neither compiles so far; upstream re-contacted

(Portage version: 2.1.10.49/git/Linux x86_64, unsigned Manifest commit)

---
 sci-biology/mosaik/ChangeLog            |    7 +++++
 sci-biology/mosaik/mosaik-2.1.33.ebuild |   33 +++++++++++++---------
 sci-biology/mosaik/mosaik-9999.ebuild   |   45 +++++++++++++++++++++++++++++++
 3 files changed, 71 insertions(+), 14 deletions(-)

diff --git a/sci-biology/mosaik/ChangeLog b/sci-biology/mosaik/ChangeLog
index 0b8561a..51f8658 100644
--- a/sci-biology/mosaik/ChangeLog
+++ b/sci-biology/mosaik/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*mosaik-9999 (15 Mar 2012)
+
+  15 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  mosaik-2.1.33.ebuild, +mosaik-9999.ebuild:
+  version bump for 2.1.33 and GIT HEAD, neither compiles so far; upstream
+  re-contacted mosaik-2.1.33.ebuild mosaik-9999.ebuild
+
 *mosaik-2.1.33 (15 Mar 2012)
 *mosaik-1.1.0021 (15 Mar 2012)
 

diff --git a/sci-biology/mosaik/mosaik-2.1.33.ebuild b/sci-biology/mosaik/mosaik-2.1.33.ebuild
index 353ecb5..172bed2 100644
--- a/sci-biology/mosaik/mosaik-2.1.33.ebuild
+++ b/sci-biology/mosaik/mosaik-2.1.33.ebuild
@@ -4,9 +4,19 @@
 
 EAPI="2"
 
+if [ "$PV" == "9999" ]; then
+	inherit git-2
+fi
+
 DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies"
 HOMEPAGE="http://code.google.com/p/mosaik-aligner/"
-SRC_URI="http://mosaik-aligner.googlecode.com/files/MOSAIK-${PV}-source.tar"
+
+if [ "$PV" == "9999" ]; then
+	EGIT_REPO_URI="http://code.google.com/p/mosaik-aligner"
+else
+	SRC_URI="http://mosaik-aligner.googlecode.com/files/MOSAIK-${PV}-source.tar
+		http://code.google.com/p/mosaik-aligner/downloads/detail?name=Mosaik%201.0%20Documentation.pdf -> Mosaik-1.0-Documentation.pdf"
+fi
 
 LICENSE="GPL-2 || ( MIT )"
 SLOT="0"
@@ -16,24 +26,19 @@ KEYWORDS="~amd64 ~x86"
 DEPEND=""
 RDEPEND=""
 
-S="${WORKDIR}/MOSAIK-${PV}-source"
-
-src_prepare() {
-	#sed -i 's/-static//' src/includes/linux.inc || die
-	echo
-}
+if [ ! "$PV" == "9999" ]; then
+	S="${WORKDIR}/MOSAIK-${PV}-source"
+fi
 
 src_compile() {
+	if [ "$PV" == "9999" ]; then
+		cd src || die
+	fi
 	emake || die
-#	emake -C MosaikTools/c++ || die
-#	emake -C MosaikTools/perl || die
 }
 
 src_install() {
-	dobin bin/* || die
-
-	insinto /usr/share/${PN}
-	doins -r MosaikTools || die
+	dobin "${WORKDIR}"/bin/* || die
 
-	dodoc README Mosaik-1.0-Documentation.pdf
+	dodoc README "${DISTDIR}"/Mosaik-1.0-Documentation.pdf
 }

diff --git a/sci-biology/mosaik/mosaik-9999.ebuild b/sci-biology/mosaik/mosaik-9999.ebuild
new file mode 100644
index 0000000..3564bc3
--- /dev/null
+++ b/sci-biology/mosaik/mosaik-9999.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mosaik/mosaik-1.0.1388.ebuild,v 1.1 2010/04/11 17:29:40 weaver Exp $
+
+EAPI="2"
+
+if [ "$PV" == "9999" ]; then
+	inherit git-2
+fi
+
+DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies"
+HOMEPAGE="http://code.google.com/p/mosaik-aligner/"
+
+if [ "$PV" == "9999" ]; then
+	EGIT_REPO_URI="http://code.google.com/p/mosaik-aligner"
+	KEYWORDS=""
+else
+	SRC_URI="http://mosaik-aligner.googlecode.com/files/MOSAIK-${PV}-source.tar
+		http://code.google.com/p/mosaik-aligner/downloads/detail?name=Mosaik%201.0%20Documentation.pdf -> Mosaik-1.0-Documentation.pdf"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="GPL-2 || ( MIT )"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND=""
+
+if [ ! "$PV" == "9999" ]; then
+	S="${WORKDIR}/MOSAIK-${PV}-source"
+fi
+
+src_compile() {
+	if [ "$PV" == "9999" ]; then
+		cd src || die
+	fi
+	emake || die
+}
+
+src_install() {
+	dobin "${WORKDIR}"/bin/* || die
+
+	dodoc README "${DISTDIR}"/Mosaik-1.0-Documentation.pdf
+}