version bump, added the pdf documentation to SRC_URI, the compile process leaks through many 'Fastq.cpp:224: error: conditional expression between distinct pointer types 'gzFile_s*' and 'FILE*' lacks a cast' messages in Fastq.cpp:224, Fastq.cpp:226, Fasta.cpp:258, Fasta.cpp:260, Fasta.cpp:266, Fasta.cpp:268, but the package itself installs and executes at least

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

5 files changed, 107 insertions, 0 deletions

diff --git a/sci-biology/mosaik/ChangeLog b/sci-biology/mosaik/ChangeLog
new file mode 100644
index 000000000..0b8561a43
--- /dev/null
+++ b/sci-biology/mosaik/ChangeLog
@@ -0,0 +1,16 @@
+# ChangeLog for sci-biology/mosaik
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*mosaik-2.1.33 (15 Mar 2012)
+*mosaik-1.1.0021 (15 Mar 2012)
+
+  15 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +mosaik-1.1.0021.ebuild, +mosaik-2.1.33.ebuild:
+  version bump, added the pdf documentation to SRC_URI, the compile process
+  leaks through many 'Fastq.cpp:224: error: conditional expression between
+  distinct pointer types 'gzFile_s*' and 'FILE*' lacks a cast' messages in
+  Fastq.cpp:224, Fastq.cpp:226, Fasta.cpp:258, Fasta.cpp:260, Fasta.cpp:266,
+  Fasta.cpp:268, but the package itself installs and executes at least
+  mosaik-1.1.0021.ebuild
+
diff --git a/sci-biology/mosaik/Manifest b/sci-biology/mosaik/Manifest
new file mode 100644
index 000000000..2f9225d43
--- /dev/null
+++ b/sci-biology/mosaik/Manifest
@@ -0,0 +1,3 @@
+DIST MOSAIK-2.1.33-source.tar 3911680 SHA256 210764cddbd8a3866976f065b912eb30fcd94d681901be93b42724708b86e2aa SHA512 9eeda8698bc929f95ff16b4e611174f631a5affb8712d582eda7e02a45f27ea8a50ffc56c6595f837af342f266a5bfe44ca1eb006d301caef671e01ed794ba20 WHIRLPOOL 89b65f5ff47dbce615f37e4ae2d3d207cde1482f3e9d4cb280cca55c399784eeb272d3af490327b3c1ac348f7d6bdc1305df67a726acea7b9e2502df02848136
+DIST Mosaik-1.0-Documentation.pdf 10589 SHA256 470e2a534668a2a8744df7b00b9b8af5a6966d2df70f0ab1a4b271bdddadae9c SHA512 b2febce1e85eea89e5ff5d9f1aae351c59574314f361b66503ec473da7641adc083e52ee739c04abfe5b074fd57271f2ca20bea215982ee3ecfce073bbfd7b38 WHIRLPOOL 764a984408590417345daf624cda3dfb5df4255f18efc8f8cfbfc61885ed14be9863eef886dacfe90562469cd6af50220c0a776653a429b888eedac86270dc06
+DIST Mosaik-1.1.0021-source.tar.bz2 7055319 SHA256 c1b7215097466b8ddfdb3d1c41ea6a46ef6d7dfd28446efc7ad8957622ff9265 SHA512 73e7ab5352468c69788008ff9807ef9de89c850e3ea08445991352d8b5e7a1e9471190429585bab28b0fe56f7dfbfd2c6027bcf0d2a78b25dac654d195acb816 WHIRLPOOL 948901d2b4437b22262b03306249d1e2986af083c1f5ab8effa07b62204fe0d8fee606f6045fafee46714bce8d0f5cf62cec3b43a757eebcc6cbad3c2904bcf5
diff --git a/sci-biology/mosaik/metadata.xml b/sci-biology/mosaik/metadata.xml
new file mode 100644
index 000000000..3302123e5
--- /dev/null
+++ b/sci-biology/mosaik/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>weaver@gentoo.org</email>
+		<name>Andrey Kislyuk</name>
+	</maintainer>
+	<herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/mosaik/mosaik-1.1.0021.ebuild b/sci-biology/mosaik/mosaik-1.1.0021.ebuild
new file mode 100644
index 000000000..932c5d0d8
--- /dev/null
+++ b/sci-biology/mosaik/mosaik-1.1.0021.ebuild
@@ -0,0 +1,40 @@
+# 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"
+
+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-${PV}-source.tar.bz2
+	http://code.google.com/p/mosaik-aligner/downloads/detail?name=Mosaik%201.0%20Documentation.pdf -> Mosaik-1.0-Documentation.pdf"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="dev-lang/swig"
+RDEPEND=""
+
+S="${WORKDIR}/mosaik-aligner"
+
+src_prepare() {
+	sed -i 's/-static//' src/includes/linux.inc || die
+}
+
+src_compile() {
+	emake -C src || die
+	emake -C MosaikTools/c++ || die
+	export PERL_CORE_DIR=/usr/lib64/perl5/5.12.4/x86_64-linux/CORE
+	emake -C MosaikTools/perl PERL_CORE_DIR=/usr/lib64/perl5/5.12.4/x86_64-linux/CORE || die
+}
+
+src_install() {
+	dobin bin/* || die
+
+	insinto /usr/share/${PN}
+	doins -r MosaikTools || die
+
+	dodoc README "${DISTDIR}"/Mosaik-1.0-Documentation.pdf
+}
diff --git a/sci-biology/mosaik/mosaik-2.1.33.ebuild b/sci-biology/mosaik/mosaik-2.1.33.ebuild
new file mode 100644
index 000000000..353ecb5cb
--- /dev/null
+++ b/sci-biology/mosaik/mosaik-2.1.33.ebuild
@@ -0,0 +1,39 @@
+# 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"
+
+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-${PV}-source.tar"
+
+LICENSE="GPL-2 || ( MIT )"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/MOSAIK-${PV}-source"
+
+src_prepare() {
+	#sed -i 's/-static//' src/includes/linux.inc || die
+	echo
+}
+
+src_compile() {
+	emake || die
+#	emake -C MosaikTools/c++ || die
+#	emake -C MosaikTools/perl || die
+}
+
+src_install() {
+	dobin bin/* || die
+
+	insinto /usr/share/${PN}
+	doins -r MosaikTools || die
+
+	dodoc README Mosaik-1.0-Documentation.pdf
+}