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

[Martin Mokrejs]

commit:     a9b6ba591d4477409c689f8612051d5be85364fa
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jan 17 12:23:55 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jan 17 12:23:55 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a9b6ba59

sci-biology/pbbam: new package needed by sci-biology/blasr

Builds and install for me, make cmake/clang deps could be
improved.

https://github.com/PacificBiosciences/pbbam/issues/25

Package-Manager: Portage-2.3.55, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 sci-biology/pbbam/metadata.xml      | 12 +++++++++
 sci-biology/pbbam/pbbam-9999.ebuild | 49 +++++++++++++++++++++++++++++++++++++
 2 files changed, 61 insertions(+)

diff --git a/sci-biology/pbbam/metadata.xml b/sci-biology/pbbam/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/pbbam/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@×××××××××××××××.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@g.o</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+</pkgmetadata>

diff --git a/sci-biology/pbbam/pbbam-9999.ebuild b/sci-biology/pbbam/pbbam-9999.ebuild
new file mode 100644
index 000000000..5593b4072
--- /dev/null
+++ b/sci-biology/pbbam/pbbam-9999.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit git-r3 multilib
+
+DESCRIPTION="PacBio modified BAM file format"
+HOMEPAGE="https://pbbam.readthedocs.io/en/latest/index.html"
+EGIT_REPO_URI="https://github.com/PacificBiosciences/pbbam.git"
+
+LICENSE="blasr"
+SLOT="0"
+IUSE="hdf5 doc"
+KEYWORDS=""
+# https://github.com/PacificBiosciences/pbbam/issues/25
+
+CDEPEND="
+	dev-util/meson
+	dev-util/ninja
+	dev-util/pkgconfig
+	>=dev-cpp/gtest-1.8.1
+	>=dev-lang/swig-3.0.5
+	doc? ( app-doc/doxygen )"
+DEPEND="
+	>=sci-libs/htslib-1.3.1:=
+	>=dev-libs/boost-1.55:=[threads]
+	hdf5? ( >=sci-libs/hdf5-1.8.12[cxx] )" # needs H5Cpp.h
+RDEPEND=""
+
+#S="${WORKDIR}/${PN}"
+
+src_compile(){
+	mkdir -p build || die
+	cd build || die
+	meson --prefix "${ED}/usr" || die
+	ninja || die
+	use doc && ( ninja doc )
+}
+
+src_install() {
+	cd build || die
+	ninja install || die
+	#dobin bin/*
+	#insinto /usr/include
+	#doins include/*
+	#insinto /usr/$(get_libdir)/${P}
+	#doins lib/*
+}