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

[Martin Mokrejs]

commit:     cef6f206bd05567e80c11b9f9b1e850f74e06731
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 28 19:23:07 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 28 20:05:19 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cef6f206

sci-biology/nanopolish: new package

Package-Manager: Portage-2.3.6, Repoman-2.3.3

 sci-biology/nanopolish/metadata.xml           | 12 +++++++
 sci-biology/nanopolish/nanopolish-9999.ebuild | 48 +++++++++++++++++++++++++++
 2 files changed, 60 insertions(+)

diff --git a/sci-biology/nanopolish/metadata.xml b/sci-biology/nanopolish/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/nanopolish/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/nanopolish/nanopolish-9999.ebuild b/sci-biology/nanopolish/nanopolish-9999.ebuild
new file mode 100644
index 000000000..92c5f41d3
--- /dev/null
+++ b/sci-biology/nanopolish/nanopolish-9999.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit git-r3
+
+DESCRIPTION="Signal-level analysis of Oxford Nanopore sequencing data"
+HOMEPAGE="https://github.com/jts/nanopolish"
+EGIT_REPO_URI="https://github.com/jts/nanopolish.git"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# HDF5 is not thread safe by default and nanopolish currently requires a threadsafe HDF5.
+# This is one reason we download the compile it ourself (the main reason is to make it
+# easier for most users). The other options cxx, fortran, mpi are not needed by nanopolish
+# (we use the C bindings in nanopolish only).
+# The bundled version of htslib in is 1.2.1 as of now although 1.5.1 already exists
+DEPEND=">=sci-libs/hdf5-1.8.14[threads]
+	>=dev-cpp/eigen-3.2.5
+	sci-libs/htslib:0
+	sci-libs/fast5"
+RDEPEND="${DEPEND}
+	sci-biology/biopython"
+
+src_prepare(){
+	default
+	rm -rf hdf5* eigen htslib || die # TODO; zap also fast5
+}
+
+src_compile(){
+	# >=gcc-4.8 but <gcc-7 is needed
+	# https://github.com/jts/nanopolish/issues/145
+	emake HDF5="noinstall" EIGEN="nofetch" HTS_LIB=-lhts HTS_INCLUDE=-I/usr/include/htslib EIGEN_INCLUDE=-I/usr/include/eigen3 # TODO: FAST5_INCLUDE=-I/usr/include/fast5
+}
+
+src_install(){
+	rm -rf lib || die # zap libs eventually compiled from the bundled copies
+	dobin nanopolish
+	# add scripts/ subdirectory to PATH
+}
+
+src_test(){
+	nanopolish_test || die
+}