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

[Martin Mokrejs]

commit:     a4e405144f304e63344c5228e1407fdff6bfab75
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr  1 21:49:26 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr  1 21:49:26 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a4e40514

sci-biology/proovread: new package

Will need more work from upstream to make it into Gentoo.

Package-Manager: Portage-2.3.27, Repoman-2.3.9

 sci-biology/proovread/metadata.xml          | 12 +++++++
 sci-biology/proovread/proovread-9999.ebuild | 50 +++++++++++++++++++++++++++++
 2 files changed, 62 insertions(+)

diff --git a/sci-biology/proovread/metadata.xml b/sci-biology/proovread/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/proovread/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/proovread/proovread-9999.ebuild b/sci-biology/proovread/proovread-9999.ebuild
new file mode 100644
index 000000000..11a78d2f8
--- /dev/null
+++ b/sci-biology/proovread/proovread-9999.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+[ "$PV" == "9999" ] && inherit git-r3
+
+DESCRIPTION="Error correct PacBio subreads using Illumina reads"
+HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread"
+if [ "$PV" == "9999" ]; then
+	EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread"
+	KEYWORDS=""
+else
+	SRC_URI=""
+	KEYWORDS="~amd64 ~x86" # issue #125
+fi
+
+LICENSE="proovread" # Artistic-2.0 or GPL-3 but not for commercial
+SLOT="0"
+IUSE=""
+
+# needs Fasta::Parser
+RDEPEND="
+	>=dev-lang/perl-5.10
+	dev-perl/Log-Log4perl
+	dev-perl/File-Which
+	>=sci-biology/ncbi-tools++-2.2.24
+	>=sci-biology/samtools-1.1"
+DEPEND="${RDEPEND}
+	>=sci-biology/shrimp-2
+	sci-biology/blasr"
+
+src_install(){
+	cd bin || die
+	dobin ChimeraToSeqFilter.pl dazz2sam ccseq bam2cns test_cfg.pl siamaera samfilter sam2cns proovread-flex proovread
+	cd ../util/bwa || die
+	dobin bwa-proovread # xa2multi.pl qualfa2fq.pl libbwa.a bwa.1
+	cd ../../util/SeqFilter || die
+	dobin bin/SeqFilter
+	cd ../../util/SeqChunker || die
+	dobin bin/*
+	# cd ../util/blasr-1.3.1 || die
+	# dobin blasr
+	# dodoc LICENSE.txt
+}
+
+pkg_postinst(){
+	einfo "Proovread uses its own, modified version of bwa as bwa-proovread"
+	einfo "with linked in libbwa.a. It also bundles shrimp2 and blasr"
+}