From e8ed9acc2ba2166aeed1ebe534271fe724ba6980 Mon Sep 17 00:00:00 2001
From: Andrew Ammerlaan <andrewammerlaan@riseup.net>
Date: Sun, 10 Jan 2021 15:04:02 +0100
Subject: sci-biology/proovread: add version 2.14.1

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
---
 sci-biology/proovread/Manifest                |  1 +
 sci-biology/proovread/proovread-2.14.1.ebuild | 52 +++++++++++++++++++++++++++
 sci-biology/proovread/proovread-9999.ebuild   | 32 ++++++++---------
 3 files changed, 68 insertions(+), 17 deletions(-)
 create mode 100644 sci-biology/proovread/Manifest
 create mode 100644 sci-biology/proovread/proovread-2.14.1.ebuild

diff --git a/sci-biology/proovread/Manifest b/sci-biology/proovread/Manifest
new file mode 100644
index 000000000..e6f75545a
--- /dev/null
+++ b/sci-biology/proovread/Manifest
@@ -0,0 +1 @@
+DIST proovread-2.14.1.tar.gz 21965507 BLAKE2B 5f9f3e6ae7f5b95a2cd9092f8ab8b53b70ac48733fe5f816fddd9b2e0957c3a8fe0bad74d317f780a628127e8a6674b238f9df9fb7908e705ff92ca7e21a8a4f SHA512 836c1da96fc90c24729d8e72610e48e6ccae5a9fc2d6fa94c32738537bbc95584c9d46b37659bbcf56cdc3c1412ca93b04c7c0a54a28a6e8cebeccd278a6f764
diff --git a/sci-biology/proovread/proovread-2.14.1.ebuild b/sci-biology/proovread/proovread-2.14.1.ebuild
new file mode 100644
index 000000000..732817308
--- /dev/null
+++ b/sci-biology/proovread/proovread-2.14.1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit perl-functions
+
+DESCRIPTION="Error correct PacBio subreads using Illumina reads"
+HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread"
+if [ "$PV" == "9999" ]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread"
+	KEYWORDS=""
+else
+	SRC_URI="https://github.com/BioInf-Wuerzburg/${PN}/releases/download/${P}/${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="Artistic-2 GPL-3 blasr"
+SLOT="0"
+
+# TODO: package shrimp and update blasr
+# blasr requires new dep libblasr, which
+# I cannot get to compile successfully
+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}"
+
+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 ../../lib || die
+	perl_domodule -r -C ${PN} *
+	cd ../util/blasr-1.3.1 || die
+	dobin blasr
+}
+
+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"
+}
diff --git a/sci-biology/proovread/proovread-9999.ebuild b/sci-biology/proovread/proovread-9999.ebuild
index d8d3dc913..732817308 100644
--- a/sci-biology/proovread/proovread-9999.ebuild
+++ b/sci-biology/proovread/proovread-9999.ebuild
@@ -1,36 +1,35 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-[ "$PV" == "9999" ] && inherit git-r3
-
-inherit perl-functions toolchain-funcs
+inherit perl-functions
 
 DESCRIPTION="Error correct PacBio subreads using Illumina reads"
 HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread"
 if [ "$PV" == "9999" ]; then
+	inherit git-r3
 	EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread"
 	KEYWORDS=""
 else
-	SRC_URI=""
-	KEYWORDS="~amd64 ~x86" # issue #125
+	SRC_URI="https://github.com/BioInf-Wuerzburg/${PN}/releases/download/${P}/${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
 fi
 
-LICENSE="Artistic-2 GPL-3"
+LICENSE="Artistic-2 GPL-3 blasr"
 SLOT="0"
-IUSE=""
 
-# needs Fasta::Parser
+# TODO: package shrimp and update blasr
+# blasr requires new dep libblasr, which
+# I cannot get to compile successfully
 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="${RDEPEND}
-	>=sci-biology/shrimp-2
-	sci-biology/blasr"
+	>=sci-biology/samtools-1.1
+"
+DEPEND="${RDEPEND}"
 
 src_install(){
 	cd bin || die
@@ -43,9 +42,8 @@ src_install(){
 	dobin bin/*
 	cd ../../lib || die
 	perl_domodule -r -C ${PN} *
-	# cd ../util/blasr-1.3.1 || die
-	# dobin blasr
-	# dodoc LICENSE.txt
+	cd ../util/blasr-1.3.1 || die
+	dobin blasr
 }
 
 pkg_postinst(){
-- 
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