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

["Andrew Ammerlaan" <andrewammerlaan@gentoo.org>]

commit:     f60510efb81dbeeb9474bb50071a0b0ed59a5964
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May  2 12:10:37 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May  2 12:15:16 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f60510ef

sci-biology/proovread: treeclean

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/proovread/metadata.xml            | 12 -------
 sci-biology/proovread/proovread-2.14.1.ebuild | 51 ---------------------------
 sci-biology/proovread/proovread-9999.ebuild   | 51 ---------------------------
 3 files changed, 114 deletions(-)

diff --git a/sci-biology/proovread/metadata.xml b/sci-biology/proovread/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/proovread/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>

diff --git a/sci-biology/proovread/proovread-2.14.1.ebuild b/sci-biology/proovread/proovread-2.14.1.ebuild
deleted file mode 100644
index be1d610b0..000000000
--- a/sci-biology/proovread/proovread-2.14.1.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# 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 [ "$PV" == "9999" ]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread"
-else
-	SRC_URI="https://github.com/BioInf-Wuerzburg/${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
deleted file mode 100644
index be1d610b0..000000000
--- a/sci-biology/proovread/proovread-9999.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# 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 [ "$PV" == "9999" ]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread"
-else
-	SRC_URI="https://github.com/BioInf-Wuerzburg/${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"
-}