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>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</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" -}
