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author | Andrew Ammerlaan <andrewammerlaan@gentoo.org> | 2023-05-02 14:10:37 +0200 |
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committer | Andrew Ammerlaan <andrewammerlaan@gentoo.org> | 2023-05-02 14:15:16 +0200 |
commit | f60510efb81dbeeb9474bb50071a0b0ed59a5964 (patch) | |
tree | 6d73de2ca0b8e832c83f2191b0d472df53b847ac /sci-biology | |
parent | sci-biology/nwalign3: treeclean (diff) | |
download | sci-f60510efb81dbeeb9474bb50071a0b0ed59a5964.tar.gz sci-f60510efb81dbeeb9474bb50071a0b0ed59a5964.tar.bz2 sci-f60510efb81dbeeb9474bb50071a0b0ed59a5964.zip |
sci-biology/proovread: treeclean
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/proovread/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/proovread/metadata.xml | 12 | ||||
-rw-r--r-- | sci-biology/proovread/proovread-2.14.1.ebuild | 51 | ||||
-rw-r--r-- | sci-biology/proovread/proovread-9999.ebuild | 51 |
4 files changed, 0 insertions, 115 deletions
diff --git a/sci-biology/proovread/Manifest b/sci-biology/proovread/Manifest deleted file mode 100644 index e6f75545a..000000000 --- a/sci-biology/proovread/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST proovread-2.14.1.tar.gz 21965507 BLAKE2B 5f9f3e6ae7f5b95a2cd9092f8ab8b53b70ac48733fe5f816fddd9b2e0957c3a8fe0bad74d317f780a628127e8a6674b238f9df9fb7908e705ff92ca7e21a8a4f SHA512 836c1da96fc90c24729d8e72610e48e6ccae5a9fc2d6fa94c32738537bbc95584c9d46b37659bbcf56cdc3c1412ca93b04c7c0a54a28a6e8cebeccd278a6f764 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" -} |