commit: 4faeb566066c8a06f19584614067ed826407c17f Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Tue Jan 25 13:33:55 2022 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Tue Jan 25 13:33:55 2022 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4faeb566
sci-biology/cortex_var: drop dead package last update 2013 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild | 51 ----------------------- sci-biology/cortex_var/metadata.xml | 15 ------- 2 files changed, 66 deletions(-) diff --git a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild deleted file mode 100644 index d368f5db3..000000000 --- a/sci-biology/cortex_var/cortex_var-1.0.5.21.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="Genotype variant discovery without reference sequence" -HOMEPAGE="http://cortexassembler.sourceforge.net/index_cortex_var.html"; # no https -SRC_URI=" - https://sourceforge.net/projects/cortexassembler/files/cortex_var/latest/CORTEX_release_v${PV}.tgz - http://cortexassembler.sourceforge.net/cortex_var_user_manual.pdf"; - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" - -# http://www.well.ox.ac.uk/project-stampy - -DEPEND=" - sci-biology/vcftools - sci-libs/gsl - sci-libs/htslib:0= - dev-lang/perl" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/CORTEX_release_v${PV}" - -src_prepare(){ - default - sed -i -e "s/ -O3 / ${CFLAGS} /" Makefile || die - sed -i -e "s#libs/gsl-1.15#${EPREFIX}/usr/include/gsl#" Makefile || die -} - -src_compile(){ - rm -rf libs/htslib libs/gsl-1.15 || die - emake -C libs/string_buffer - emake STRING_BUF_PATH="${S}/libs/string_buffer" HTS_PATH="/usr/include/" -C libs/seq_file - emake NUM_COLS=1 MAXK=31 cortex_var -} - -src_install(){ - bash install.sh || die - perl_set_version - perl_domodule scripts/analyse_variants/bioinf-perl/lib/* scripts/calling/* - echo \ - "PATH=${EPREFIX}/usr/share/${PN}/scripts/analyse_variants/needleman_wunsch" \ - > "${T}/99${PN}" || die - doenvd "${T}/99${PN}" - dodoc "${DISTDIR}"/cortex_var_user_manual.pdf -} diff --git a/sci-biology/cortex_var/metadata.xml b/sci-biology/cortex_var/metadata.xml deleted file mode 100644 index a2867d6fd..000000000 --- a/sci-biology/cortex_var/metadata.xml +++ /dev/null @@ -1,15 +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> - <upstream> - <remote-id type="sourceforge">cortexassembler</remote-id> - </upstream> -</pkgmetadata>
