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Tue, 23 Mar 2021 09:27:32 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 0FE6C46C for ; Tue, 23 Mar 2021 09:27:31 +0000 (UTC) From: "Andrew Ammerlaan" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Andrew Ammerlaan" Message-ID: <1616491639.864b2c5e4f51a2894e0a87dbf777c2c056a2cfa1.andrewammerlaan@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/kraken/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/kraken/kraken-1.1.1-r1.ebuild sci-biology/kraken/kraken-1.1.1-r2.ebuild sci-biology/kraken/kraken-2.1.1.ebuild X-VCS-Directories: sci-biology/kraken/ X-VCS-Committer: andrewammerlaan X-VCS-Committer-Name: Andrew Ammerlaan X-VCS-Revision: 864b2c5e4f51a2894e0a87dbf777c2c056a2cfa1 X-VCS-Branch: master Date: Tue, 23 Mar 2021 09:27:31 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 90c81839-7535-42ab-b4df-b17bd325cf49 X-Archives-Hash: e5770dba465b017025a901b80a6cd984 commit: 864b2c5e4f51a2894e0a87dbf777c2c056a2cfa1 Author: Andrew Ammerlaan riseup net> AuthorDate: Tue Mar 23 09:27:19 2021 +0000 Commit: Andrew Ammerlaan riseup net> CommitDate: Tue Mar 23 09:27:19 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=864b2c5e sci-biology/kraken: add kraken version 2 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> ...raken-1.1.1-r1.ebuild => kraken-1.1.1-r2.ebuild} | 9 +++------ .../{kraken-1.1.1-r1.ebuild => kraken-2.1.1.ebuild} | 21 +++++++++++---------- 2 files changed, 14 insertions(+), 16 deletions(-) diff --git a/sci-biology/kraken/kraken-1.1.1-r1.ebuild b/sci-biology/kraken/kraken-1.1.1-r2.ebuild similarity index 85% copy from sci-biology/kraken/kraken-1.1.1-r1.ebuild copy to sci-biology/kraken/kraken-1.1.1-r2.ebuild index fb97ab47e..3dd599b83 100644 --- a/sci-biology/kraken/kraken-1.1.1-r1.ebuild +++ b/sci-biology/kraken/kraken-1.1.1-r2.ebuild @@ -7,11 +7,10 @@ inherit perl-functions DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups" HOMEPAGE="https://ccb.jhu.edu/software/kraken" -SRC_URI="https://github.com/DerrickWood/kraken/archive/v1.0.tar.gz -> ${P}.tar.gz - https://ccb.jhu.edu/software/kraken/MANUAL.html -> ${P}_MANUAL.html" +SRC_URI="https://github.com/DerrickWood/kraken/archive/v${PV}.tar.gz -> ${P}.tar.gz" LICENSE="GPL-3" -SLOT="0" +SLOT="1" KEYWORDS="~amd64" DEPEND="" @@ -21,8 +20,6 @@ RDEPEND="${DEPEND} sci-biology/jellyfish:1 " -S="${WORKDIR}/${PN}-1.0" - src_prepare(){ default sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i src/Makefile || die @@ -34,7 +31,7 @@ src_compile(){ } src_install(){ - dodoc "${DISTDIR}/${P}_MANUAL.html" + dodoc -r docs perl_set_version perl_domodule destdir/*.pm dosym ../../"${VENDOR_LIB//${EPREFIX/}}/krakenlib.pm" /usr/bin/krakenlib.pm diff --git a/sci-biology/kraken/kraken-1.1.1-r1.ebuild b/sci-biology/kraken/kraken-2.1.1.ebuild similarity index 74% rename from sci-biology/kraken/kraken-1.1.1-r1.ebuild rename to sci-biology/kraken/kraken-2.1.1.ebuild index fb97ab47e..0991f94fa 100644 --- a/sci-biology/kraken/kraken-1.1.1-r1.ebuild +++ b/sci-biology/kraken/kraken-2.1.1.ebuild @@ -6,35 +6,36 @@ EAPI=7 inherit perl-functions DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups" -HOMEPAGE="https://ccb.jhu.edu/software/kraken" -SRC_URI="https://github.com/DerrickWood/kraken/archive/v1.0.tar.gz -> ${P}.tar.gz - https://ccb.jhu.edu/software/kraken/MANUAL.html -> ${P}_MANUAL.html" +HOMEPAGE="https://ccb.jhu.edu/software/kraken2/" +SRC_URI="https://github.com/DerrickWood/kraken2/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" -LICENSE="GPL-3" -SLOT="0" +LICENSE="MIT" +SLOT="2" KEYWORDS="~amd64" +# TODO: somehow avoid the file conflict with kraken-1 DEPEND="" RDEPEND="${DEPEND} + sci-biology/ncbi-tools++ dev-lang/perl net-misc/wget - sci-biology/jellyfish:1 + !sci-biology/kraken:1 " -S="${WORKDIR}/${PN}-1.0" +S="${WORKDIR}/${PN}2-${PV}" src_prepare(){ default sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i src/Makefile || die - echo "exit 0" >> install_kraken.sh || die + echo "exit 0" >> install_kraken2.sh || die } src_compile(){ - ./install_kraken.sh destdir || die + ./install_kraken2.sh destdir || die } src_install(){ - dodoc "${DISTDIR}/${P}_MANUAL.html" + dodoc -r docs perl_set_version perl_domodule destdir/*.pm dosym ../../"${VENDOR_LIB//${EPREFIX/}}/krakenlib.pm" /usr/bin/krakenlib.pm