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Sun, 10 Jan 2021 14:04:12 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 6EBE83A6 for ; Sun, 10 Jan 2021 14:04:11 +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: <1610287442.e8ed9acc2ba2166aeed1ebe534271fe724ba6980.andrewammerlaan@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/proovread/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/proovread/proovread-2.14.1.ebuild sci-biology/proovread/proovread-9999.ebuild X-VCS-Directories: sci-biology/proovread/ X-VCS-Committer: andrewammerlaan X-VCS-Committer-Name: Andrew Ammerlaan X-VCS-Revision: e8ed9acc2ba2166aeed1ebe534271fe724ba6980 X-VCS-Branch: master Date: Sun, 10 Jan 2021 14:04:11 +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: 0926086d-e907-4a20-b6db-6dadb04bfb99 X-Archives-Hash: 96d39d73ecfa8e613ff25b61a3c3727a commit: e8ed9acc2ba2166aeed1ebe534271fe724ba6980 Author: Andrew Ammerlaan riseup net> AuthorDate: Sun Jan 10 14:04:02 2021 +0000 Commit: Andrew Ammerlaan riseup net> CommitDate: Sun Jan 10 14:04:02 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e8ed9acc sci-biology/proovread: add version 2.14.1 Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> ...oovread-9999.ebuild => proovread-2.14.1.ebuild} | 32 ++++++++++------------ sci-biology/proovread/proovread-9999.ebuild | 32 ++++++++++------------ 2 files changed, 30 insertions(+), 34 deletions(-) diff --git a/sci-biology/proovread/proovread-9999.ebuild b/sci-biology/proovread/proovread-2.14.1.ebuild similarity index 68% copy from sci-biology/proovread/proovread-9999.ebuild copy to sci-biology/proovread/proovread-2.14.1.ebuild index d8d3dc913..732817308 100644 --- a/sci-biology/proovread/proovread-9999.ebuild +++ b/sci-biology/proovread/proovread-2.14.1.ebuild @@ -1,36 +1,35 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -[ "$PV" == "9999" ] && inherit git-r3 - -inherit perl-functions toolchain-funcs +inherit perl-functions DESCRIPTION="Error correct PacBio subreads using Illumina reads" HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread" if [ "$PV" == "9999" ]; then + inherit git-r3 EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread" KEYWORDS="" else - SRC_URI="" - KEYWORDS="~amd64 ~x86" # issue #125 + SRC_URI="https://github.com/BioInf-Wuerzburg/${PN}/releases/download/${P}/${P}.tar.gz" + KEYWORDS="~amd64 ~x86" fi -LICENSE="Artistic-2 GPL-3" +LICENSE="Artistic-2 GPL-3 blasr" SLOT="0" -IUSE="" -# needs Fasta::Parser +# TODO: package shrimp and update blasr +# blasr requires new dep libblasr, which +# I cannot get to compile successfully RDEPEND=" >=dev-lang/perl-5.10 dev-perl/Log-Log4perl dev-perl/File-Which >=sci-biology/ncbi-tools++-2.2.24 - >=sci-biology/samtools-1.1" -DEPEND="${RDEPEND} - >=sci-biology/shrimp-2 - sci-biology/blasr" + >=sci-biology/samtools-1.1 +" +DEPEND="${RDEPEND}" src_install(){ cd bin || die @@ -43,9 +42,8 @@ src_install(){ dobin bin/* cd ../../lib || die perl_domodule -r -C ${PN} * - # cd ../util/blasr-1.3.1 || die - # dobin blasr - # dodoc LICENSE.txt + cd ../util/blasr-1.3.1 || die + dobin blasr } pkg_postinst(){ diff --git a/sci-biology/proovread/proovread-9999.ebuild b/sci-biology/proovread/proovread-9999.ebuild index d8d3dc913..732817308 100644 --- a/sci-biology/proovread/proovread-9999.ebuild +++ b/sci-biology/proovread/proovread-9999.ebuild @@ -1,36 +1,35 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -[ "$PV" == "9999" ] && inherit git-r3 - -inherit perl-functions toolchain-funcs +inherit perl-functions DESCRIPTION="Error correct PacBio subreads using Illumina reads" HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread" if [ "$PV" == "9999" ]; then + inherit git-r3 EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread" KEYWORDS="" else - SRC_URI="" - KEYWORDS="~amd64 ~x86" # issue #125 + SRC_URI="https://github.com/BioInf-Wuerzburg/${PN}/releases/download/${P}/${P}.tar.gz" + KEYWORDS="~amd64 ~x86" fi -LICENSE="Artistic-2 GPL-3" +LICENSE="Artistic-2 GPL-3 blasr" SLOT="0" -IUSE="" -# needs Fasta::Parser +# 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="${RDEPEND} - >=sci-biology/shrimp-2 - sci-biology/blasr" + >=sci-biology/samtools-1.1 +" +DEPEND="${RDEPEND}" src_install(){ cd bin || die @@ -43,9 +42,8 @@ src_install(){ dobin bin/* cd ../../lib || die perl_domodule -r -C ${PN} * - # cd ../util/blasr-1.3.1 || die - # dobin blasr - # dodoc LICENSE.txt + cd ../util/blasr-1.3.1 || die + dobin blasr } pkg_postinst(){