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From: "Andrew Ammerlaan" <andrewammerlaan@riseup.net>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/proovread/
Date: Sun, 10 Jan 2021 14:04:11 +0000 (UTC)	[thread overview]
Message-ID: <1610287442.e8ed9acc2ba2166aeed1ebe534271fe724ba6980.andrewammerlaan@gentoo> (raw)

commit:     e8ed9acc2ba2166aeed1ebe534271fe724ba6980
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 10 14:04:02 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> 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 <andrewammerlaan <AT> 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(){


             reply	other threads:[~2021-01-10 14:04 UTC|newest]

Thread overview: 6+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2021-01-10 14:04 Andrew Ammerlaan [this message]
  -- strict thread matches above, loose matches on Subject: below --
2023-05-02 12:15 [gentoo-commits] proj/sci:master commit in: sci-biology/proovread/ Andrew Ammerlaan
2021-03-20 11:03 Andrew Ammerlaan
2018-04-02 20:26 Justin Lecher
2018-04-01 22:17 Martin Mokrejs
2018-04-01 21:49 Martin Mokrejs

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