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(){
next 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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