[gentoo-commits] proj/sci:master commit in: sci-biology/nextclip/

[gentoo-commits] proj/sci:master commit in: sci-biology/nextclip/

[Martin Mokrejs]

commit:     c6e01bee05d3b6a88b906f5e6a4c93892ef43bcd
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 17 22:47:07 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 17 22:47:07 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c6e01bee

sci-biology/nextclip: new package

It does not do a proper alignment so no surprise it does
not work well (see github issues from several users).

Also, the nextclip binary triggers a QA issue (opened as
github issue #22) due to writable and executable sections.

Package-Manager: Portage-2.3.19, Repoman-2.3.6

 sci-biology/nextclip/metadata.xml          | 12 +++++++++
 sci-biology/nextclip/nextclip-1.3.1.ebuild | 41 ++++++++++++++++++++++++++++++
 2 files changed, 53 insertions(+)

diff --git a/sci-biology/nextclip/metadata.xml b/sci-biology/nextclip/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/nextclip/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+</pkgmetadata>

diff --git a/sci-biology/nextclip/nextclip-1.3.1.ebuild b/sci-biology/nextclip/nextclip-1.3.1.ebuild
new file mode 100644
index 000000000..3efbb61c6
--- /dev/null
+++ b/sci-biology/nextclip/nextclip-1.3.1.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit flag-o-matic toolchain-funcs
+
+DESCRIPTION="Split Illumina Nextera long mate-pairs"
+HOMEPAGE="https://github.com/richardmleggett/nextclip
+	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3928519"
+SRC_URI="https://github.com/richardmleggett/nextclip/archive/NextClip_v1.3.1.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	>=dev-lang/R-2.12.2
+	>=sci-biology/bwa-0.6.1
+	dev-texlive/texlive-latex"
+
+S="${WORKDIR}"/"${PN}"-NextClip_v"${PV}"
+
+src_prepare(){
+	default
+	sed -e 's/$(ARCH)//;s/$(MACFLAG)//' -i Makefile || die
+	sed -e "s/CC=gcc/$(tc-getCC)/;s/-Wall -O3/${CFLAGS}/" -i Makefile || die
+}
+
+src_compile(){
+	emake all
+}
+
+src_install(){
+	dobin bin/nextclip
+	insinto /usr/share/"${PN}"
+	doins scripts/*
+	dodoc nextclipmanual.pdf README.md
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/nextclip/

[Andrew Ammerlaan]

commit:     62e674ce4653c925b0413789bc612484063870b1
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 12:51:39 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 12:51:39 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=62e674ce

sci-biology/nextclip: EAPI bump

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/nextclip/nextclip-1.3.1.ebuild | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/sci-biology/nextclip/nextclip-1.3.1.ebuild b/sci-biology/nextclip/nextclip-1.3.1.ebuild
index 3efbb61c6..74b1f78b4 100644
--- a/sci-biology/nextclip/nextclip-1.3.1.ebuild
+++ b/sci-biology/nextclip/nextclip-1.3.1.ebuild
@@ -1,7 +1,7 @@
-# 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
 
 inherit flag-o-matic toolchain-funcs
 
@@ -13,7 +13,6 @@ SRC_URI="https://github.com/richardmleggett/nextclip/archive/NextClip_v1.3.1.tar
 LICENSE="GPL-3+"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}