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

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

[Martin Mokrejs]

commit:     ffae3c61b35c5d4a47c5a3fd48b912775a19818b
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Feb 19 17:56:33 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Feb 19 17:56:33 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ffae3c61

sci-biology/lumpy-sv: use CDEPEND for cmake

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/lumpy-sv/lumpy-sv-9999.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild b/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild
index 7c2fea620..c6154555c 100644
--- a/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild
+++ b/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild
@@ -16,7 +16,8 @@ KEYWORDS=""
 IUSE=""
 
 # contains bundled htslib
-DEPEND="dev-util/cmake"
+CDEPEND="dev-util/cmake"
+DEPEND=""
 RDEPEND="${DEPEND}"
 
 src_install(){

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

[Martin Mokrejs]

commit:     d3b79fddef20a7acf8d8cc6a49ca46830424065c
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Feb 19 17:53:40 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Feb 19 17:53:40 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d3b79fdd

sci-biology/lumpy-sv: new package, inventing installation layout

https://github.com/arq5x/lumpy-sv/issues/168

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/lumpy-sv/lumpy-sv-9999.ebuild | 39 +++++++++++++++++++++++++++++++
 sci-biology/lumpy-sv/metadata.xml         | 12 ++++++++++
 2 files changed, 51 insertions(+)

diff --git a/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild b/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild
new file mode 100644
index 000000000..7c2fea620
--- /dev/null
+++ b/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit git-r3
+
+DESCRIPTION="Probabilistic framework for structural variant discovery"
+HOMEPAGE="https://github.com/arq5x/lumpy-sv"
+EGIT_REPO_URI="https://github.com/arq5x/lumpy-sv.git"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# contains bundled htslib
+DEPEND="dev-util/cmake"
+RDEPEND="${DEPEND}"
+
+src_install(){
+	cat > "${T}"/99lumpy-sv <<- EOF
+	LUMPY_HOME=${EPREFIX}/usr/share/lumpy-sv
+	PAIREND_DISTRO=${EPREFIX}/usr/share/lumpy-sv/scripts/pairend_distro.py
+	BAMGROUPREADS=${EPREFIX}/usr/share/lumpy-sv/scripts/bamkit/bamgroupreads.py
+	BAMFILTERRG=${EPREFIX}/usr/share/lumpy-sv/scripts/bamkit/bamfilterrg.py
+	BAMLIBS=${EPREFIX}/usr/share/lumpy-sv/scripts/bamkit/bamlibs.py
+	EOF
+	doenvd "${T}"/99lumpy-sv
+	rm -f bin/lumpyexpress.config
+	dobin bin/*
+	insinto /usr/share/lumpy-sv/scripts
+	for f in lumpy lumpy_filter lumpyexpress; do
+		rm bin/"$f" || die
+	done
+	doins scripts/*
+	dodoc README.md
+}

diff --git a/sci-biology/lumpy-sv/metadata.xml b/sci-biology/lumpy-sv/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/lumpy-sv/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>

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

[Martin Mokrejs]

commit:     48c6d4a6e09db35e06cbcd8cafd5d3471aaf4526
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Feb 19 18:41:59 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Feb 19 18:41:59 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=48c6d4a6

sci-biology/lumpy-sv: more tweaks to the install procedure

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/lumpy-sv/lumpy-sv-9999.ebuild | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild b/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild
index c6154555c..c7c37c2a0 100644
--- a/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild
+++ b/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild
@@ -32,9 +32,13 @@ src_install(){
 	rm -f bin/lumpyexpress.config
 	dobin bin/*
 	insinto /usr/share/lumpy-sv/scripts
-	for f in lumpy lumpy_filter lumpyexpress; do
-		rm bin/"$f" || die
+	for f in lumpyexpress lumpyexpress.config; do
+		rm scripts/"$f" || die
 	done
 	doins scripts/*
 	dodoc README.md
+	insinto /usr/share/lumpy-sv/scripts/bamkit
+	cd scripts/bamkit || die
+	doins *.py sectosupp
+	newdoc README.md README_bamkit.md
 }

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

[Andrew Ammerlaan]

commit:     b0ebcbef4027efb671812d1c0d9be250935b3c2b
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 11:55:27 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 11:55:27 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b0ebcbef

sci-biology/lumpy-sv: EAPI bump, fix build

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

 ...{lumpy-sv-9999.ebuild => lumpy-sv-0.3.1.ebuild} | 28 ++++++++++------------
 1 file changed, 13 insertions(+), 15 deletions(-)

diff --git a/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild b/sci-biology/lumpy-sv/lumpy-sv-0.3.1.ebuild
similarity index 64%
rename from sci-biology/lumpy-sv/lumpy-sv-9999.ebuild
rename to sci-biology/lumpy-sv/lumpy-sv-0.3.1.ebuild
index 4c565c0c0..f98892b95 100644
--- a/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild
+++ b/sci-biology/lumpy-sv/lumpy-sv-0.3.1.ebuild
@@ -1,24 +1,26 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
-
-inherit git-r3
+EAPI=7
 
 DESCRIPTION="Probabilistic framework for structural variant discovery"
 HOMEPAGE="https://github.com/arq5x/lumpy-sv"
-EGIT_REPO_URI="https://github.com/arq5x/lumpy-sv.git"
+SRC_URI="https://github.com/arq5x/lumpy-sv/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
 
-# contains bundled htslib
-CDEPEND="dev-util/cmake"
-DEPEND=""
+DEPEND="sci-libs/htslib"
 RDEPEND="${DEPEND}"
 
+src_prepare() {
+	default
+	# do not build bundled htslib, link to system lib
+	sed -i -e 's/lumpy_filter: htslib/lumpy_filter:/g' Makefile || die
+	sed -i -e 's/-I..\/..\/lib\/htslib\///' -e 's/..\/..\/lib\/htslib\/libhts.a/-lhts/g' src/filter/Makefile || die
+}
+
 src_install(){
 	cat > "${T}"/99lumpy-sv <<- EOF
 	LUMPY_HOME=${EPREFIX}/usr/share/lumpy-sv
@@ -35,9 +37,5 @@ src_install(){
 		rm scripts/"$f" || die
 	done
 	doins scripts/*
-	dodoc README.md
-	insinto /usr/share/lumpy-sv/scripts/bamkit
-	cd scripts/bamkit || die
-	doins *.py sectosupp
-	newdoc README.md README_bamkit.md
+	einstalldocs
 }