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

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

[Martin Mokrejs]

commit:     57aaac2250383519cf73bc1d9d3fc20a1a3c8240
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Feb 24 13:57:44 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Feb 24 13:57:44 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=57aaac22

sci-biology/verifyBamID: new package, would benefit unbundling of libStatGen

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/verifyBamID/metadata.xml             | 12 ++++++++
 sci-biology/verifyBamID/verifyBamID-1.1.3.ebuild | 39 ++++++++++++++++++++++++
 2 files changed, 51 insertions(+)

diff --git a/sci-biology/verifyBamID/metadata.xml b/sci-biology/verifyBamID/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/verifyBamID/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/verifyBamID/verifyBamID-1.1.3.ebuild b/sci-biology/verifyBamID/verifyBamID-1.1.3.ebuild
new file mode 100644
index 000000000..dfea2c485
--- /dev/null
+++ b/sci-biology/verifyBamID/verifyBamID-1.1.3.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 toolchain-funcs
+
+DESCRIPTION="Verify sample identity/mix and genotype concordance"
+HOMEPAGE="http://genome.sph.umich.edu/wiki/VerifyBamID"
+SRC_URI="https://github.com/statgen/verifyBamID/archive/v1.1.3.tar.gz -> ${P}.tar.gz
+	https://github.com/statgen/libStatGen/archive/v1.0.13.tar.gz -> libStatGen-1.0.13.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+# DEPEND="sci-libs/libStatGen" # TODO: currently it uses its own bundled copy
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	default
+	# unpack ./libStatGen-1.0.13/ contents
+	gzip -dc "${DISTDIR}"/libStatGen-1.0.13.tar.gz | tar xf - || die
+	ln -s libStatGen-1.0.13 libStatGen || die
+	cd "${WORKDIR}" || die
+	ln -s libStatGen-1.0.13 libStatGen || die
+}
+
+src_compile(){
+	# LIB_PATH_GENERAL="${EPREFIX}"/usr/"$(get_libdir)" emake
+	LIB_PATH_GENERAL="../libStatGen-1.0.13" emake
+}
+
+src_install(){
+	dobin bin/verifyBamID
+}

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

[Andrew Ammerlaan]

commit:     85ea7cd26bde63d5c0b0157bb2f10214006aec89
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 16:09:45 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 16:09:45 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=85ea7cd2

sci-biology/verifyBamID: EAPI bump, bump libStatGen version

fixes build failure

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

 sci-biology/verifyBamID/verifyBamID-1.1.3.ebuild | 21 ++++++++++-----------
 1 file changed, 10 insertions(+), 11 deletions(-)

diff --git a/sci-biology/verifyBamID/verifyBamID-1.1.3.ebuild b/sci-biology/verifyBamID/verifyBamID-1.1.3.ebuild
index 040816a76..2a6759c54 100644
--- a/sci-biology/verifyBamID/verifyBamID-1.1.3.ebuild
+++ b/sci-biology/verifyBamID/verifyBamID-1.1.3.ebuild
@@ -1,19 +1,18 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit toolchain-funcs
 
 DESCRIPTION="Verify sample identity/mix and genotype concordance"
 HOMEPAGE="http://genome.sph.umich.edu/wiki/VerifyBamID"
-SRC_URI="https://github.com/statgen/verifyBamID/archive/v1.1.3.tar.gz -> ${P}.tar.gz
-	https://github.com/statgen/libStatGen/archive/v1.0.13.tar.gz -> libStatGen-1.0.13.tar.gz"
+SRC_URI="https://github.com/statgen/verifyBamID/archive/v${PV}.tar.gz -> ${P}.tar.gz
+	https://github.com/statgen/libStatGen/archive/v1.0.15.tar.gz -> libStatGen-1.0.15.tar.gz"
 
 LICENSE="GPL-3+"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 # DEPEND="sci-libs/libStatGen" # TODO: currently it uses its own bundled copy
 DEPEND=""
@@ -21,18 +20,18 @@ RDEPEND="${DEPEND}"
 
 src_prepare(){
 	# unpack ./libStatGen-1.0.13/ contents
-	gzip -dc "${DISTDIR}"/libStatGen-1.0.13.tar.gz | tar xf - || die
-	ln -s libStatGen-1.0.13 libStatGen || die
+	gzip -dc "${DISTDIR}"/libStatGen-1.0.15.tar.gz | tar xf - || die
+	ln -s libStatGen-1.0.15 libStatGen || die
 	cd "${WORKDIR}" || die
-	ln -s libStatGen-1.0.13 libStatGen || die
+	ln -s libStatGen-1.0.15 libStatGen || die
 	sed -e 's/-Werror//' -i verifyBamID-1.1.3/src/Makefile || die
-	sed -e 's/-Werror//' -i verifyBamID-1.1.3/libStatGen-1.0.13/general/Makefile || die
-	eapply_user
+	sed -e 's/-Werror//' -i verifyBamID-1.1.3/libStatGen-1.0.15/general/Makefile || die
+	default
 }
 
 src_compile(){
 	# LIB_PATH_GENERAL="${EPREFIX}"/usr/"$(get_libdir)" emake
-	LIB_PATH_GENERAL="../libStatGen-1.0.13" emake USER_WARNINGS=' '
+	LIB_PATH_GENERAL="../libStatGen-1.0.15" emake USER_WARNINGS=' '
 }
 
 src_install(){