* [gentoo-commits] proj/sci:master commit in: sci-biology/ngs/
@ 2022-01-15 11:04 Andrew Ammerlaan
0 siblings, 0 replies; 4+ messages in thread
From: Andrew Ammerlaan @ 2022-01-15 11:04 UTC (permalink / raw
To: gentoo-commits
commit: 2d893e4f6dd9835a92f032448ebafe0cf6877760
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 15 11:01:14 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sat Jan 15 11:01:14 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2d893e4f
sci-biology/ngs: add new dep of sra-tools
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/ngs/metadata.xml | 12 +++++++++++
sci-biology/ngs/ngs-2.11.2.ebuild | 42 +++++++++++++++++++++++++++++++++++++++
2 files changed, 54 insertions(+)
diff --git a/sci-biology/ngs/metadata.xml b/sci-biology/ngs/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/ngs/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/ngs/ngs-2.11.2.ebuild b/sci-biology/ngs/ngs-2.11.2.ebuild
new file mode 100644
index 000000000..d398d6f96
--- /dev/null
+++ b/sci-biology/ngs/ngs-2.11.2.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit python-single-r1
+
+DESCRIPTION="NGS Language Bindings "
+HOMEPAGE="https://github.com/ncbi/ngs"
+SRC_URI="https://github.com/ncbi/ngs/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}
+ sci-biology/bamtools
+"
+RDEPEND="${DEPEND}
+ virtual/jre:*
+"
+
+src_configure() {
+ # this is some non-standard configure script
+ ./configure || die
+}
+
+src_install() {
+ dodir /usr/include
+ dodir /etc/profile.d
+ # Hard way around hard coded paths
+ find . -type f -exec sed -i \
+ -e "s:/usr/local:${ED}/usr:g" \
+ -e "s:/etc:${ED}/etc:g" \
+ -e "s:/usr/lib:${ED}/usr/lib:g" \
+ -e "s:/usr/include:${ED}/usr/include:g" \
+ -e "s:setup.py -q install:setup.py install --root="${D}":g" \
+ {} \; || die
+ default
+}
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ngs/
@ 2022-01-15 11:52 Andrew Ammerlaan
0 siblings, 0 replies; 4+ messages in thread
From: Andrew Ammerlaan @ 2022-01-15 11:52 UTC (permalink / raw
To: gentoo-commits
commit: 4ba2a854b240019039ba956765fe0ae7683de289
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 15 11:52:31 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sat Jan 15 11:52:31 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4ba2a854
sci-biology/ngs: add missing dep on java compiler
Closes: https://github.com/gentoo/sci/issues/1134
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/ngs/ngs-2.11.2.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/ngs/ngs-2.11.2.ebuild b/sci-biology/ngs/ngs-2.11.2.ebuild
index d398d6f96..04e788b93 100644
--- a/sci-biology/ngs/ngs-2.11.2.ebuild
+++ b/sci-biology/ngs/ngs-2.11.2.ebuild
@@ -17,6 +17,7 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}
sci-biology/bamtools
+ virtual/jdk:*
"
RDEPEND="${DEPEND}
virtual/jre:*
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ngs/
@ 2022-01-15 14:38 Andrew Ammerlaan
0 siblings, 0 replies; 4+ messages in thread
From: Andrew Ammerlaan @ 2022-01-15 14:38 UTC (permalink / raw
To: gentoo-commits
commit: ccdbe2a7bbec5dc1c4e303f9e4003f22e1d7ee49
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 15 14:38:15 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sat Jan 15 14:38:15 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ccdbe2a7
sci-biology/ngs: properly use the java eclass
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/ngs/ngs-2.11.2.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/ngs/ngs-2.11.2.ebuild b/sci-biology/ngs/ngs-2.11.2.ebuild
index 04e788b93..8675ae22a 100644
--- a/sci-biology/ngs/ngs-2.11.2.ebuild
+++ b/sci-biology/ngs/ngs-2.11.2.ebuild
@@ -4,7 +4,7 @@
EAPI=8
PYTHON_COMPAT=( python3_{8..10} )
-inherit python-single-r1
+inherit python-single-r1 java-pkg-2
DESCRIPTION="NGS Language Bindings "
HOMEPAGE="https://github.com/ncbi/ngs"
@@ -17,10 +17,10 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}
sci-biology/bamtools
- virtual/jdk:*
+ virtual/jdk:1.8
"
RDEPEND="${DEPEND}
- virtual/jre:*
+ virtual/jre:1.8
"
src_configure() {
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ngs/
@ 2025-05-06 13:53 Alexander Puck Neuwirth
0 siblings, 0 replies; 4+ messages in thread
From: Alexander Puck Neuwirth @ 2025-05-06 13:53 UTC (permalink / raw
To: gentoo-commits
commit: c3475d9f4afad55d57ce8c09e8051281784f7950
Author: Alexander Puck Neuwirth <alexander <AT> neuwirth-informatik <DOT> de>
AuthorDate: Mon May 5 23:34:19 2025 +0000
Commit: Alexander Puck Neuwirth <alexander <AT> neuwirth-informatik <DOT> de>
CommitDate: Tue May 6 13:52:10 2025 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c3475d9f
sci-biology/ngs: treeclean
Signed-off-by: Alexander Puck Neuwirth <alexander <AT> neuwirth-informatik.de>
sci-biology/ngs/metadata.xml | 15 --------------
sci-biology/ngs/ngs-2.11.2.ebuild | 43 ---------------------------------------
2 files changed, 58 deletions(-)
diff --git a/sci-biology/ngs/metadata.xml b/sci-biology/ngs/metadata.xml
deleted file mode 100644
index f165e6cbc..000000000
--- a/sci-biology/ngs/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?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>
- <upstream>
- <remote-id type="github">ncbi/ngs</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/ngs/ngs-2.11.2.ebuild b/sci-biology/ngs/ngs-2.11.2.ebuild
deleted file mode 100644
index 0574c5076..000000000
--- a/sci-biology/ngs/ngs-2.11.2.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-inherit python-single-r1 java-pkg-2
-
-DESCRIPTION="NGS Language Bindings "
-HOMEPAGE="https://github.com/ncbi/ngs"
-SRC_URI="https://github.com/ncbi/ngs/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="~amd64"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
- sci-biology/bamtools
- virtual/jdk:1.8
-"
-RDEPEND="${DEPEND}
- virtual/jre:1.8
-"
-
-src_configure() {
- # this is some non-standard configure script
- ./configure || die
-}
-
-src_install() {
- dodir /usr/include
- dodir /etc/profile.d
- # Hard way around hard coded paths
- find . -type f -exec sed -i \
- -e "s:/usr/local:${ED}/usr:g" \
- -e "s:/etc:${ED}/etc:g" \
- -e "s:/usr/lib:${ED}/usr/lib:g" \
- -e "s:/usr/include:${ED}/usr/include:g" \
- -e "s:setup.py -q install:setup.py install --root="${D}":g" \
- {} \; || die
- default
-}
^ permalink raw reply related [flat|nested] 4+ messages in thread
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