* [gentoo-commits] proj/sci:master commit in: sci-biology/hisat2/
@ 2017-03-26 14:45 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2017-03-26 14:45 UTC (permalink / raw
To: gentoo-commits
commit: 869844b94cd59135cc3a85c0a42aafcf815f413e
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 26 09:18:45 2017 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar 26 09:18:45 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=869844b9
sci-biology/hisat2: Properly support python
Drop stray CVS header line
Package-Manager: Portage-2.3.5, Repoman-2.3.2
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/hisat2/hisat2-2.0.5.ebuild | 13 ++++++++-----
1 file changed, 8 insertions(+), 5 deletions(-)
diff --git a/sci-biology/hisat2/hisat2-2.0.5.ebuild b/sci-biology/hisat2/hisat2-2.0.5.ebuild
index a8a81a26f..d200a57ac 100644
--- a/sci-biology/hisat2/hisat2-2.0.5.ebuild
+++ b/sci-biology/hisat2/hisat2-2.0.5.ebuild
@@ -1,13 +1,15 @@
# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Id$
EAPI=6
-inherit eutils
+PYTHON_COMPAT=( python2_7 )
+
+inherit python-r1
DESCRIPTION="Align DNA reads to a population of genomes"
-HOMEPAGE="https://ccb.jhu.edu/software/hisat2
+HOMEPAGE="
+ https://ccb.jhu.edu/software/hisat2
https://github.com/infphilo/hisat2"
SRC_URI="ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/${P}-source.zip"
@@ -16,7 +18,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="cpu_flags_x86_sse2"
-DEPEND=""
+DEPEND="${PYTHON_DEPS}"
RDEPEND="${DEPEND}"
PATCHES=( "${FILESDIR}"/${P}-respect_CXXFLAGS.patch )
@@ -44,7 +46,8 @@ src_compile(){
}
src_install(){
- dobin hisat2 hisat2-build hisat2-inspect hisat2-build-s hisat2-build-l hisat2-align-s hisat2-align-l hisat2-inspect-s hisat2-inspect-l *.py
+ dobin hisat2{,-build,-inspect,-build-s,-build-l,-align-s,-align-l,-inspect-s,-inspect-l}
+ python_foreach_impl python_doscript *.py
insinto /usr/share/"${PN}"/scripts
doins scripts/*.sh
dodoc MANUAL TUTORIAL
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/hisat2/
@ 2021-01-19 16:26 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 16:26 UTC (permalink / raw
To: gentoo-commits
commit: eca3014fae9e6a22196e2cf57f270b3ad46f591a
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 16:20:31 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 16:20:31 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=eca3014f
sci-biology/hisat2: depend on unzip
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/hisat2/hisat2-2.2.1.ebuild | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/sci-biology/hisat2/hisat2-2.2.1.ebuild b/sci-biology/hisat2/hisat2-2.2.1.ebuild
index 5532d2b71..2b4bd91f5 100644
--- a/sci-biology/hisat2/hisat2-2.2.1.ebuild
+++ b/sci-biology/hisat2/hisat2-2.2.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -16,9 +16,11 @@ SRC_URI="https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi/download ->
LICENSE="GPL-3+"
SLOT="0"
KEYWORDS="~amd64 ~x86"
+
IUSE="cpu_flags_x86_sse2"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-DEPEND="${PYTHON_DEPS}"
+DEPEND="${PYTHON_DEPS} app-arch/unzip"
RDEPEND="${DEPEND}"
PATCHES=( "${FILESDIR}"/${P}-respect_CXXFLAGS.patch )
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/hisat2/
@ 2021-03-06 12:08 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-03-06 12:08 UTC (permalink / raw
To: gentoo-commits
commit: a1945ac9b929f5720f2df22b7866dbc980fe5f4c
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar 6 12:08:00 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar 6 12:08:00 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a1945ac9
sci-biology/hisat2: EAPI bump
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/hisat2/hisat2-2.2.1.ebuild | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/sci-biology/hisat2/hisat2-2.2.1.ebuild b/sci-biology/hisat2/hisat2-2.2.1.ebuild
index 9c14faf23..8841bd445 100644
--- a/sci-biology/hisat2/hisat2-2.2.1.ebuild
+++ b/sci-biology/hisat2/hisat2-2.2.1.ebuild
@@ -1,17 +1,17 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-PYTHON_COMPAT=( python3_{7,8} )
+PYTHON_COMPAT=( python3_{7,8,9} )
inherit python-r1
DESCRIPTION="Align DNA reads to a population of genomes"
HOMEPAGE="
https://ccb.jhu.edu/software/hisat2
- https://github.com/infphilo/hisat2"
-SRC_URI="https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi/download -> ${P}.zip"
+ https://github.com/DaehwanKimLab/hisat2"
+SRC_URI="https://github.com/DaehwanKimLab/hisat2/archive/v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-3+"
SLOT="0"
@@ -20,7 +20,7 @@ KEYWORDS="~amd64 ~x86"
IUSE="cpu_flags_x86_sse2"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-DEPEND="${PYTHON_DEPS} app-arch/unzip"
+DEPEND="${PYTHON_DEPS}"
RDEPEND="${DEPEND}"
PATCHES=( "${FILESDIR}"/${P}-respect_CXXFLAGS.patch )
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/hisat2/
@ 2023-04-20 3:16 Horea Christian
0 siblings, 0 replies; 6+ messages in thread
From: Horea Christian @ 2023-04-20 3:16 UTC (permalink / raw
To: gentoo-commits
commit: 4a09c787c1cebef14bc0400404207920fc8d93b5
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Apr 20 03:16:30 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Apr 20 03:16:30 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4a09c787
sci-biology/hisat2: update HOMEPAGE
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/hisat2/hisat2-2.2.1.ebuild | 2 +-
sci-biology/hisat2/metadata.xml | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/hisat2/hisat2-2.2.1.ebuild b/sci-biology/hisat2/hisat2-2.2.1.ebuild
index 8841bd445..d54858576 100644
--- a/sci-biology/hisat2/hisat2-2.2.1.ebuild
+++ b/sci-biology/hisat2/hisat2-2.2.1.ebuild
@@ -9,7 +9,7 @@ inherit python-r1
DESCRIPTION="Align DNA reads to a population of genomes"
HOMEPAGE="
- https://ccb.jhu.edu/software/hisat2
+ https://daehwankimlab.github.io/hisat2
https://github.com/DaehwanKimLab/hisat2"
SRC_URI="https://github.com/DaehwanKimLab/hisat2/archive/v${PV}.tar.gz -> ${P}.tar.gz"
diff --git a/sci-biology/hisat2/metadata.xml b/sci-biology/hisat2/metadata.xml
index 2a70cba7e..7954bc741 100644
--- a/sci-biology/hisat2/metadata.xml
+++ b/sci-biology/hisat2/metadata.xml
@@ -10,6 +10,6 @@
<name>Gentoo Biology Project</name>
</maintainer>
<upstream>
- <remote-id type="github">infphilo/hisat2</remote-id>
+ <remote-id type="github">DaehwanKimLab/hisat2</remote-id>
</upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/hisat2/
@ 2023-04-20 3:23 Horea Christian
0 siblings, 0 replies; 6+ messages in thread
From: Horea Christian @ 2023-04-20 3:23 UTC (permalink / raw
To: gentoo-commits
commit: a2510336fc30abbe7678120d6df4dabe9043d4b5
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Apr 20 03:23:08 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Apr 20 03:23:08 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a2510336
sci-biology/hisat2: update EAPI 7 -> 8
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/hisat2/hisat2-2.2.1.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/hisat2/hisat2-2.2.1.ebuild b/sci-biology/hisat2/hisat2-2.2.1.ebuild
index d54858576..ce46f7daa 100644
--- a/sci-biology/hisat2/hisat2-2.2.1.ebuild
+++ b/sci-biology/hisat2/hisat2-2.2.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{9..11} )
inherit python-r1
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/hisat2/
@ 2023-05-02 12:25 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2023-05-02 12:25 UTC (permalink / raw
To: gentoo-commits
commit: 17dc620f2e5c13aea2fbe89236f9dffa899cb2e2
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May 2 12:23:29 2023 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May 2 12:23:29 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=17dc620f
sci-biology/hisat2: disable py3.9
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/hisat2/hisat2-2.2.1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/hisat2/hisat2-2.2.1.ebuild b/sci-biology/hisat2/hisat2-2.2.1.ebuild
index ce46f7daa..9a30d7aef 100644
--- a/sci-biology/hisat2/hisat2-2.2.1.ebuild
+++ b/sci-biology/hisat2/hisat2-2.2.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..11} )
inherit python-r1
^ permalink raw reply related [flat|nested] 6+ messages in thread
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