* [gentoo-commits] proj/sci:master commit in: sci-biology/kmergenie/
@ 2015-03-13 16:23 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-03-13 16:23 UTC (permalink / raw
To: gentoo-commits
commit: e8031d7da1b7dd9040cd4876c146f2190fc3734a
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 13 16:22:43 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 13 16:22:43 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e8031d7d
new package; the k-mer size is set during compilation, use 'k=121 emerge kmergenie' to set your k-mer size
Package-Manager: portage-2.2.15
sci-biology/kmergenie/ChangeLog | 10 +++++++
sci-biology/kmergenie/kmergenie-1.6950.ebuild | 40 +++++++++++++++++++++++++++
sci-biology/kmergenie/metadata.xml | 9 ++++++
3 files changed, 59 insertions(+)
diff --git a/sci-biology/kmergenie/ChangeLog b/sci-biology/kmergenie/ChangeLog
new file mode 100644
index 0000000..482c032
--- /dev/null
+++ b/sci-biology/kmergenie/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/kmergenie
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*kmergenie-1.6950 (13 Mar 2015)
+
+ 13 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +kmergenie-1.6950.ebuild, +metadata.xml:
+ new package; the k-mer size is set during compilation, use 'k=121 emerge
+ kmergenie' to set your k-mer size
diff --git a/sci-biology/kmergenie/kmergenie-1.6950.ebuild b/sci-biology/kmergenie/kmergenie-1.6950.ebuild
new file mode 100644
index 0000000..91abe45
--- /dev/null
+++ b/sci-biology/kmergenie/kmergenie-1.6950.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+DESCRIPTION="Estimate best k-mer length to be used in novo assemblies (default set during compilation is 121)"
+HOMEPAGE="http://kmergenie.bx.psu.edu/"
+SRC_URI="http://kmergenie.bx.psu.edu/"${P}".tar.gz"
+
+LICENSE="CeCILL-1.1"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="dev-lang/R"
+RDEPEND="${DEPEND}"
+
+# Type `make` in the KmerGenie directory
+# To enable larger values of k, e.g. 200, type `make clean ; make k=200`.
+#
+# usage: ./kmergenie reads_file
+
+src_prepare(){
+ sed -e 's#-O4##' -i makefile || die
+}
+
+src_compile(){
+ make -j 1 || die
+}
+
+src_install(){
+ dobin kmergenie
+ dodoc README
+ # TODO: install also the python files
+}
diff --git a/sci-biology/kmergenie/metadata.xml b/sci-biology/kmergenie/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/kmergenie/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/kmergenie/
@ 2015-03-18 13:06 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-03-18 13:06 UTC (permalink / raw
To: gentoo-commits
commit: 72636efc7346f744696721df0c86bbb01273864b
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 18 13:04:47 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 18 13:04:47 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=72636efc
install the real binary, add dependency of external python module; the DEPEND line still needs a fix: DEPEND: Invalid atom (Invalid use dep: ''), token 1
Package-Manager: portage-2.2.15
sci-biology/kmergenie/ChangeLog | 5 +++++
sci-biology/kmergenie/kmergenie-1.6950.ebuild | 7 +++++--
2 files changed, 10 insertions(+), 2 deletions(-)
diff --git a/sci-biology/kmergenie/ChangeLog b/sci-biology/kmergenie/ChangeLog
index 482c032..93a1fa9 100644
--- a/sci-biology/kmergenie/ChangeLog
+++ b/sci-biology/kmergenie/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ kmergenie-1.6950.ebuild:
+ install the real binary, add dependency of external python module; the DEPEND
+ line still needs a fix: DEPEND: Invalid atom (Invalid use dep: ''), token 1
+
*kmergenie-1.6950 (13 Mar 2015)
13 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/kmergenie/kmergenie-1.6950.ebuild b/sci-biology/kmergenie/kmergenie-1.6950.ebuild
index 91abe45..46f37da 100644
--- a/sci-biology/kmergenie/kmergenie-1.6950.ebuild
+++ b/sci-biology/kmergenie/kmergenie-1.6950.ebuild
@@ -17,7 +17,9 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE=""
-DEPEND="dev-lang/R"
+# dev-python/docopt[${PYTHON_USEDEP}]
+DEPEND="dev-python/docopt
+ dev-lang/R"
RDEPEND="${DEPEND}"
# Type `make` in the KmerGenie directory
@@ -27,6 +29,7 @@ RDEPEND="${DEPEND}"
src_prepare(){
sed -e 's#-O4##' -i makefile || die
+ sed -e 's#third_party.##' -i kmergenie || die
}
src_compile(){
@@ -34,7 +37,7 @@ src_compile(){
}
src_install(){
- dobin kmergenie
+ dobin kmergenie specialk
dodoc README
# TODO: install also the python files
}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/kmergenie/
@ 2015-03-30 16:42 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-03-30 16:42 UTC (permalink / raw
To: gentoo-commits
commit: 4d653b1c16ed43c5fc7f86ab5d2e93e71573cae2
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 30 16:41:32 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 30 16:41:32 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4d653b1c
sci-biology/kmergenie: version bump
Package-Manager: portage-2.2.18
sci-biology/kmergenie/ChangeLog | 6 ++++++
.../kmergenie/{kmergenie-1.6950.ebuild => kmergenie-1.6971.ebuild} | 0
2 files changed, 6 insertions(+)
diff --git a/sci-biology/kmergenie/ChangeLog b/sci-biology/kmergenie/ChangeLog
index 93a1fa9..72b81bf 100644
--- a/sci-biology/kmergenie/ChangeLog
+++ b/sci-biology/kmergenie/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*kmergenie-1.6971 (30 Mar 2015)
+
+ 30 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +kmergenie-1.6971.ebuild, -kmergenie-1.6950.ebuild:
+ sci-biology/kmergenie: version bump
+
18 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
kmergenie-1.6950.ebuild:
install the real binary, add dependency of external python module; the DEPEND
diff --git a/sci-biology/kmergenie/kmergenie-1.6950.ebuild b/sci-biology/kmergenie/kmergenie-1.6971.ebuild
similarity index 100%
rename from sci-biology/kmergenie/kmergenie-1.6950.ebuild
rename to sci-biology/kmergenie/kmergenie-1.6971.ebuild
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/kmergenie/
@ 2015-04-29 22:42 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-04-29 22:42 UTC (permalink / raw
To: gentoo-commits
commit: 3b2e9d01b911d23d49e3bea49c71647d536effaa
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Apr 29 22:41:35 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Apr 29 22:41:35 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3b2e9d01
sci-biology/kmergenie: fix installation of launcher script
Package-Manager: portage-2.2.18
sci-biology/kmergenie/ChangeLog | 4 ++++
sci-biology/kmergenie/kmergenie-1.6971.ebuild | 2 ++
2 files changed, 6 insertions(+)
diff --git a/sci-biology/kmergenie/ChangeLog b/sci-biology/kmergenie/ChangeLog
index 72b81bf..198a4ff 100644
--- a/sci-biology/kmergenie/ChangeLog
+++ b/sci-biology/kmergenie/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 29 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ kmergenie-1.6971.ebuild:
+ sci-biology/kmergenie: fix installation of launcher script
+
*kmergenie-1.6971 (30 Mar 2015)
30 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/kmergenie/kmergenie-1.6971.ebuild b/sci-biology/kmergenie/kmergenie-1.6971.ebuild
index 46f37da..6081505 100644
--- a/sci-biology/kmergenie/kmergenie-1.6971.ebuild
+++ b/sci-biology/kmergenie/kmergenie-1.6971.ebuild
@@ -40,4 +40,6 @@ src_install(){
dobin kmergenie specialk
dodoc README
# TODO: install also the python files
+ insinto /usr/share/${PN}/R
+ doins scripts/*
}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/kmergenie/
@ 2021-02-13 11:16 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-02-13 11:16 UTC (permalink / raw
To: gentoo-commits
commit: b82fc54234ed593fafb5a8426eb540d680b0e8da
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Feb 13 11:16:07 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Feb 13 11:16:07 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b82fc542
sci-biology/kmergenie: version bump, correctly depend on python
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/kmergenie/kmergenie-1.6971.ebuild | 44 ---------------------------
sci-biology/kmergenie/kmergenie-1.7048.ebuild | 22 ++++++++++++++
2 files changed, 22 insertions(+), 44 deletions(-)
diff --git a/sci-biology/kmergenie/kmergenie-1.6971.ebuild b/sci-biology/kmergenie/kmergenie-1.6971.ebuild
deleted file mode 100644
index a451dc8c6..000000000
--- a/sci-biology/kmergenie/kmergenie-1.6971.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-PYTHON_COMPAT=( python{2_6,2_7} )
-
-DESCRIPTION="Estimate best k-mer length to be used in novo assemblies"
-HOMEPAGE="http://kmergenie.bx.psu.edu/"
-SRC_URI="http://kmergenie.bx.psu.edu/"${P}".tar.gz"
-
-LICENSE="CeCILL-1.1"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-# dev-python/docopt[${PYTHON_USEDEP}]
-DEPEND="dev-python/docopt
- dev-lang/R"
-RDEPEND="${DEPEND}"
-
-# Type `make` in the KmerGenie directory
-# To enable larger values of k, e.g. 200, type `make clean ; make k=200`.
-#
-# usage: ./kmergenie reads_file
-
-src_prepare(){
- sed -e 's#-O4##' -i makefile || die
- sed -e 's#third_party.##' -i kmergenie || die
-}
-
-src_compile(){
- make -j 1 || die
-}
-
-src_install(){
- dobin kmergenie specialk
- dodoc README
- # TODO: install also the python files
- insinto /usr/share/${PN}/R
- doins scripts/*
-}
diff --git a/sci-biology/kmergenie/kmergenie-1.7048.ebuild b/sci-biology/kmergenie/kmergenie-1.7048.ebuild
new file mode 100644
index 000000000..3a0d6a105
--- /dev/null
+++ b/sci-biology/kmergenie/kmergenie-1.7048.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7,8,9} )
+
+inherit distutils-r1
+
+DESCRIPTION="Estimate best k-mer length to be used in novo assemblies"
+HOMEPAGE="http://kmergenie.bx.psu.edu/"
+SRC_URI="http://kmergenie.bx.psu.edu/${P}.tar.gz"
+
+LICENSE="CeCILL-1.1"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="
+ dev-python/docopt[${PYTHON_USEDEP}]
+ dev-lang/R
+"
+RDEPEND="${DEPEND}"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/kmergenie/
@ 2023-05-02 12:15 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2023-05-02 12:15 UTC (permalink / raw
To: gentoo-commits
commit: 2ac756fa05f57ab928a0ad0863f166e661e20fd8
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May 2 12:08:34 2023 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May 2 12:15:11 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2ac756fa
sci-biology/kmergenie: treeclean
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/kmergenie/kmergenie-1.7048.ebuild | 22 ----------------------
sci-biology/kmergenie/metadata.xml | 12 ------------
2 files changed, 34 deletions(-)
diff --git a/sci-biology/kmergenie/kmergenie-1.7048.ebuild b/sci-biology/kmergenie/kmergenie-1.7048.ebuild
deleted file mode 100644
index 3a0d6a105..000000000
--- a/sci-biology/kmergenie/kmergenie-1.7048.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Estimate best k-mer length to be used in novo assemblies"
-HOMEPAGE="http://kmergenie.bx.psu.edu/"
-SRC_URI="http://kmergenie.bx.psu.edu/${P}.tar.gz"
-
-LICENSE="CeCILL-1.1"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND="
- dev-python/docopt[${PYTHON_USEDEP}]
- dev-lang/R
-"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/kmergenie/metadata.xml b/sci-biology/kmergenie/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/kmergenie/metadata.xml
+++ /dev/null
@@ -1,12 +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>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 6+ messages in thread
end of thread, other threads:[~2023-05-02 12:15 UTC | newest]
Thread overview: 6+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2015-03-30 16:42 [gentoo-commits] proj/sci:master commit in: sci-biology/kmergenie/ Martin Mokrejs
-- strict thread matches above, loose matches on Subject: below --
2023-05-02 12:15 Andrew Ammerlaan
2021-02-13 11:16 Andrew Ammerlaan
2015-04-29 22:42 Martin Mokrejs
2015-03-18 13:06 Martin Mokrejs
2015-03-13 16:23 Martin Mokrejs
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox