* [gentoo-commits] proj/sci:master commit in: sci-biology/ampliconnoise/
@ 2015-01-07 21:49 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-01-07 21:49 UTC (permalink / raw
To: gentoo-commits
commit: 6be36f56d69cd44520a4fb498055558511f65e3b
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 7 21:48:51 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 7 21:48:51 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6be36f56
initial ebuild for a new package
Package-Manager: portage-2.2.7
---
sci-biology/ampliconnoise/ChangeLog | 10 ++++++++++
sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild | 20 ++++++++++++++++++++
sci-biology/ampliconnoise/metadata.xml | 9 +++++++++
3 files changed, 39 insertions(+)
diff --git a/sci-biology/ampliconnoise/ChangeLog b/sci-biology/ampliconnoise/ChangeLog
new file mode 100644
index 0000000..eb6ffaa
--- /dev/null
+++ b/sci-biology/ampliconnoise/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/ampliconnoise
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*ampliconnoise-1.27 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +ampliconnoise-1.27.ebuild:
+ initial ebuild
+
diff --git a/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild b/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
new file mode 100644
index 0000000..a53392b
--- /dev/null
+++ b/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Noise removal from pyrosequenced amplicons"
+HOMEPAGE="http://code.google.com/p/ampliconnoise/"
+SRC_URI="http://ampliconnoise.googlecode.com/files/AmpliconNoiseV"${PV}".tar.gz
+ http://ampliconnoise.googlecode.com/files/TutorialV1.22.tar.gz
+ http://ampliconnoise.googlecode.com/files/DiversityEstimates.tar.gz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
diff --git a/sci-biology/ampliconnoise/metadata.xml b/sci-biology/ampliconnoise/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/ampliconnoise/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/ampliconnoise/
@ 2015-02-18 16:41 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2015-02-18 16:41 UTC (permalink / raw
To: gentoo-commits
commit: 52a009c1ce8b1b94dba9daf61062318ea2f52eea
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 13:46:50 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 13:46:50 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=52a009c1
sci-biology/ampliconnoise: drop Useless blank line on last line
Package-Manager: portage-2.2.17
---
sci-biology/ampliconnoise/ChangeLog | 4 +++-
sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild | 7 ++-----
2 files changed, 5 insertions(+), 6 deletions(-)
diff --git a/sci-biology/ampliconnoise/ChangeLog b/sci-biology/ampliconnoise/ChangeLog
index eb6ffaa..ca695eb 100644
--- a/sci-biology/ampliconnoise/ChangeLog
+++ b/sci-biology/ampliconnoise/ChangeLog
@@ -2,9 +2,11 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 Feb 2015; Justin Lecher <jlec@gentoo.org> ampliconnoise-1.27.ebuild:
+ sci-biology/ampliconnoise: drop Useless blank line on last line
+
*ampliconnoise-1.27 (07 Jan 2015)
07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ampliconnoise-1.27.ebuild:
initial ebuild
-
diff --git a/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild b/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
index a53392b..8e51b1c 100644
--- a/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
+++ b/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
@@ -6,7 +6,8 @@ EAPI=5
DESCRIPTION="Noise removal from pyrosequenced amplicons"
HOMEPAGE="http://code.google.com/p/ampliconnoise/"
-SRC_URI="http://ampliconnoise.googlecode.com/files/AmpliconNoiseV"${PV}".tar.gz
+SRC_URI="
+ http://ampliconnoise.googlecode.com/files/AmpliconNoiseV${PV}.tar.gz
http://ampliconnoise.googlecode.com/files/TutorialV1.22.tar.gz
http://ampliconnoise.googlecode.com/files/DiversityEstimates.tar.gz"
@@ -14,7 +15,3 @@ LICENSE="LGPL-3"
SLOT="0"
KEYWORDS="~amd64"
IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ampliconnoise/
@ 2016-07-11 16:29 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2016-07-11 16:29 UTC (permalink / raw
To: gentoo-commits
commit: aa0c9614f6649cb743fdfe98d9dc08e84f753ace
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jul 11 16:28:47 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jul 11 16:28:47 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=aa0c9614
sci-biology/ampliconnoise: partial ebuild fixes
Package-Manager: portage-2.2.28
sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild | 15 ++++++++++++++-
1 file changed, 14 insertions(+), 1 deletion(-)
diff --git a/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild b/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
index 1addbb5..9cc43ca 100644
--- a/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
+++ b/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
DESCRIPTION="Noise removal from pyrosequenced amplicons"
HOMEPAGE="http://code.google.com/p/ampliconnoise/"
@@ -15,3 +15,16 @@ LICENSE="LGPL-3"
SLOT="0"
KEYWORDS="~amd64"
IUSE=""
+
+S="${WORKDIR}/AmpliconNoiseV1.27"
+
+src_compile(){
+ emake
+ cd ../DiversityEstimates || die
+ emake
+}
+
+src_install(){
+ default
+ dodoc "${WORKDIR}"/TutorialV1.22/Tutorial.ppt "${WORKDIR}"/TutorialV1.22/SmallTwins.*
+}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ampliconnoise/
@ 2016-07-11 16:30 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2016-07-11 16:30 UTC (permalink / raw
To: gentoo-commits
commit: 2b29d5c3ff51dba080faeac42d0902ef08a9e4e5
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jul 11 16:30:19 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jul 11 16:30:19 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2b29d5c3
sci-biology/ampliconnoise: oops, drop KEYWORDS
Package-Manager: portage-2.2.28
sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild b/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
index 9cc43ca..40909fd 100644
--- a/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
+++ b/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
@@ -13,7 +13,7 @@ SRC_URI="
LICENSE="LGPL-3"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
IUSE=""
S="${WORKDIR}/AmpliconNoiseV1.27"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ampliconnoise/
@ 2016-07-12 17:02 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2016-07-12 17:02 UTC (permalink / raw
To: gentoo-commits
commit: 34e693f2fc0529853c8af20bc738dcda6a4f68c8
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jul 12 17:02:43 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jul 12 17:02:43 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=34e693f2
sci-biology/ampliconnoise: more ebuild tweaks
Package-Manager: portage-2.2.28
sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild | 20 +++++++++++++++++---
1 file changed, 17 insertions(+), 3 deletions(-)
diff --git a/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild b/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
index 40909fd..16af117 100644
--- a/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
+++ b/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -14,11 +14,22 @@ SRC_URI="
LICENSE="LGPL-3"
SLOT="0"
KEYWORDS=""
-IUSE=""
+IUSE="mpi"
+RDEPEND="
+ mpi? ( virtual/mpi )
+ sci-libs/gsl
+ sci-biology/mafft
+ sci-biology/usearch-bin
+ dev-haskell/biosff || ( sci-biology/flower )"
+ # sci-biology/flower::haskell installs renamed binaries to avoid file collision
+ # unfortunately flower executable from the two packages
+ # dev-haskell/biosff::science vs. sci-biology/flower::haskell
+ # do not offer same cmdline options (upstream did not sync the two packages)
S="${WORKDIR}/AmpliconNoiseV1.27"
src_compile(){
+ # FIXME: the Makefile forcibly calls 'mpicc'
emake
cd ../DiversityEstimates || die
emake
@@ -26,5 +37,8 @@ src_compile(){
src_install(){
default
- dodoc "${WORKDIR}"/TutorialV1.22/Tutorial.ppt "${WORKDIR}"/TutorialV1.22/SmallTwins.*
+ dodoc "${WORKDIR}"/TutorialV1.22/Tutorial.ppt "${WORKDIR}"/TutorialV1.22/SmallTwins.* Doc.pdf
+ mv bin "${DESTDIR}/${EPREFIX}"/usr/ || die
+ insinto /usr/share/"${PN}"/scripts
+ doins Scripts/*.pl Scripts/*.sh
}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ampliconnoise/
@ 2020-09-27 9:19 Horea Christian
0 siblings, 0 replies; 6+ messages in thread
From: Horea Christian @ 2020-09-27 9:19 UTC (permalink / raw
To: gentoo-commits
commit: ecf1b90b64015fb2b9c1684c7ddd1c3b98fc01e1
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 27 09:18:53 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Sep 27 09:18:53 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ecf1b90b
sci-biology/ampliconnoise: removed discontinued package
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
.../ampliconnoise/ampliconnoise-1.27.ebuild | 43 ----------------------
sci-biology/ampliconnoise/metadata.xml | 12 ------
2 files changed, 55 deletions(-)
diff --git a/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild b/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
deleted file mode 100644
index 5555cf4c6..000000000
--- a/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Noise removal from pyrosequenced amplicons"
-HOMEPAGE="http://code.google.com/p/ampliconnoise/"
-SRC_URI="
- http://ampliconnoise.googlecode.com/files/AmpliconNoiseV${PV}.tar.gz
- http://ampliconnoise.googlecode.com/files/TutorialV1.22.tar.gz
- http://ampliconnoise.googlecode.com/files/DiversityEstimates.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE="mpi"
-RDEPEND="
- mpi? ( virtual/mpi )
- sci-libs/gsl
- sci-biology/mafft
- sci-biology/usearch-bin
- dev-haskell/biosff || ( sci-biology/flower )"
- # sci-biology/flower::haskell installs renamed binaries to avoid file collision
- # unfortunately flower executable from the two packages
- # dev-haskell/biosff::science vs. sci-biology/flower::haskell
- # do not offer same cmdline options (upstream did not sync the two packages)
-
-S="${WORKDIR}/AmpliconNoiseV1.27"
-
-src_compile(){
- # FIXME: the Makefile forcibly calls 'mpicc'
- emake
- cd ../DiversityEstimates || die
- emake
-}
-
-src_install(){
- default
- dodoc "${WORKDIR}"/TutorialV1.22/Tutorial.ppt "${WORKDIR}"/TutorialV1.22/SmallTwins.* Doc.pdf
- mv bin "${DESTDIR}/${EPREFIX}"/usr/ || die
- insinto /usr/share/"${PN}"/scripts
- doins Scripts/*.pl Scripts/*.sh
-}
diff --git a/sci-biology/ampliconnoise/metadata.xml b/sci-biology/ampliconnoise/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/ampliconnoise/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
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