[gentoo-commits] proj/sci:master commit in: sci-biology/ampliconnoise/
commit: ecf1b90b64015fb2b9c1684c7ddd1c3b98fc01e1
Author: Horea Christian chymera eu>
AuthorDate: Sun Sep 27 09:18:53 2020 +
Commit: Horea Christian gmail com>
CommitDate: Sun Sep 27 09:18:53 2020 +
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 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 cf4c6..0
--- 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..0
--- a/sci-biology/ampliconnoise/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- mmokr...@fold.natur.cuni.cz
- Martin Mokrejs
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
[gentoo-commits] proj/sci:master commit in: sci-biology/ampliconnoise/
commit: 34e693f2fc0529853c8af20bc738dcda6a4f68c8
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Tue Jul 12 17:02:43 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Jul 12 17:02:43 2016 +
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
}
[gentoo-commits] proj/sci:master commit in: sci-biology/ampliconnoise/
commit: 2b29d5c3ff51dba080faeac42d0902ef08a9e4e5
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Mon Jul 11 16:30:19 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Jul 11 16:30:19 2016 +
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"
[gentoo-commits] proj/sci:master commit in: sci-biology/ampliconnoise/
commit: aa0c9614f6649cb743fdfe98d9dc08e84f753ace
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Mon Jul 11 16:28:47 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Jul 11 16:28:47 2016 +
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.*
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/ampliconnoise/
commit: 52a009c1ce8b1b94dba9daf61062318ea2f52eea
Author: Justin Lecher jlec AT gentoo DOT org
AuthorDate: Wed Feb 18 13:46:50 2015 +
Commit: Justin Lecher jlec AT gentoo DOT org
CommitDate: Wed Feb 18 13:46:50 2015 +
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 j...@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 mmokr...@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}
-
[gentoo-commits] proj/sci:master commit in: sci-biology/ampliconnoise/
commit: 6be36f56d69cd44520a4fb49808511f65e3b
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Wed Jan 7 21:48:51 2015 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Wed Jan 7 21:48:51 2015 +
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 000..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 mmokr...@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 000..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 000..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
+ herdsci-biology/herd
+ maintainer
+emailmmokr...@fold.natur.cuni.cz/email
+nameMartin Mokrejs/name
+ /maintainer
+/pkgmetadata
