* [gentoo-commits] proj/sci:master commit in: sci-biology/arachne/
@ 2016-03-30 20:24 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2016-03-30 20:24 UTC (permalink / raw
To: gentoo-commits
commit: c0c2589594db6900b277d68628ece4d62254e1ae
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 30 20:22:23 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 30 20:22:23 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c0c25895
sci-biology/arachne: new package; does not compile (upstream contacted) and the LICENSE is not exactly MIT?
Package-Manager: portage-2.2.28
sci-biology/arachne/arachne-46233.ebuild | 41 ++++++++++++++++++++++++++++++++
sci-biology/arachne/metadata.xml | 12 ++++++++++
2 files changed, 53 insertions(+)
diff --git a/sci-biology/arachne/arachne-46233.ebuild b/sci-biology/arachne/arachne-46233.ebuild
new file mode 100644
index 0000000..71fc0b8
--- /dev/null
+++ b/sci-biology/arachne/arachne-46233.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+DESCRIPTION="Whole genome shotgun assembler for Sanger read lengths (overlap-layout-contig)"
+HOMEPAGE="https://www.broadinstitute.org/crd/wiki
+ http://genome.cshlp.org/content/12/1/177.abstract"
+SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ARACHNE/latest_source_code/${P}.tar.gz"
+
+LICENSE="MIT" # not exactly MIT ... hence no KEYWORDS
+SLOT="0"
+KEYWORDS=""
+IUSE="doc openmp"
+
+DEPEND="dev-libs/xerces-c
+ doc? ( virtual/latex-base app-text/dvipsk )"
+RDEPEND="${DEPEND}"
+
+# needs >=g++-4.7 but does not compile with 5.3.0
+
+# --disable-openmp to disable requirement for OpenMP-capable compiler
+src_configure() {
+ local myconf=()
+ use openmp || myconf+=( --disable-openmp )
+ econf ${myconf[@]}
+}
+
+# set the following environment variables
+# http://www.broadinstitute.org/crd/wiki/index.php/Setup
+#
+# ARACHNE_PRE
+# ARACHNE_BIN_DIR
+# ARACHNE_PRETTY_HELP
+
+pkg_postinst(){
+ einfo "Please add these to your ~/.bashrc"
+ einfo "limit stacksize 100000"
+ einfo "limit datasize unlimited"
+}
diff --git a/sci-biology/arachne/metadata.xml b/sci-biology/arachne/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/arachne/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>
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/arachne/
@ 2016-04-08 18:25 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2016-04-08 18:25 UTC (permalink / raw
To: gentoo-commits
commit: 11ab19e99ad2647fd06eb3da6fc8ad427ba7cc1a
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 8 18:22:58 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 8 18:22:58 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=11ab19e9
sci-biology/arachne: improve package description
Package-Manager: portage-2.2.28
sci-biology/arachne/arachne-46233.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/arachne/arachne-46233.ebuild b/sci-biology/arachne/arachne-46233.ebuild
index a5eda4d..2b56ae9 100644
--- a/sci-biology/arachne/arachne-46233.ebuild
+++ b/sci-biology/arachne/arachne-46233.ebuild
@@ -4,7 +4,7 @@
EAPI=5
-DESCRIPTION="Whole genome shotgun OLC assembler for Sanger read lengths (overlap-layout-contig)"
+DESCRIPTION="Whole genome shotgun OLC assembler for Sanger reads (overlap-layout-contig)"
HOMEPAGE="https://www.broadinstitute.org/crd/wiki
http://genome.cshlp.org/content/12/1/177.abstract"
SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ARACHNE/latest_source_code/${P}.tar.gz"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/arachne/
@ 2016-04-08 18:25 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2016-04-08 18:25 UTC (permalink / raw
To: gentoo-commits
commit: 339c586d63abe1fad29ec3e6baac5920f38e8060
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 8 18:22:12 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 8 18:22:12 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=339c586d
sci-biology/arachne: improve package description
Package-Manager: portage-2.2.28
sci-biology/arachne/arachne-46233.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/arachne/arachne-46233.ebuild b/sci-biology/arachne/arachne-46233.ebuild
index 71fc0b8..a5eda4d 100644
--- a/sci-biology/arachne/arachne-46233.ebuild
+++ b/sci-biology/arachne/arachne-46233.ebuild
@@ -4,7 +4,7 @@
EAPI=5
-DESCRIPTION="Whole genome shotgun assembler for Sanger read lengths (overlap-layout-contig)"
+DESCRIPTION="Whole genome shotgun OLC assembler for Sanger read lengths (overlap-layout-contig)"
HOMEPAGE="https://www.broadinstitute.org/crd/wiki
http://genome.cshlp.org/content/12/1/177.abstract"
SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ARACHNE/latest_source_code/${P}.tar.gz"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/arachne/
@ 2021-01-20 8:40 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-01-20 8:40 UTC (permalink / raw
To: gentoo-commits
commit: df56637412debd360e81205a6ccf6bbe5fbc948f
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Jan 20 08:37:00 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Jan 20 08:37:00 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=df566374
sci-biology/arachne: update homepage
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/arachne/arachne-46233.ebuild | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/sci-biology/arachne/arachne-46233.ebuild b/sci-biology/arachne/arachne-46233.ebuild
index 9efa4a5d4..ec7a59aa1 100644
--- a/sci-biology/arachne/arachne-46233.ebuild
+++ b/sci-biology/arachne/arachne-46233.ebuild
@@ -1,11 +1,10 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=5
DESCRIPTION="Whole genome shotgun OLC assembler for Sanger reads (overlap-layout-contig)"
-HOMEPAGE="https://www.broadinstitute.org/crd/wiki
- http://genome.cshlp.org/content/12/1/177.abstract"
+HOMEPAGE="https://genome.cshlp.org/content/12/1/177.abstract"
SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ARACHNE/latest_source_code/${P}.tar.gz"
LICENSE="MIT" # not exactly MIT ... hence no KEYWORDS
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/arachne/
@ 2021-02-01 9:40 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-02-01 9:40 UTC (permalink / raw
To: gentoo-commits
commit: f479536b47aa45c35818d45d2652672ed3136a00
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Feb 1 09:40:31 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Feb 1 09:40:31 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f479536b
sci-biology/arachne: EAPI bump
license is MIT as far as I can tell, does not compile though
so no keywords yet
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/arachne/arachne-46233.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/arachne/arachne-46233.ebuild b/sci-biology/arachne/arachne-46233.ebuild
index ec7a59aa1..b34d00134 100644
--- a/sci-biology/arachne/arachne-46233.ebuild
+++ b/sci-biology/arachne/arachne-46233.ebuild
@@ -1,13 +1,13 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
DESCRIPTION="Whole genome shotgun OLC assembler for Sanger reads (overlap-layout-contig)"
HOMEPAGE="https://genome.cshlp.org/content/12/1/177.abstract"
SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ARACHNE/latest_source_code/${P}.tar.gz"
-LICENSE="MIT" # not exactly MIT ... hence no KEYWORDS
+LICENSE="MIT"
SLOT="0"
KEYWORDS=""
IUSE="doc openmp"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/arachne/
@ 2022-01-25 13:36 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2022-01-25 13:36 UTC (permalink / raw
To: gentoo-commits
commit: 716876a2c96656ae74a3694152cca46abfa7190f
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 13:36:16 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 13:36:16 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=716876a2
sci-biology/arachne: drop dead package
unfetchable
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/arachne/arachne-46233.ebuild | 39 --------------------------------
sci-biology/arachne/metadata.xml | 12 ----------
2 files changed, 51 deletions(-)
diff --git a/sci-biology/arachne/arachne-46233.ebuild b/sci-biology/arachne/arachne-46233.ebuild
deleted file mode 100644
index b34d00134..000000000
--- a/sci-biology/arachne/arachne-46233.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Whole genome shotgun OLC assembler for Sanger reads (overlap-layout-contig)"
-HOMEPAGE="https://genome.cshlp.org/content/12/1/177.abstract"
-SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ARACHNE/latest_source_code/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE="doc openmp"
-
-DEPEND="dev-libs/xerces-c
- doc? ( virtual/latex-base app-text/dvipsk )"
-RDEPEND="${DEPEND}"
-
-# needs >=g++-4.7 but does not compile with 5.3.0
-
-# --disable-openmp to disable requirement for OpenMP-capable compiler
-src_configure() {
- local myconf=()
- use openmp || myconf+=( --disable-openmp )
- econf ${myconf[@]}
-}
-
-# set the following environment variables
-# http://www.broadinstitute.org/crd/wiki/index.php/Setup
-#
-# ARACHNE_PRE
-# ARACHNE_BIN_DIR
-# ARACHNE_PRETTY_HELP
-
-pkg_postinst(){
- einfo "Please add these to your ~/.bashrc"
- einfo "limit stacksize 100000"
- einfo "limit datasize unlimited"
-}
diff --git a/sci-biology/arachne/metadata.xml b/sci-biology/arachne/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/arachne/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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