* [gentoo-commits] proj/sci:master commit in: sci-biology/symap/
@ 2013-08-29 15:52 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2013-08-29 15:52 UTC (permalink / raw
To: gentoo-commits
commit: 36a3d4107693d6146159efeb83e1f8024da0a6e6
Author: Martin Mokrejš <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Thu Aug 29 15:39:26 2013 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Aug 29 15:39:26 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=36a3d410
Not yet completed ebuild for a new package
---
sci-biology/symap/ChangeLog | 9 +++++++++
sci-biology/symap/symap-4.0.ebuild | 31 +++++++++++++++++++++++++++++++
2 files changed, 40 insertions(+)
diff --git a/sci-biology/symap/ChangeLog b/sci-biology/symap/ChangeLog
new file mode 100644
index 0000000..9677e2f
--- /dev/null
+++ b/sci-biology/symap/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/symap
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*symap-4.0 (29 Aug 2013)
+
+ 29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +symap-4.0.ebuild:
+ Not yet working.
+
diff --git a/sci-biology/symap/symap-4.0.ebuild b/sci-biology/symap/symap-4.0.ebuild
new file mode 100644
index 0000000..c7434a0
--- /dev/null
+++ b/sci-biology/symap/symap-4.0.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+DESCRIPTION="Synteny Mapping and Analysis Program between chromosomes, contigs and physical maps"
+HOMEPAGE="http://www.agcol.arizona.edu/software/symap/"
+SRC_URI="symap_40.tar.gz"
+
+LICENSE="GPLv2-symap"
+SLOT="0"
+KEYWORDS=""
+#KEYWORDS="~x86 ~amd64"
+IUSE=""
+
+RESTRICT="fetch"
+
+pkg_nofetch() {
+ einfo "Please register and download symap_${PV}.tar.gz (110MB)"
+ einfo "at http://www.agcol.arizona.edu/software/symap/v"${PV}"/download/"
+ einfo 'and place it in '${DISTDIR}
+}
+
+
+DEPEND="sci-biology/blat
+ sci-biology/mummer
+ sci-biology/muscle"
+RDEPEND="${DEPEND}
+ dev-lang/java"
+
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/symap/
@ 2014-01-06 19:57 Justin Lecher
0 siblings, 0 replies; 4+ messages in thread
From: Justin Lecher @ 2014-01-06 19:57 UTC (permalink / raw
To: gentoo-commits
commit: 4ef7b895cc703f68836185428d4762885e1ab60c
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 6 19:40:32 2014 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan 6 19:40:32 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4ef7b895
sci-biology/symap: Fix wrong license
Package-Manager: portage-2.2.8
---
sci-biology/symap/ChangeLog | 5 ++++-
sci-biology/symap/metadata.xml | 5 +++++
sci-biology/symap/symap-4.0.ebuild | 19 +++++++++----------
3 files changed, 18 insertions(+), 11 deletions(-)
diff --git a/sci-biology/symap/ChangeLog b/sci-biology/symap/ChangeLog
index 9677e2f..e17a576 100644
--- a/sci-biology/symap/ChangeLog
+++ b/sci-biology/symap/ChangeLog
@@ -1,7 +1,10 @@
# ChangeLog for sci-biology/symap
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 06 Jan 2014; Justin Lecher <jlec@gentoo.org> symap-4.0.ebuild, +metadata.xml:
+ Fix wrong license
+
*symap-4.0 (29 Aug 2013)
29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +symap-4.0.ebuild:
diff --git a/sci-biology/symap/metadata.xml b/sci-biology/symap/metadata.xml
new file mode 100644
index 0000000..897aa2e
--- /dev/null
+++ b/sci-biology/symap/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+</pkgmetadata>
diff --git a/sci-biology/symap/symap-4.0.ebuild b/sci-biology/symap/symap-4.0.ebuild
index c7434a0..55cc0c6 100644
--- a/sci-biology/symap/symap-4.0.ebuild
+++ b/sci-biology/symap/symap-4.0.ebuild
@@ -1,14 +1,14 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
DESCRIPTION="Synteny Mapping and Analysis Program between chromosomes, contigs and physical maps"
HOMEPAGE="http://www.agcol.arizona.edu/software/symap/"
SRC_URI="symap_40.tar.gz"
-LICENSE="GPLv2-symap"
+LICENSE="GPL-2"
SLOT="0"
KEYWORDS=""
#KEYWORDS="~x86 ~amd64"
@@ -17,15 +17,14 @@ IUSE=""
RESTRICT="fetch"
pkg_nofetch() {
- einfo "Please register and download symap_${PV}.tar.gz (110MB)"
- einfo "at http://www.agcol.arizona.edu/software/symap/v"${PV}"/download/"
- einfo 'and place it in '${DISTDIR}
+ elog "Please register and download symap_${PV}.tar.gz (110MB)"
+ elog "at http://www.agcol.arizona.edu/software/symap/v${PV}/download/"
+ elog "and place it in ${DISTDIR}"
}
-
-DEPEND="sci-biology/blat
+DEPEND="
+ sci-biology/blat
sci-biology/mummer
sci-biology/muscle"
RDEPEND="${DEPEND}
- dev-lang/java"
-
+ virtual/jre"
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/symap/
@ 2021-02-04 7:45 Andrew Ammerlaan
0 siblings, 0 replies; 4+ messages in thread
From: Andrew Ammerlaan @ 2021-02-04 7:45 UTC (permalink / raw
To: gentoo-commits
commit: 4d0370cad9584f28fe77059521a641287a501d88
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Feb 4 07:45:17 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Feb 4 07:45:17 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4d0370ca
sci-biology/symap: version bump, EAIP bump
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/symap/symap-4.0.ebuild | 29 --------------------------
sci-biology/symap/symap-5.0.6.ebuild | 40 ++++++++++++++++++++++++++++++++++++
2 files changed, 40 insertions(+), 29 deletions(-)
diff --git a/sci-biology/symap/symap-4.0.ebuild b/sci-biology/symap/symap-4.0.ebuild
deleted file mode 100644
index bc485ff04..000000000
--- a/sci-biology/symap/symap-4.0.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Synteny Mapping and Analysis Program"
-HOMEPAGE="http://www.agcol.arizona.edu/software/symap/"
-SRC_URI="symap_40.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-#KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
- elog "Please register and download symap_${PV}.tar.gz (110MB)"
- elog "at http://www.agcol.arizona.edu/software/symap/v${PV}/download/"
- elog "and place it in ${DISTDIR}"
-}
-
-DEPEND="
- sci-biology/blat
- sci-biology/mummer
- sci-biology/muscle"
-RDEPEND="${DEPEND}
- virtual/jre"
diff --git a/sci-biology/symap/symap-5.0.6.ebuild b/sci-biology/symap/symap-5.0.6.ebuild
new file mode 100644
index 000000000..58b444b3d
--- /dev/null
+++ b/sci-biology/symap/symap-5.0.6.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Synteny Mapping and Analysis Program"
+HOMEPAGE="http://www.agcol.arizona.edu/software/symap/ https://github.com/csoderlund/SyMAP"
+SRC_URI="https://github.com/csoderlund/SyMAP/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+# error: package netscape.javascript does not exist
+KEYWORDS=""
+
+DEPEND="
+ sci-biology/blat
+ sci-biology/mummer
+ sci-biology/muscle"
+RDEPEND="${DEPEND}
+ >=virtual/jre-1.7:*"
+
+S="${WORKDIR}/SyMAP-${PV}/java"
+
+src_unpack() {
+ default
+ cd "${S}"
+ tar xvf classes_ext.tar.gz
+ cd ../
+ tar xvf ext.tar.gz
+}
+
+src_prepare() {
+ default
+ sed -e 's/#JAVA_PATH=\/usr/JAVA_PATH=\/usr/g' -i Makefile || die
+}
+
+src_compile() {
+ emake class_dirs
+ emake
+}
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/symap/
@ 2022-01-25 10:27 Andrew Ammerlaan
0 siblings, 0 replies; 4+ messages in thread
From: Andrew Ammerlaan @ 2022-01-25 10:27 UTC (permalink / raw
To: gentoo-commits
commit: 1369d67182d9d6e00895f5895fea8511fff61d89
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 10:27:19 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 10:27:19 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1369d671
sci-biology/symap: drop dead package
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/symap/metadata.xml | 8 --------
sci-biology/symap/symap-5.0.6.ebuild | 40 ------------------------------------
2 files changed, 48 deletions(-)
diff --git a/sci-biology/symap/metadata.xml b/sci-biology/symap/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/sci-biology/symap/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/symap/symap-5.0.6.ebuild b/sci-biology/symap/symap-5.0.6.ebuild
deleted file mode 100644
index 58b444b3d..000000000
--- a/sci-biology/symap/symap-5.0.6.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Synteny Mapping and Analysis Program"
-HOMEPAGE="http://www.agcol.arizona.edu/software/symap/ https://github.com/csoderlund/SyMAP"
-SRC_URI="https://github.com/csoderlund/SyMAP/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-# error: package netscape.javascript does not exist
-KEYWORDS=""
-
-DEPEND="
- sci-biology/blat
- sci-biology/mummer
- sci-biology/muscle"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.7:*"
-
-S="${WORKDIR}/SyMAP-${PV}/java"
-
-src_unpack() {
- default
- cd "${S}"
- tar xvf classes_ext.tar.gz
- cd ../
- tar xvf ext.tar.gz
-}
-
-src_prepare() {
- default
- sed -e 's/#JAVA_PATH=\/usr/JAVA_PATH=\/usr/g' -i Makefile || die
-}
-
-src_compile() {
- emake class_dirs
- emake
-}
^ permalink raw reply related [flat|nested] 4+ messages in thread
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