* [gentoo-commits] proj/sci:master commit in: sci-biology/seaview/
@ 2012-01-30 0:57 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2012-01-30 0:57 UTC (permalink / raw
To: gentoo-commits
commit: 2fcbf893286791d9d0139b9250938d57df54c65a
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jan 30 00:57:29 2012 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jan 30 00:57:29 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2fcbf893
sci-biology/seaview: version bump; add missing symlink so that the C++ header can be found; remove calll to xft-config and use pkg-config instead; set our Gentoo FLTK path (not include path) to /usr/include/fltk-1 so that svg.o gets included during linking, otherwise we get undefined reference to svg_tree_save(FD_nj_plot*)
(Portage version: 2.1.10.44/git/Linux x86_64, unsigned Manifest commit)
---
sci-biology/seaview/ChangeLog | 13 ++++++
sci-biology/seaview/metadata.xml | 16 +++++++
sci-biology/seaview/seaview-4.3.3.ebuild | 69 ++++++++++++++++++++++++++++++
3 files changed, 98 insertions(+), 0 deletions(-)
diff --git a/sci-biology/seaview/ChangeLog b/sci-biology/seaview/ChangeLog
new file mode 100644
index 0000000..cd6851b
--- /dev/null
+++ b/sci-biology/seaview/ChangeLog
@@ -0,0 +1,13 @@
+# ChangeLog for sci-biology/seaview
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*seaview-4.3.3 (30 Jan 2012)
+
+ 30 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +seaview-4.3.3.ebuild, +metadata.xml:
+ version bump; add missing symlink so that the C++ header can be found; remove
+ calll to xft-config and use pkg-config instead; set our Gentoo FLTK path (not
+ include path) to /usr/include/fltk-1 so that svg.o gets included during
+ linking, otherwise we get undefined reference to svg_tree_save(FD_nj_plot*)
+
diff --git a/sci-biology/seaview/metadata.xml b/sci-biology/seaview/metadata.xml
new file mode 100644
index 0000000..0c1ebc3
--- /dev/null
+++ b/sci-biology/seaview/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer>
+ <email>weaver@gentoo.org</email>
+ <name>Andrey Kislyuk</name>
+ </maintainer>
+ <herd>sci-biology</herd>
+ <longdescription>
+ SeaView is a graphical multiple sequence alignment editor developped by
+ Manolo Gouy. SeaView is able to read and write various alignment
+ formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to
+ manually edit the alignment, and also to run DOT-PLOT or CLUSTALW
+ programs to locally improve the alignment.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/seaview/seaview-4.3.3.ebuild b/sci-biology/seaview/seaview-4.3.3.ebuild
new file mode 100644
index 0000000..b2cfe65
--- /dev/null
+++ b/sci-biology/seaview/seaview-4.3.3.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/seaview/seaview-4.2.5.ebuild,v 1.5 2011/03/20 20:02:27 jlec Exp $
+
+EAPI="2"
+
+inherit toolchain-funcs multilib eutils base
+
+DESCRIPTION="A graphical multiple sequence alignment editor"
+HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html"
+SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/${PN}_${PV}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+xft"
+
+DEPEND="x11-libs/fltk:1
+ xft? ( x11-libs/libXft
+ x11-libs/fltk:1[xft] )"
+RDEPEND="${DEPEND}
+ sci-biology/clustalw
+ || ( sci-libs/libmuscle sci-biology/muscle )
+ sci-biology/phyml"
+
+S="${WORKDIR}/${PN}"
+
+src_prepare() {
+ # respect CXXFLAGS (package uses them as CFLAGS)
+ sed -i \
+ -e "s:^CXX.*:CXX = $(tc-getCXX):" \
+ -e "s:\$(OPT):${CXXFLAGS}:" \
+ -e "s:^OPT:#OPT:" \
+ -e "s:^FLTK = /usr/include:FLTK = /usr/include/fltk-1:" \
+ -e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \
+ -e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \
+ -e "s:^USE_XFT:#USE_XFT:" \
+ -e "s:^#HELPFILE:HELPFILE:" \
+ -e "s:/usr/share/doc/seaview/seaview.htm:/usr/share/seaview/seaview.htm:" \
+ -e "s:^#PHYMLNAME:PHYMLNAME:" \
+ Makefile || die "sed failed while editing Makefile"
+
+ if use xft; then
+ sed -i \
+ -e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $(pkg-config --cflags xft):" \
+ -e "s:-lXft:$(pkg-config --libs xft):" \
+ Makefile || die "sed failed while editing Makefile to enable xft"
+ else
+ sed -i -e "s:-lXft::" Makefile || die
+ fi
+ cd FL || die
+ ln -sf . FL
+ base_src_prepare
+}
+
+src_install() {
+ dobin seaview || die
+
+ # /usr/share/seaview/seaview.html is hardcoded in the binary, see Makefile
+ insinto /usr/share/seaview
+ doins example.nxs seaview.html
+
+ insinto /usr/share/seaview/images
+ doins seaview.xpm || die
+
+ make_desktop_entry seaview Seaview
+
+ doman seaview.1 || die
+}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/seaview/
@ 2012-01-30 1:07 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2012-01-30 1:07 UTC (permalink / raw
To: gentoo-commits
commit: a665728b09699f8ce9648783a95af1ef9d9961a6
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jan 30 01:07:19 2012 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jan 30 01:07:19 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a665728b
sci-biology/seaview: and the path to the helpfile was corrected in the Makefile to match intended location specified in ebuild
---
sci-biology/seaview/ChangeLog | 4 ++++
1 files changed, 4 insertions(+), 0 deletions(-)
diff --git a/sci-biology/seaview/ChangeLog b/sci-biology/seaview/ChangeLog
index cd6851b..0197a4e 100644
--- a/sci-biology/seaview/ChangeLog
+++ b/sci-biology/seaview/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 30 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ChangeLog:
+ and the path to the helpfile was corrected in the Makefile to match intended
+ location specified in ebuild
+
*seaview-4.3.3 (30 Jan 2012)
30 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/seaview/
@ 2012-10-07 9:18 Justin Lecher
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher @ 2012-10-07 9:18 UTC (permalink / raw
To: gentoo-commits
commit: 4be3f8d76bdfbd5e62a9e5dd877e7e4b923b5c4b
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Aug 26 13:10:59 2012 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Aug 26 13:10:59 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4be3f8d7
better version in tree
---
sci-biology/seaview/ChangeLog | 17 -------
sci-biology/seaview/metadata.xml | 16 -------
sci-biology/seaview/seaview-4.3.3.ebuild | 69 ------------------------------
3 files changed, 0 insertions(+), 102 deletions(-)
diff --git a/sci-biology/seaview/ChangeLog b/sci-biology/seaview/ChangeLog
deleted file mode 100644
index 0197a4e..0000000
--- a/sci-biology/seaview/ChangeLog
+++ /dev/null
@@ -1,17 +0,0 @@
-# ChangeLog for sci-biology/seaview
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
- 30 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ChangeLog:
- and the path to the helpfile was corrected in the Makefile to match intended
- location specified in ebuild
-
-*seaview-4.3.3 (30 Jan 2012)
-
- 30 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- +seaview-4.3.3.ebuild, +metadata.xml:
- version bump; add missing symlink so that the C++ header can be found; remove
- calll to xft-config and use pkg-config instead; set our Gentoo FLTK path (not
- include path) to /usr/include/fltk-1 so that svg.o gets included during
- linking, otherwise we get undefined reference to svg_tree_save(FD_nj_plot*)
-
diff --git a/sci-biology/seaview/metadata.xml b/sci-biology/seaview/metadata.xml
deleted file mode 100644
index 0c1ebc3..0000000
--- a/sci-biology/seaview/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer>
- <email>weaver@gentoo.org</email>
- <name>Andrey Kislyuk</name>
- </maintainer>
- <herd>sci-biology</herd>
- <longdescription>
- SeaView is a graphical multiple sequence alignment editor developped by
- Manolo Gouy. SeaView is able to read and write various alignment
- formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to
- manually edit the alignment, and also to run DOT-PLOT or CLUSTALW
- programs to locally improve the alignment.
- </longdescription>
-</pkgmetadata>
diff --git a/sci-biology/seaview/seaview-4.3.3.ebuild b/sci-biology/seaview/seaview-4.3.3.ebuild
deleted file mode 100644
index b2cfe65..0000000
--- a/sci-biology/seaview/seaview-4.3.3.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/seaview/seaview-4.2.5.ebuild,v 1.5 2011/03/20 20:02:27 jlec Exp $
-
-EAPI="2"
-
-inherit toolchain-funcs multilib eutils base
-
-DESCRIPTION="A graphical multiple sequence alignment editor"
-HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html"
-SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/${PN}_${PV}.tar.gz"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+xft"
-
-DEPEND="x11-libs/fltk:1
- xft? ( x11-libs/libXft
- x11-libs/fltk:1[xft] )"
-RDEPEND="${DEPEND}
- sci-biology/clustalw
- || ( sci-libs/libmuscle sci-biology/muscle )
- sci-biology/phyml"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
- # respect CXXFLAGS (package uses them as CFLAGS)
- sed -i \
- -e "s:^CXX.*:CXX = $(tc-getCXX):" \
- -e "s:\$(OPT):${CXXFLAGS}:" \
- -e "s:^OPT:#OPT:" \
- -e "s:^FLTK = /usr/include:FLTK = /usr/include/fltk-1:" \
- -e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \
- -e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \
- -e "s:^USE_XFT:#USE_XFT:" \
- -e "s:^#HELPFILE:HELPFILE:" \
- -e "s:/usr/share/doc/seaview/seaview.htm:/usr/share/seaview/seaview.htm:" \
- -e "s:^#PHYMLNAME:PHYMLNAME:" \
- Makefile || die "sed failed while editing Makefile"
-
- if use xft; then
- sed -i \
- -e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $(pkg-config --cflags xft):" \
- -e "s:-lXft:$(pkg-config --libs xft):" \
- Makefile || die "sed failed while editing Makefile to enable xft"
- else
- sed -i -e "s:-lXft::" Makefile || die
- fi
- cd FL || die
- ln -sf . FL
- base_src_prepare
-}
-
-src_install() {
- dobin seaview || die
-
- # /usr/share/seaview/seaview.html is hardcoded in the binary, see Makefile
- insinto /usr/share/seaview
- doins example.nxs seaview.html
-
- insinto /usr/share/seaview/images
- doins seaview.xpm || die
-
- make_desktop_entry seaview Seaview
-
- doman seaview.1 || die
-}
^ permalink raw reply related [flat|nested] 3+ messages in thread
end of thread, other threads:[~2012-10-07 9:19 UTC | newest]
Thread overview: 3+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2012-10-07 9:18 [gentoo-commits] proj/sci:master commit in: sci-biology/seaview/ Justin Lecher
-- strict thread matches above, loose matches on Subject: below --
2012-01-30 1:07 Martin Mokrejs
2012-01-30 0:57 Martin Mokrejs
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox