reinit the tree, so we can have metadata

5 files changed, 253 insertions, 0 deletions

diff --git a/sci-biology/seaview/Manifest b/sci-biology/seaview/Manifest
new file mode 100644
index 000000000000..cc814b318224
--- /dev/null
+++ b/sci-biology/seaview/Manifest
@@ -0,0 +1,9 @@
+DIST seaview_4.3.5.tar.gz 309530 SHA256 38050d6792eb799d61e5e849f76971a9c7d45f467e5c04fbc4363062d8e7100d SHA512 b20c018da9a29d79fe0393fed5d29117729492ea8f36e72d4aeb98044a3de4a13331bd29e76ca552a08f6da764e57e69f9fb0325fc031551514d7a54b56c849a WHIRLPOOL 82fc7324bf1d934d69712629808d6b4178a5f2cdcf25351fb2fe2784f9cea0c1ec0aaaba7a3a08c84795108eb049394ceaab052af8cc0efbb0975064fa4e80e0
+DIST seaview_4.5.4.tar.gz 420608 SHA256 f4569ad7f1d8de2b141175b1122f036cb45f55f8e9e59e42d6026668e091e7ed SHA512 a8a2e49a13f87ae4279311068147169b1e17874e9ce5787003b854c7271efc7a128db6916bb883a9b7b0b90f855fe40d83c77e9fd9f5751464e04346b9923301 WHIRLPOOL c52f7ac9d7d4c85d7670bdb3a87c9ba94904b25e11583ad8abf3de9f43fa3967d64b96d447ebb5ebe614053c4de64828d1c3c5763c64dc269e78fb3c49151886
+DIST seaview_4.6.tar.gz 424258 SHA256 6826a41bf2980922add66857abe42e3e6a19f0d1bb13845252745db7740c37bc SHA512 e005d9dcc9e03c5636404e94f0059f7d4a9289fe77ecdab765e3ca2b59d826b8711a344f3824d079383a7ede0fe17b3b06694dfb7b709bb6a0a1e38cef6ee1d6 WHIRLPOOL 50375ee836de8de50556a69054baa841f27025d679ce65953aee55d69c89129246eef8896b5833b5874cbdcbc55900dd4e37d4814c4f0a90097cb8c37f0ef1ae
+EBUILD seaview-4.3.5.ebuild 2013 SHA256 a5e3ed9063835147e1227e4094941d7ffa34ba5ba44da9b4fd3b3e5aa55420ac SHA512 41eeabeb570a22219f7ad649a4eb127b94a253f914ea6637fcce518da3607e3fb42b528d3aa436f6b86e54b695d31900b29558ec0696c1e4bf3264c42cdfc945 WHIRLPOOL 26e9c72ac903782291e131da4d52059a4b1c79becacd431d00b0726272bc4e7f844626bede2fc7e36a28ccccfcb3a4b0e975d00c3c62d8dd45b39ba99542c597
+EBUILD seaview-4.5.4.ebuild 2013 SHA256 a5e3ed9063835147e1227e4094941d7ffa34ba5ba44da9b4fd3b3e5aa55420ac SHA512 41eeabeb570a22219f7ad649a4eb127b94a253f914ea6637fcce518da3607e3fb42b528d3aa436f6b86e54b695d31900b29558ec0696c1e4bf3264c42cdfc945 WHIRLPOOL 26e9c72ac903782291e131da4d52059a4b1c79becacd431d00b0726272bc4e7f844626bede2fc7e36a28ccccfcb3a4b0e975d00c3c62d8dd45b39ba99542c597
+EBUILD seaview-4.6.ebuild 1997 SHA256 6b57bec3393355d016145f9104ac66b33497cbe1787a9430e45b353739528c1b SHA512 5768df52c205ccfaa4d2d52ec753125dd77eb91a7b0be959dbc67aca00c0a66dc3f13b125d073450a81a06eea29880503981942042c77a0c6e1bb8f19f070cb8 WHIRLPOOL e666cc8ce9ee43e8ae7a9321d7eb5ecc557036aa464354c1a0b0d278d465968be73f77f7a2ea51e1b01eadf0f112973d07022c74ae60c5abcb09e75b1707c83f
+MISC ChangeLog 3587 SHA256 4ed7e21c12bc6710319fe46602e6ee30c7436d79a6f5afe8273b754b35f74d5d SHA512 394452bc63381d8c47434cbbba52c40692b89157581a1c1466e5c7199e48d2e938e051ac1bc1d6819f0f2fd555868cc24ff0342c3d015d65548abbb37910891f WHIRLPOOL 4b68d6fa54617fb9308f52727bfa656e22d3550166b3b9a9ca4965a9a52d14368774d7bb9f4a8df43d0a34cc7c243d39b0f8a0efe8d99b05f1d4dcbd844277a0
+MISC ChangeLog-2015 8783 SHA256 0981ab2b9f7546a936e0e57ad0322f7007fc6a83e2b93f230acf665ac333d2bd SHA512 eb595983a51fc83a0d46ced9a6a5416ed2f61e7f1b33b8eeefbbb6979f486fba7582ce01a104ac28626d3ff17b7d4898613e09027f3d6f70bd42fb8e81b649f4 WHIRLPOOL 68f6eeda8f16a080a49467520b832a54341e9fbf265ac7e22d1e51f0f192edeecfc49e2716a860f2229577a194b90d2719756e6400e09b7ee68e91807a2fc19c
+MISC metadata.xml 628 SHA256 1f936b9abe506aa04d855215dc6e7b0ea4a22abb2c464872b0f92dd6c2fe53ad SHA512 5ea98118394152f404bf39d35f3e5daf759e5a2107ea43141f7e8e54109ad0f41476e0cd820bcbde057bab96c4680be86cf8c25eacd4b6ec06122b633c062ad4 WHIRLPOOL d0c9e2cab8953fb461bf72802665030b15823cb3cf09611b8dab6f7d71d0c3b131f5f16e324f72310b61caf0484e3947eaf689aba5a58b322ac834e1a62dcac1
diff --git a/sci-biology/seaview/metadata.xml b/sci-biology/seaview/metadata.xml
new file mode 100644
index 000000000000..7e8eb04c0ab0
--- /dev/null
+++ b/sci-biology/seaview/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <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-4.3.5.ebuild b/sci-biology/seaview/seaview-4.3.5.ebuild
new file mode 100644
index 000000000000..33ee6f65ccbd
--- /dev/null
+++ b/sci-biology/seaview/seaview-4.3.5.ebuild
@@ -0,0 +1,76 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit eutils multilib toolchain-funcs
+
+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"
+
+CDEPEND="
+	sys-libs/zlib
+	x11-libs/fltk:1
+	x11-libs/libX11
+	xft? (
+		x11-libs/libXft
+		x11-libs/fltk:1[xft] )"
+RDEPEND="${CDEPEND}
+	sci-biology/clustalw
+	|| ( sci-libs/libmuscle sci-biology/muscle )
+	sci-biology/phyml"
+DEPEND="${CDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}/${PN}"
+
+src_prepare() {
+	# respect CXXFLAGS (package uses them as CFLAGS)
+	sed \
+		-e "s:^CC.*:CC = $(tc-getCC):" \
+		-e "s:^CXX.*:CXX = $(tc-getCXX):" \
+		-e "s:\$(OPT):${CXXFLAGS}:" \
+		-e "s:^OPT:#OPT:" \
+		-e "s:^FLTK = .*$:FLTK = ${EPREFIX}/usr/include/fltk-1:" \
+		-e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \
+		-e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \
+		-e "s:^USE_XFT:#USE_XFT:" \
+		-e "s:^#HELPFILE:HELPFILE:" \
+		-e "s:/usr/share/doc/seaview/seaview.htm:${EPREFIX}/usr/share/seaview/seaview.htm:" \
+		-e "s:^#PHYMLNAME:PHYMLNAME:" \
+		-e 's:-lXinerama::g' \
+		-e 's:-lpng::g' \
+		-e 's:-ljpeg::g' \
+		-e 's:-lfontconfig::g' \
+		-i Makefile || die "sed failed while editing Makefile"
+
+	if use xft; then
+		sed \
+			-e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $($(tc-getPKG_CONFIG) --cflags xft):" \
+			-e "s:-lXft:$($(tc-getPKG_CONFIG) --libs xft):" \
+			-i Makefile || die "sed failed while editing Makefile to enable xft"
+	else
+		sed -i -e "s:-lXft::" Makefile || die
+	fi
+}
+
+src_install() {
+	dobin seaview
+
+	# /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
+
+	make_desktop_entry seaview Seaview
+
+	doman seaview.1
+}
diff --git a/sci-biology/seaview/seaview-4.5.4.ebuild b/sci-biology/seaview/seaview-4.5.4.ebuild
new file mode 100644
index 000000000000..33ee6f65ccbd
--- /dev/null
+++ b/sci-biology/seaview/seaview-4.5.4.ebuild
@@ -0,0 +1,76 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit eutils multilib toolchain-funcs
+
+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"
+
+CDEPEND="
+	sys-libs/zlib
+	x11-libs/fltk:1
+	x11-libs/libX11
+	xft? (
+		x11-libs/libXft
+		x11-libs/fltk:1[xft] )"
+RDEPEND="${CDEPEND}
+	sci-biology/clustalw
+	|| ( sci-libs/libmuscle sci-biology/muscle )
+	sci-biology/phyml"
+DEPEND="${CDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}/${PN}"
+
+src_prepare() {
+	# respect CXXFLAGS (package uses them as CFLAGS)
+	sed \
+		-e "s:^CC.*:CC = $(tc-getCC):" \
+		-e "s:^CXX.*:CXX = $(tc-getCXX):" \
+		-e "s:\$(OPT):${CXXFLAGS}:" \
+		-e "s:^OPT:#OPT:" \
+		-e "s:^FLTK = .*$:FLTK = ${EPREFIX}/usr/include/fltk-1:" \
+		-e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \
+		-e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \
+		-e "s:^USE_XFT:#USE_XFT:" \
+		-e "s:^#HELPFILE:HELPFILE:" \
+		-e "s:/usr/share/doc/seaview/seaview.htm:${EPREFIX}/usr/share/seaview/seaview.htm:" \
+		-e "s:^#PHYMLNAME:PHYMLNAME:" \
+		-e 's:-lXinerama::g' \
+		-e 's:-lpng::g' \
+		-e 's:-ljpeg::g' \
+		-e 's:-lfontconfig::g' \
+		-i Makefile || die "sed failed while editing Makefile"
+
+	if use xft; then
+		sed \
+			-e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $($(tc-getPKG_CONFIG) --cflags xft):" \
+			-e "s:-lXft:$($(tc-getPKG_CONFIG) --libs xft):" \
+			-i Makefile || die "sed failed while editing Makefile to enable xft"
+	else
+		sed -i -e "s:-lXft::" Makefile || die
+	fi
+}
+
+src_install() {
+	dobin seaview
+
+	# /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
+
+	make_desktop_entry seaview Seaview
+
+	doman seaview.1
+}
diff --git a/sci-biology/seaview/seaview-4.6.ebuild b/sci-biology/seaview/seaview-4.6.ebuild
new file mode 100644
index 000000000000..4ad8ad61b72b
--- /dev/null
+++ b/sci-biology/seaview/seaview-4.6.ebuild
@@ -0,0 +1,77 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit eutils toolchain-funcs
+
+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"
+
+RDEPEND="
+	sys-libs/zlib
+	x11-libs/fltk:1
+	x11-libs/libX11
+	xft? (
+		x11-libs/libXft
+		x11-libs/fltk:1[xft] )
+	sci-biology/clustalw:2
+	|| ( sci-libs/libmuscle sci-biology/muscle )
+	sci-biology/phyml"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}/${PN}"
+
+src_prepare() {
+	default
+
+	# respect CXXFLAGS (package uses them as CFLAGS)
+	sed \
+		-e "s:^CC.*:CC = $(tc-getCC):" \
+		-e "s:^CXX.*:CXX = $(tc-getCXX):" \
+		-e "s:\$(OPT):${CXXFLAGS}:" \
+		-e "s:^OPT:#OPT:" \
+		-e "s:^FLTK = .*$:FLTK = ${EPREFIX}/usr/include/fltk-1:" \
+		-e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \
+		-e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \
+		-e "s:^USE_XFT:#USE_XFT:" \
+		-e "s:^#HELPFILE:HELPFILE:" \
+		-e "s:/usr/share/doc/seaview/seaview.htm:${EPREFIX}/usr/share/seaview/seaview.htm:" \
+		-e "s:^#PHYMLNAME:PHYMLNAME:" \
+		-e 's:-lXinerama::g' \
+		-e 's:-lpng::g' \
+		-e 's:-ljpeg::g' \
+		-e 's:-lfontconfig::g' \
+		-i Makefile || die "sed failed while editing Makefile"
+
+	if use xft; then
+		sed \
+			-e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $($(tc-getPKG_CONFIG) --cflags xft):" \
+			-e "s:-lXft:$($(tc-getPKG_CONFIG) --libs xft):" \
+			-i Makefile || die "sed failed while editing Makefile to enable xft"
+	else
+		sed -i -e "s:-lXft::" Makefile || die
+	fi
+}
+
+src_install() {
+	dobin seaview
+
+	# /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
+
+	make_desktop_entry seaview Seaview
+
+	doman seaview.1
+}