reinit the tree, so we can have metadata

5 files changed, 219 insertions, 0 deletions

diff --git a/sci-chemistry/theseus/Manifest b/sci-chemistry/theseus/Manifest
new file mode 100644
index 000000000000..d3a37f389528
--- /dev/null
+++ b/sci-chemistry/theseus/Manifest
@@ -0,0 +1,9 @@
+DIST theseus_2.0.6.tar.gz 1257560 SHA256 f63f4d5fd9ce9d30048312e31807a1a413b433e2bbcfd0cefb3703f455551c23 SHA512 70604c468eb841b92e77a3e91cd57120b96c171512fb1cc31a407b7c4816150dfa31ec123fb9568a842e623f3252c60df0dc53d40fa2a4aece6e3c77039f4696 WHIRLPOOL 01c73e5bec0f4e9a98cd926a15f3213f30d20db10a500e88cfa54e31b92324d3fb741899c30c5c45e8d5a2d31eb68e742113b29a077f70430cf7acda9c02bc54
+DIST theseus_3.0.0.tar.gz 1213574 SHA256 4e474efabf1cfc9a48e96e86ac9e5b0f8035b57677017542e66478759bdc7866 SHA512 251e6273624126406609691e1205d9693c18dcbc8c81e10c77101ac4a1b6bdffcb56a47fd5fdc7ed6ed4fa107c2ed26b03a1780f951f9cc69a25c0722996e7b2 WHIRLPOOL 5a15c0f5270411114ebbca4fc9cad1e4db0449d1e6d8d1693f1e58d6a54f61b401cc6a2df2539d2ca34dd4dc52a09e1c45c0af8b80eb5c8916d8f168bf536ad3
+DIST theseus_3.3.0.tar.gz 22548124 SHA256 3cfd4f906717f9cb8e77f689fc97059b32df355c0696077034ea99a485e3f2fe SHA512 1fba3e8019a40214defdae13d4721d170ee698337d8efd4e872af22f8ab3cb1fdd52fa9f19a858ee51bc98150692af0c6016033feb0d76f29acaf7fffbb430e2 WHIRLPOOL c1baf4daea1e2a0c78b73d8d91ff735aa9bb82bd6edf533aab0f9d20a9e82b7f61fdf8c4b09c92b58447f686e954b6eaf7f02d7c9e5304c8d52b4c09b6d323af
+EBUILD theseus-2.0.6.ebuild 1449 SHA256 6a73f8b5cb38a26472f5b4588c9c3c507d13d86ec879b7db7c37c1be503d3f98 SHA512 35fce318510a70da251151061013e52dc0c16b0bdb8aed4ecd1dca2deb53a662290d4700a5df3bfa755c785e8b481cdd7f83a2263a3823823261044079e69a26 WHIRLPOOL 544a8d7f6b18d8da80f57c04a20d24a8734a45b9916e8f5fb330a5263416f79dd56413be851c12e584ebb14fed546c48cbda06016efbc593f59c96c2b67871cc
+EBUILD theseus-3.0.0.ebuild 1503 SHA256 aeacc8a235a96451545179aa398d6501cfd03a5c60800b2f5cce4a46e9a4dc88 SHA512 cb2824c8e5fff646ffd6523cb47385143e366ad19e92685b411d4f3ac8827d16260da048e29666ce3aa7a328d3ee136ef309e5443e252dac1862f987bac74bda WHIRLPOOL 141f3375a419c25fe84c1200c78f9a10d7cefca0fccc78bc7e575d514802f6569315826cec3d028b9a3c0cf14712272b05ad05c53e228f554a2683c04f4ebe6f
+EBUILD theseus-3.3.0.ebuild 1503 SHA256 aeacc8a235a96451545179aa398d6501cfd03a5c60800b2f5cce4a46e9a4dc88 SHA512 cb2824c8e5fff646ffd6523cb47385143e366ad19e92685b411d4f3ac8827d16260da048e29666ce3aa7a328d3ee136ef309e5443e252dac1862f987bac74bda WHIRLPOOL 141f3375a419c25fe84c1200c78f9a10d7cefca0fccc78bc7e575d514802f6569315826cec3d028b9a3c0cf14712272b05ad05c53e228f554a2683c04f4ebe6f
+MISC ChangeLog 2676 SHA256 5de717cb694416f8de834b556fbf92c448a8f206a3ad1a04f879e3f696392efd SHA512 829d5fd143fd890f84cdc76477e5751b439f882cee5f777405d5c48cac44db1a2bbf0b244a68dc510ba55522a3a4de2794bf926b930c545c759ae6423735e580 WHIRLPOOL e0af631987b9e06bf56648f09348d5c8f7164a453858f34f0215b4e85509d2f2dd631f913def416358bfabb67eac6c70fe6ea0637756374bd409938ebaedd3d2
+MISC ChangeLog-2015 1688 SHA256 37b31fd290437d848279ffd703a98710a93c0f5e2df6d8821e619542cfcf93bd SHA512 776e93efc0052180316f4c234a13f29b498c83797c3c1ae5040861c3990494baa04be52881a952b2a8514068a9ccb9b993951074a6b0a2e11c9283b301d54a62 WHIRLPOOL 6ada67fe0de5ff0cb7cb8eb86fa01ab7ddc84cbd44212a39199191f459b7b7f596a6885acdfc0d55fdc8412b6b5175bfc9bc2cd607a32248e72482950b0501ed
+MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269
diff --git a/sci-chemistry/theseus/metadata.xml b/sci-chemistry/theseus/metadata.xml
new file mode 100644
index 000000000000..8937bad0b175
--- /dev/null
+++ b/sci-chemistry/theseus/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-chemistry@gentoo.org</email>
+    <name>Gentoo Chemistry Project</name>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/theseus/theseus-2.0.6.ebuild b/sci-chemistry/theseus/theseus-2.0.6.ebuild
new file mode 100644
index 000000000000..7c3f3783602c
--- /dev/null
+++ b/sci-chemistry/theseus/theseus-2.0.6.ebuild
@@ -0,0 +1,64 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit multilib toolchain-funcs
+
+DESCRIPTION="Maximum likelihood superpositioning and analysis of macromolecular structures"
+HOMEPAGE="http://www.theseus3d.org/"
+SRC_URI="http://www.theseus3d.org/src/${PN}_${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+RDEPEND="
+	sci-libs/gsl
+	|| (
+		sci-biology/muscle
+		sci-biology/probcons
+		sci-biology/mafft
+		sci-biology/t-coffee
+		sci-biology/kalign
+		sci-biology/clustalw:2
+		)"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}"/${PN}_src/
+
+src_prepare() {
+	cat >> make.inc <<- EOF
+	ARCH = $(tc-getAR)
+	ARCHFLAGS = -rvs
+	RANLIB = $(tc-getRANLIB)
+	LOCALLIBDIR = "${EPREFIX}/usr/$(get_libdir)
+	SYSLIBS = $(pkg-config --libs gsl) -lpthread
+	LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus
+	LIBDIR = -L./lib
+	INSTALLDIR = "${ED}"/usr/bin
+	OPT =
+	WARN =
+	CFLAGS = ${CFLAGS} \$(WARN)
+	CC = $(tc-getCC)
+	EOF
+
+	sed \
+		-e 's|theseus:|theseus: libs|g' \
+		-e '/-o theseus/s:$(CC):$(CC) ${LDFLAGS}:g' \
+		-i Makefile || die
+
+	sed \
+		-e 's:/usr/bin/sed:sed:g' \
+		-e "s:/usr/local/bin/:/usr/bin/:g" \
+		-e "s:/usr/bin/:${EPREFIX}/usr/bin/:g" \
+		-i theseus_align || die
+}
+
+src_install() {
+	dobin theseus theseus_align
+	dodoc theseus_man.pdf README AUTHORS
+	use examples && insinto /usr/share/${PN} && doins -r examples
+}
diff --git a/sci-chemistry/theseus/theseus-3.0.0.ebuild b/sci-chemistry/theseus/theseus-3.0.0.ebuild
new file mode 100644
index 000000000000..9eebccc8bc96
--- /dev/null
+++ b/sci-chemistry/theseus/theseus-3.0.0.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit multilib toolchain-funcs
+
+DESCRIPTION="Maximum likelihood superpositioning and analysis of macromolecular structures"
+HOMEPAGE="http://www.theseus3d.org/"
+SRC_URI="http://www.theseus3d.org/src/${PN}_${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+RDEPEND="
+	sci-libs/gsl
+	|| (
+		sci-biology/muscle
+		sci-biology/probcons
+		sci-biology/mafft
+		sci-biology/t-coffee
+		sci-biology/kalign
+		sci-biology/clustalw:2
+		)"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}"/${PN}_src/
+
+src_prepare() {
+	cat >> make.inc <<- EOF
+	ARCH = $(tc-getAR)
+	ARCHFLAGS = -rvs
+	RANLIB = $(tc-getRANLIB)
+	LOCALLIBDIR = "${EPREFIX}/usr/$(get_libdir)
+	SYSLIBS = $(pkg-config --libs gsl) -lpthread
+	LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus
+	LIBDIR = -L./lib
+	INSTALLDIR = "${ED}"/usr/bin
+	OPT =
+	WARN =
+	CFLAGS = ${CFLAGS} -std=c11 \$(WARN)
+	CC = $(tc-getCC)
+	EOF
+
+	sed \
+		-e 's|theseus:|theseus: libs|g' \
+		-e '/-o theseus/s:$(CC):$(CC) ${LDFLAGS}:g' \
+		-i Makefile || die
+
+	sed \
+		-e 's:/usr/bin/sed:sed:g' \
+		-e "s:/usr/local/bin/:/usr/bin/:g" \
+		-e "s:/usr/bin/:${EPREFIX}/usr/bin/:g" \
+		-i theseus_align || die
+}
+
+src_compile () {
+	emake ltheseus
+	default
+}
+
+src_install() {
+	dobin theseus theseus_align
+	dodoc theseus_man.pdf README AUTHORS
+	use examples && insinto /usr/share/${PN} && doins -r examples
+}
diff --git a/sci-chemistry/theseus/theseus-3.3.0.ebuild b/sci-chemistry/theseus/theseus-3.3.0.ebuild
new file mode 100644
index 000000000000..9eebccc8bc96
--- /dev/null
+++ b/sci-chemistry/theseus/theseus-3.3.0.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit multilib toolchain-funcs
+
+DESCRIPTION="Maximum likelihood superpositioning and analysis of macromolecular structures"
+HOMEPAGE="http://www.theseus3d.org/"
+SRC_URI="http://www.theseus3d.org/src/${PN}_${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+RDEPEND="
+	sci-libs/gsl
+	|| (
+		sci-biology/muscle
+		sci-biology/probcons
+		sci-biology/mafft
+		sci-biology/t-coffee
+		sci-biology/kalign
+		sci-biology/clustalw:2
+		)"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}"/${PN}_src/
+
+src_prepare() {
+	cat >> make.inc <<- EOF
+	ARCH = $(tc-getAR)
+	ARCHFLAGS = -rvs
+	RANLIB = $(tc-getRANLIB)
+	LOCALLIBDIR = "${EPREFIX}/usr/$(get_libdir)
+	SYSLIBS = $(pkg-config --libs gsl) -lpthread
+	LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus
+	LIBDIR = -L./lib
+	INSTALLDIR = "${ED}"/usr/bin
+	OPT =
+	WARN =
+	CFLAGS = ${CFLAGS} -std=c11 \$(WARN)
+	CC = $(tc-getCC)
+	EOF
+
+	sed \
+		-e 's|theseus:|theseus: libs|g' \
+		-e '/-o theseus/s:$(CC):$(CC) ${LDFLAGS}:g' \
+		-i Makefile || die
+
+	sed \
+		-e 's:/usr/bin/sed:sed:g' \
+		-e "s:/usr/local/bin/:/usr/bin/:g" \
+		-e "s:/usr/bin/:${EPREFIX}/usr/bin/:g" \
+		-i theseus_align || die
+}
+
+src_compile () {
+	emake ltheseus
+	default
+}
+
+src_install() {
+	dobin theseus theseus_align
+	dodoc theseus_man.pdf README AUTHORS
+	use examples && insinto /usr/share/${PN} && doins -r examples
+}