proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

5 files changed, 216 insertions, 0 deletions

diff --git a/sci-chemistry/theseus/Manifest b/sci-chemistry/theseus/Manifest
new file mode 100644
index 000000000000..9708bc4e5cf6
--- /dev/null
+++ b/sci-chemistry/theseus/Manifest
@@ -0,0 +1,3 @@
+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
diff --git a/sci-chemistry/theseus/metadata.xml b/sci-chemistry/theseus/metadata.xml
new file mode 100644
index 000000000000..ae9ec7c5f6a4
--- /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>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>jlec@gentoo.org</email>
+  </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..56d58ae9fb9e
--- /dev/null
+++ b/sci-chemistry/theseus/theseus-2.0.6.ebuild
@@ -0,0 +1,65 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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..ed80be95d26b
--- /dev/null
+++ b/sci-chemistry/theseus/theseus-3.0.0.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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..ed80be95d26b
--- /dev/null
+++ b/sci-chemistry/theseus/theseus-3.3.0.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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
+}