From 56bd759df1d0c750a065b8c845e93d5dfa6b549d Mon Sep 17 00:00:00 2001 From: "Robin H. Johnson" Date: Sat, 8 Aug 2015 13:49:04 -0700 Subject: proj/gentoo: Initial commit MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 X-Thanks: Alec Warner - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring - wrote much python to improve cvs2svn X-Thanks: Rich Freeman - validation scripts X-Thanks: Patrick Lauer - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed --- sci-chemistry/theseus/Manifest | 3 ++ sci-chemistry/theseus/metadata.xml | 8 ++++ sci-chemistry/theseus/theseus-2.0.6.ebuild | 65 +++++++++++++++++++++++++++ sci-chemistry/theseus/theseus-3.0.0.ebuild | 70 ++++++++++++++++++++++++++++++ sci-chemistry/theseus/theseus-3.3.0.ebuild | 70 ++++++++++++++++++++++++++++++ 5 files changed, 216 insertions(+) create mode 100644 sci-chemistry/theseus/Manifest create mode 100644 sci-chemistry/theseus/metadata.xml create mode 100644 sci-chemistry/theseus/theseus-2.0.6.ebuild create mode 100644 sci-chemistry/theseus/theseus-3.0.0.ebuild create mode 100644 sci-chemistry/theseus/theseus-3.3.0.ebuild (limited to 'sci-chemistry/theseus') 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 @@ + + + + sci-chemistry + + jlec@gentoo.org + + 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 +} -- cgit v1.2.3-65-gdbad