From: Justin Lecher Date: Sat, 3 Jul 2010 13:32:41 +0000 (+0000) Subject: Initial addition X-Git-Url: http://git.tremily.us/gitweb.cgi?a=commitdiff_plain;h=e44eb0108002deb7690b9e0240235d7e0ae4e5ce;p=gentoo.git Initial addition Package-Manager: portage-2.2_rc67/cvs/Linux x86_64 --- diff --git a/sci-chemistry/phaser/ChangeLog b/sci-chemistry/phaser/ChangeLog new file mode 100644 index 000000000000..e0e3fbf871ed --- /dev/null +++ b/sci-chemistry/phaser/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-chemistry/phaser +# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/phaser/ChangeLog,v 1.1 2010/07/03 13:32:41 jlec Exp $ + +*phaser-2.1.4 (03 Jul 2010) + + 03 Jul 2010; Justin Lecher +phaser-2.1.4.ebuild, + +files/phaser-2.1.4-chmod.patch, +metadata.xml: + Initial addition + diff --git a/sci-chemistry/phaser/Manifest b/sci-chemistry/phaser/Manifest new file mode 100644 index 000000000000..103eb8c13dbf --- /dev/null +++ b/sci-chemistry/phaser/Manifest @@ -0,0 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +AUX phaser-2.1.4-chmod.patch 555 RMD160 97aac303973819050a02e7513f7d5b05edf0b4ce SHA1 6e3514e29e68f3e82797655edaeeb08e5d103dae SHA256 7dbdf50a096448283400e5026b5e3366420e7d124f8a4f85396604bb43d7a3be +DIST ccp4-6.1.13-phaser-cctbx-src.tar.gz 22021353 RMD160 7523142c284815d407da9ae99b8ca122f8bcb25c SHA1 4f56b3fd9b44eb4a88af9f00527a2739cb3c62a0 SHA256 e6c4365cb34da5ce2dd5f1e74b8927258064016194446163418c8a3139a4b804 +EBUILD phaser-2.1.4.ebuild 2842 RMD160 9fac6ff28f167e4030e07ccf5d757e0d07b06496 SHA1 21481f4386f80964dd24a50e7b47fd196091a0b4 SHA256 3d748afea18bf6a71bcb841e8ca1f8afc45964a8f570e53704cfe9ea8bb078a6 +MISC ChangeLog 379 RMD160 42b4dcd9999d720114cefe7b95a136dbc95bbc1b SHA1 34473d8829b678d2abfa6372168b2bd18fdd63b7 SHA256 47ea6906d510e3b42ed326e3afac0f34e1c3d560d3e8ad9812fa520ccadcb626 +MISC metadata.xml 200 RMD160 89d5a5da0eb89f1fcf71ccf61190c871f369f322 SHA1 859c9d3058407bbf3a2a8d468f73e2ce7debe539 SHA256 939542523093a72e36d31bcd538511217b8695021f9c3099c8ddb43132845e66 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.15 (GNU/Linux) + +iEYEARECAAYFAkwvO/4ACgkQgAnW8HDreRasXwCeMKMWIJNORghRN2ietaYMYgg5 +7nEAoJVHgzsY+icBbZxlPnsc6m60c7Q7 +=LcqX +-----END PGP SIGNATURE----- diff --git a/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch b/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch new file mode 100644 index 000000000000..5311cb332785 --- /dev/null +++ b/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch @@ -0,0 +1,13 @@ +diff --git a/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py b/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py +index 3b1bd3a..8939a74 100755 +--- a/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py ++++ b/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py +@@ -802,8 +802,6 @@ class environment: + else: + action = self.write_bin_sh_dispatcher + ext = "" +- try: os.chmod(source_file, 0755) +- except OSError: pass + target_file_ext = target_file + ext + remove_or_rename(target_file_ext) + try: action(source_file, target_file_ext) diff --git a/sci-chemistry/phaser/metadata.xml b/sci-chemistry/phaser/metadata.xml new file mode 100644 index 000000000000..c94b0217ca5e --- /dev/null +++ b/sci-chemistry/phaser/metadata.xml @@ -0,0 +1,8 @@ + + + sci-chemistry + + jlec@gentoo.org + ccp4 maintainer + + diff --git a/sci-chemistry/phaser/phaser-2.1.4.ebuild b/sci-chemistry/phaser/phaser-2.1.4.ebuild new file mode 100644 index 000000000000..8457c6c55b87 --- /dev/null +++ b/sci-chemistry/phaser/phaser-2.1.4.ebuild @@ -0,0 +1,121 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/phaser/phaser-2.1.4.ebuild,v 1.1 2010/07/03 13:32:41 jlec Exp $ + +EAPI="3" + +PYTHON_DEPEND="2" + +inherit base flag-o-matic python + +CCP4VER="6.1.13" + +DESCRIPTION="A program for phasing macromolecular crystal structures" +HOMEPAGE="http://www-structmed.cimr.cam.ac.uk/phaser" +SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/${CCP4VER}/ccp4-${CCP4VER}-${PN}-cctbx-src.tar.gz" + +LICENSE="|| ( phaser phaser-com ccp4 )" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="openmp" + +RDEPEND="" +DEPEND="${RDEPEND} + app-shells/tcsh" + +S="${WORKDIR}"/ccp4-${CCP4VER} + +PATCHES=( + "${FILESDIR}"/phaser-2.1.4-chmod.patch + "${FILESDIR}"/phaser-2.1.4-ldflags.patch + ) + +pkg_setup() { + python_set_active_version 2 +} + +src_prepare() { + base_src_prepare + + use openmp && append-flags -fopenmp + + for i in ${CXXFLAGS}; do + OPTS="${OPTS} \"${i}\"," + done + + OPTS=${OPTS%,} + + sed -i \ + -e "s:opts = \[.*\]$:opts = \[${OPTS}\]:g" \ + "${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die + + for i in ${LDFLAGS}; do + OPTSLD="${OPTSLD} \"${i}\"," + done + + sed -i \ + -e "s:env_etc.shlinkflags .* \"-shared\":env_etc.shlinkflags = \[ ${OPTSLD} \"-shared\"\]:g" \ + -e "s:\[\"-static:\[${OPTSLD} \"-static:g" \ + "${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die + +} + +src_configure() { + local compiler + local mtype + local mversion + local nproc + + # Valid compilers are win32_cl, sunos_CC, unix_gcc, unix_ecc, + # unix_icc, unix_icpc, tru64_cxx, hp_ux11_aCC, irix_CC, + # darwin_c++, darwin_gcc. The build systems seems to prepend + # unix_ all by itself. Can this be derived from $(tc-getCC)? + compiler=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)') + + # Breaks cross compilation. + mtype=$(src/${PN}/bin/machine_type) + mversion=$(src/${PN}/bin/machine_version) + + einfo "Creating build directory" + mkdir build + cd build + ln -sf "${S}/lib/cctbx/cctbx_sources/scons" scons + ln -sf "${S}/lib/cctbx/cctbx_sources/libtbx" libtbx + + einfo "Configuring phaser components" + $(PYTHON) "libtbx/configure.py" \ + --build=release \ + --compiler=${compiler} \ + --repository="${S}"/src/${PN}/source \ + --repository="${S}"/lib/cctbx/cctbx_sources \ + --static_libraries \ + ccp4io="${S}" \ + mmtbx \ + phaser || die "configure.py failed" +} + +src_compile() { + nproc=`echo "-j1 ${MAKEOPTS}" \ + | sed -e "s/.*\(-j\s*\|--jobs=\)\([0-9]\+\).*/\2/"` + + cd build + einfo "Setting up build environment" + source setpaths.sh + + einfo "Compiling phaser components" + libtbx.scons -j ${nproc} || die "libtbx.scons failed" +} + +src_install() { + dobin build/exe/phaser || die + + cat >> "${T}"/53${PN} <<- EOF + PHASER="${EPREFIX}/usr/bin" + PHASER_ENVIRONMENT="1" + PHASER_MTYPE="${mtype}" + PHASER_MVERSION="${mversion}" + PHASER_VERSION="${PV}" + EOF + + doenvd "${T}"/53${PN} || die +}