Initial addition

(Portage version: 2.2_rc67/cvs/Linux x86_64)

4 files changed, 152 insertions, 0 deletions

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 <jlec@gentoo.org> +phaser-2.1.4.ebuild,
+  +files/phaser-2.1.4-chmod.patch, +metadata.xml:
+  Initial addition
+
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 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<pkgmetadata>
+	<herd>sci-chemistry</herd>
+<maintainer>
+  <email>jlec@gentoo.org</email>
+	<description>ccp4 maintainer</description>
+</maintainer>
+</pkgmetadata>
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
+}