diff options
Diffstat (limited to 'sci-chemistry')
| -rw-r--r-- | sci-chemistry/refmac/ChangeLog | 10 | ||||
| -rw-r--r-- | sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild | 72 | ||||
| -rw-r--r-- | sci-chemistry/refmac/refmac-5.6.0102-r1.ebuild | 74 |
3 files changed, 155 insertions, 1 deletions
diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog index 4be8055aa360..b3b528407a98 100644 --- a/sci-chemistry/refmac/ChangeLog +++ b/sci-chemistry/refmac/ChangeLog @@ -1,6 +1,14 @@ # ChangeLog for sci-chemistry/refmac # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.41 2011/01/28 15:39:11 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.42 2011/01/31 21:14:39 dberkholz Exp $ + +*refmac-5.6.0102-r1 (31 Jan 2011) +*refmac-5.5.0110-r3 (31 Jan 2011) + + 31 Jan 2011; Donnie Berkholz <dberkholz@gentoo.org>; + +refmac-5.5.0110-r3.ebuild, +refmac-5.6.0102-r1.ebuild: + Fix for ARP/wARP. It looked for Refmac in a location where we didn't have it, + so make another symlink. *refmac-5.6.0102 (28 Jan 2011) diff --git a/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild b/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild new file mode 100644 index 000000000000..683dcf8cb2a7 --- /dev/null +++ b/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild,v 1.1 2011/01/31 21:14:39 dberkholz Exp $ + +EAPI="2" + +inherit base toolchain-funcs versionator + +DESCRIPTION="Macromolecular crystallographic refinement program" +HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac" +SRC_URI=" + ${HOMEPAGE}/data/refmac_stable/refmac_${PV}.tar.gz + test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )" + +SLOT="0" +LICENSE="ccp4" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + sci-chemistry/makecif + >=sci-libs/ccp4-libs-6.1.3-r7 + sci-libs/mmdb + <sci-libs/monomer-db-1 + virtual/blas + virtual/lapack" +DEPEND="${RDEPEND}" + +S="${WORKDIR}" + +PATCHES=( + "${FILESDIR}"/${PV}-allow-dynamic-linking.patch + ) + +src_prepare() { + base_src_prepare + use test && epatch "${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-test.log.patch +} + +src_compile() { + emake \ + FC=$(tc-getFC) \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + COPTIM="${CFLAGS}" \ + FOPTIM="${FFLAGS:- -O2}" \ + VERSION="" \ + XFFLAGS="-fno-second-underscore" \ + LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \ + LLIBLAPACK="$(pkg-config --libs lapack blas)" \ + ${PN} libcheck || die +} + +src_test() { + einfo "Starting tests ..." + source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh" + export PATH="${WORKDIR}/test-framework/scripts:${S}:${PATH}" + export CCP4_TEST="${WORKDIR}"/test-framework + export CCP4_SCR="${T}" + ln -sf refmac "${S}"/refmac5 + sed '/^ANISOU/d' -i ${CCP4_TEST}/data/pdb/1vr7.pdb + ccp4-run-thorough-tests -v test_refmac5 || die +} + +src_install() { + exeinto /usr/libexec/ccp4/bin/ + doexe ${PN} || die + dosym refmac /usr/libexec/ccp4/bin/refmac5 || die + dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN} || die + dosym refmac /usr/bin/refmac5 || die + dodoc refmac_keywords.pdf bugs_and_features.pdf || die +} diff --git a/sci-chemistry/refmac/refmac-5.6.0102-r1.ebuild b/sci-chemistry/refmac/refmac-5.6.0102-r1.ebuild new file mode 100644 index 000000000000..8415ebd6e428 --- /dev/null +++ b/sci-chemistry/refmac/refmac-5.6.0102-r1.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0102-r1.ebuild,v 1.1 2011/01/31 21:14:39 dberkholz Exp $ + +EAPI="2" + +inherit base toolchain-funcs versionator + +MY_PV="$(get_version_component_range 1-2)_source_v${PV}" + +DESCRIPTION="Macromolecular crystallographic refinement program" +HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac" +SRC_URI=" + ${HOMEPAGE}/data/refmac_experimental/${PN}${MY_PV}.tar.gz + test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )" + +SLOT="0" +LICENSE="ccp4" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + >=sci-libs/ccp4-libs-6.1.3-r7 + sci-libs/mmdb + >sci-libs/monomer-db-1 + virtual/blas + virtual/lapack" +DEPEND="${RDEPEND}" + +S="${WORKDIR}" + +PATCHES=( + "${FILESDIR}"/${PV}-allow-dynamic-linking.patch + ) + +src_prepare() { + base_src_prepare + use test && epatch "${FILESDIR}"/5.5-test.log.patch +} + +src_compile() { + emake \ + FC=$(tc-getFC) \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + COPTIM="${CFLAGS}" \ + FOPTIM="${FFLAGS:- -O2}" \ + VERSION="" \ + XFFLAGS="-fno-second-underscore" \ + LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \ + LLIBLAPACK="$(pkg-config --libs lapack blas)" \ + || die +} + +src_test() { + einfo "Starting tests ..." + source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh" + export PATH="${WORKDIR}/test-framework/scripts:${S}:${PATH}" + export CCP4_TEST="${WORKDIR}"/test-framework + export CCP4_SCR="${T}" + ln -sf refmac "${S}"/refmac5 + sed '/^ANISOU/d' -i ${CCP4_TEST}/data/pdb/1vr7.pdb + ccp4-run-thorough-tests -v test_refmac5 || die +} + +src_install() { + for i in refmac libcheck FreeTwin header2matr; do + exeinto /usr/libexec/ccp4/bin/ + doexe ${i} || die + dosym ../libexec/ccp4/bin/${i} /usr/bin/${i} + done + dosym refmac /usr/bin/refmac5 || die + dosym refmac /usr/libexec/ccp4/bin/refmac5 || die +} |