From 71c06bcd5e268b61f523b446939643321c9fa120 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Sun, 28 Mar 2010 13:37:10 +0000 Subject: New ebuild #309105 (Portage version: 2.2_rc67/cvs/Linux x86_64) --- sci-chemistry/balbes/ChangeLog | 11 +++ sci-chemistry/balbes/balbes-1.0.0_p100317.ebuild | 63 +++++++++++++++ .../balbes/files/1.0.0_p100317-ldflags.patch | 91 ++++++++++++++++++++++ sci-chemistry/balbes/metadata.xml | 17 ++++ 4 files changed, 182 insertions(+) create mode 100644 sci-chemistry/balbes/ChangeLog create mode 100644 sci-chemistry/balbes/balbes-1.0.0_p100317.ebuild create mode 100644 sci-chemistry/balbes/files/1.0.0_p100317-ldflags.patch create mode 100644 sci-chemistry/balbes/metadata.xml (limited to 'sci-chemistry/balbes') diff --git a/sci-chemistry/balbes/ChangeLog b/sci-chemistry/balbes/ChangeLog new file mode 100644 index 000000000000..e55d12500d01 --- /dev/null +++ b/sci-chemistry/balbes/ChangeLog @@ -0,0 +1,11 @@ +# ChangeLog for sci-chemistry/balbes +# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/balbes/ChangeLog,v 1.1 2010/03/28 13:37:10 jlec Exp $ + +*balbes-1.0.0_p100317 (28 Mar 2010) + + 28 Mar 2010; Justin Lecher (jlec) + +files/1.0.0_p100317-ldflags.patch, +balbes-1.0.0_p100317.ebuild, + +metadata.xml: + New ebuild #309105 + diff --git a/sci-chemistry/balbes/balbes-1.0.0_p100317.ebuild b/sci-chemistry/balbes/balbes-1.0.0_p100317.ebuild new file mode 100644 index 000000000000..2af860d6906c --- /dev/null +++ b/sci-chemistry/balbes/balbes-1.0.0_p100317.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/balbes/balbes-1.0.0_p100317.ebuild,v 1.1 2010/03/28 13:37:10 jlec Exp $ + +EAPI="3" + +FORTRAN="gfortran ifort" +CCP4VER="6.1.3" +PYTHON_DEPEND="2" + +inherit eutils fortran python + +DESCRIPTION="Automated molecular replacement (MR) pipeline" +HOMEPAGE="http://www.ysbl.york.ac.uk/~fei/balbes/index.html" +SRC_URI=" + mirror://gentoo/${P}.tar.gz + ftp://ftp.ccp4.ac.uk/ccp4/${CCP4VER}/ccp4-${CCP4VER}-core-src.tar.gz" + +SLOT="0" +KEYWORDS="~amd64 ~x86" +LICENSE="ccp4" +IUSE="" + +COMMON_DEPEND="sci-libs/ccp4-libs" +RDEPEND=" + ${COMMON_DEPEND} + ~sci-libs/balbes-db-${CCP4VER} + !<=sci-chemistry/ccp4-apps-6.1.3-r1" +DEPEND="${COMMON_DEPEND}" + +S="${WORKDIR}"/src + +src_unpack() { + unpack ${P}.tar.gz + tar xvzf "${DISTDIR}"/ccp4-${CCP4VER}-core-src.tar.gz ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py/balbes + python_convert_shebangs 2 "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py/balbes +} + +src_prepare() { + mkdir "${WORKDIR}"/bin || die + epatch "${FILESDIR}"/${PV}-ldflags.patch +} + +src_compile() { + # incomplete targets: + # dimer_search_db domain_search_db domain align3 + targets="search_db get_structure_db manage_db search_dm dom2ch + save_si get_pdb_list_db update_db + update_dom_db bl2mtz check_file_db fobs2cif sol_check + get_trns p2s check_cell alt_sg + align cell_list create_bins + get_pdb_list_db get_ch get_nm get_mod" + emake \ + BLANC_FORT="${FORTRANC} ${FFLAGS}" \ + ${targets} || die +} + +src_install() { + dobin \ + "${WORKDIR}"/bin/* \ + "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py/balbes \ + || die +} diff --git a/sci-chemistry/balbes/files/1.0.0_p100317-ldflags.patch b/sci-chemistry/balbes/files/1.0.0_p100317-ldflags.patch new file mode 100644 index 000000000000..e1d09b7f3c33 --- /dev/null +++ b/sci-chemistry/balbes/files/1.0.0_p100317-ldflags.patch @@ -0,0 +1,91 @@ +diff --git a/makefile b/makefile +index baaceb5..139037e 100755 +--- a/makefile ++++ b/makefile +@@ -201,58 +201,58 @@ save_seg_id.o: save_seg_id.f + $(BLANC_FORT) -c save_seg_id.f + + sdb_l: $(OBJDB_S) +- $(BLANC_FORT) -o ../bin/search_DB $(OBJDB_S) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/search_DB $(OBJDB_S) + tdb_l: $(OBJDB_T) +- $(BLANC_FORT) -o ../bin/get_structure_DB $(OBJDB_T) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_structure_DB $(OBJDB_T) + mdb_l: $(OBJDB_M) +- $(BLANC_FORT) -o ../bin/manage_DB $(OBJDB_M) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/manage_DB $(OBJDB_M) + mdm_l: $(OBJDB_MD) +- $(BLANC_FORT) -o ../bin/search_DOM $(OBJDB_MD) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/search_DOM $(OBJDB_MD) + d2c_l: $(OBJDB_A) +- $(BLANC_FORT) -o ../bin/domain2chain $(OBJDB_A) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/domain2chain $(OBJDB_A) + upd_l: $(OBJDB_U) +- $(BLANC_FORT) -o ../bin/update_DB $(OBJDB_U) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/update_DB $(OBJDB_U) + dom_l: $(OBJDB_V) +- $(BLANC_FORT) -o ../bin/update_domain_DB $(OBJDB_V) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/update_domain_DB $(OBJDB_V) + ddb_l: $(OBJDB_D) +- $(BLANC_FORT) -o ../bin/dimer_search $(OBJDB_D) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/dimer_search $(OBJDB_D) + dmdb_l: $(OBJDB_N) +- $(BLANC_FORT) -o ../bin/domain_search $(OBJDB_N) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/domain_search $(OBJDB_N) + gdb_l: $(OBJDB_G) +- $(BLANC_FORT) -o ../bin/get_pdb_list $(OBJDB_G) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_pdb_list $(OBJDB_G) + b2m_l: blanc2mtz.o libutils.o +- $(BLANC_FORT) -o ../bin/blanc2mtz blanc2mtz.o libutils.o $(CLIB)/libccp4f.a $(CLIB)/libccp4c.a ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/blanc2mtz blanc2mtz.o libutils.o -lccp4f -lccp4c + f2c_l: f2cif.o libutils.o +- $(BLANC_FORT) -o ../bin/f2cif f2cif.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/f2cif f2cif.o libutils.o + chf_l: check_file_DB.o libutils.o +- $(BLANC_FORT) -o ../bin/check_file_DB check_file_DB.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/check_file_DB check_file_DB.o libutils.o + chc_l: check_cell_sg.o libutils.o +- $(BLANC_FORT) -o ../bin/check_cell_sg check_cell_sg.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/check_cell_sg check_cell_sg.o libutils.o + asl_l: alt_sg_list.o libutils.o +- $(BLANC_FORT) -o ../bin/alt_sg_list alt_sg_list.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/alt_sg_list alt_sg_list.o libutils.o + sc_l: $(OBJDB_C) +- $(BLANC_FORT) -o ../bin/solution_check $(OBJDB_C) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/solution_check $(OBJDB_C) + gt_l: $(OBJDB_R) +- $(BLANC_FORT) -o ../bin/get_trans $(OBJDB_R) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_trans $(OBJDB_R) + dmn_l: domain.o libutils.o +- $(BLANC_FORT) -o ../bin/domain domain.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/domain domain.o libutils.o + pack: pdb_pack.o libutils.o +- $(BLANC_FORT) -o ../bin/pdb_pack pdb_pack.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/pdb_pack pdb_pack.o libutils.o + p2s_l: $(OBJDB_P) +- $(BLANC_FORT) -o ../bin/pdb2s $(OBJDB_P) ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/pdb2s $(OBJDB_P) + aln_l: align_DB.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/align_DB align_DB.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/align_DB align_DB.o DB_subr.o libutils.o + aln3_l: align_DB_new.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/align_DB_new align_DB_new.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/align_DB_new align_DB_new.o DB_subr.o libutils.o + cell_l: create_cell_list.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/create_cell_list create_cell_list.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/create_cell_list create_cell_list.o DB_subr.o libutils.o + getch_l: get_chain.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/get_chain get_chain.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_chain get_chain.o DB_subr.o libutils.o + getnmr_l: get_nmr.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/get_nmr get_nmr.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_nmr get_nmr.o DB_subr.o libutils.o + getmod_l: get_model.o libutils.o +- $(BLANC_FORT) -o ../bin/get_model get_model.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_model get_model.o libutils.o + crb_l: create_binaries.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/create_binaries create_binaries.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/create_binaries create_binaries.o DB_subr.o libutils.o + save_si_l: save_seg_id.o DB_subr.o libutils.o +- $(BLANC_FORT) -o ../bin/save_seg_id save_seg_id.o DB_subr.o libutils.o ++ $(BLANC_FORT) ${LDFLAGS} -o ../bin/save_seg_id save_seg_id.o DB_subr.o libutils.o diff --git a/sci-chemistry/balbes/metadata.xml b/sci-chemistry/balbes/metadata.xml new file mode 100644 index 000000000000..e1c959f9fd3a --- /dev/null +++ b/sci-chemistry/balbes/metadata.xml @@ -0,0 +1,17 @@ + + + sci-chemistry + + jlec@gentoo.org + + + BALBES is a system for solving protein structures using x-ray + crystalographic data. Molecular Replacement(MR) is its core + scientific method. BALBES aims to integrate all components, + necessary for finding a solution structure by MR, into one system. + It consists of a database, scientific programs and a python + pipeline. The system is automated so that it needs no user's + intervention when running complicated combination of jobs such + as model searching, molecular replacement and refinement. + + -- cgit v1.2.3-65-gdbad