From 97ca5ad9e5cff6dd9521f95ba14c3f01e80324f1 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Sun, 28 Mar 2010 13:37:10 +0000 Subject: [PATCH] New ebuild #309105 Package-Manager: portage-2.2_rc67/cvs/Linux x86_64 --- sci-chemistry/balbes/ChangeLog | 11 +++ sci-chemistry/balbes/Manifest | 16 ++++ .../balbes/balbes-1.0.0_p100317.ebuild | 63 +++++++++++++ .../balbes/files/1.0.0_p100317-ldflags.patch | 91 +++++++++++++++++++ sci-chemistry/balbes/metadata.xml | 17 ++++ sci-chemistry/ccp4/Manifest | 12 +-- 6 files changed, 204 insertions(+), 6 deletions(-) create mode 100644 sci-chemistry/balbes/ChangeLog create mode 100644 sci-chemistry/balbes/Manifest 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 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/Manifest b/sci-chemistry/balbes/Manifest new file mode 100644 index 000000000000..c371dd763cba --- /dev/null +++ b/sci-chemistry/balbes/Manifest @@ -0,0 +1,16 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +AUX 1.0.0_p100317-ldflags.patch 4625 RMD160 4fbb03a04e537d6f718fce4ca071e690df86aead SHA1 6edda34cad028233d0aadd57c4e174e51846a88c SHA256 5a7381573dbb548444f706c6b647e71a85728c5d40e03210a659d3abe90705b4 +DIST balbes-1.0.0_p100317.tar.gz 506464 RMD160 5fbb018b33d539734b5421951178c62847f58acf SHA1 a6907d1762c12c63f71bfb9fbb9d601d4271cda6 SHA256 c5bf6c2086e1a3d7d380e5501c0cffdb91cbf77c74d2951dd345273f21921d0c +DIST ccp4-6.1.3-core-src.tar.gz 242134076 RMD160 e9b7deb0766fb95d5e8946881f20e086f0896fe9 SHA1 ee5ada892694db5dc9b2d7d2330b4ac694f56580 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 +EBUILD balbes-1.0.0_p100317.ebuild 1697 RMD160 ecb66d464872e3570e2ee168b222ded556c68311 SHA1 2613061764bbcd70eaf6f1740e5e5275e5802037 SHA256 26949c27a53bace850f3017042aa30dc17238ddd003579bdf4a9d29ea1ffbffa +MISC ChangeLog 409 RMD160 d7c3892479cd5965cce61db936029b915e937ffe SHA1 5e272b9337c321b0a8eae8df2aa4ceb9fd8ec6a8 SHA256 925589d5ad19a23c1d2867d6fbfbf8096448ebb9b55c161d536ce6a8bf5c3735 +MISC metadata.xml 699 RMD160 964f68eb52b2551c0632c527b35db898b874c5dd SHA1 341a49a79324f693a523d85647bf7b44a6e24908 SHA256 0b4c1aed85a6a421f6e2ec9e74213c2461c47286a61858001f8779b1803698d6 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.14 (GNU/Linux) + +iEYEARECAAYFAkuvW4wACgkQgAnW8HDreRZiZQCfdtmwgeyt0GC78xzyAc6r9nP3 +4dkAoKFGfLmEJntPsWrEpigTpW5HFd41 +=gmLW +-----END PGP SIGNATURE----- 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. + + diff --git a/sci-chemistry/ccp4/Manifest b/sci-chemistry/ccp4/Manifest index 78614c025f55..c9c3361cfd05 100644 --- a/sci-chemistry/ccp4/Manifest +++ b/sci-chemistry/ccp4/Manifest @@ -43,13 +43,13 @@ DIST util_windows.tcl-r1.27-r1.27.2.1.diff 1486 RMD160 06b5598bcff7da11e19ec62c7 EBUILD ccp4-6.0.1-r1.ebuild 13681 RMD160 881038127962bb7aea4f9f77b4cc5b8c170dd688 SHA1 34d43786b53b4adfeec8740036cd2a9081823452 SHA256 bfda422f6d798d29c22faf86b789e4ac5db9799508d027e3428a8f264d286fc7 EBUILD ccp4-6.0.2-r1.ebuild 14094 RMD160 e273884aea608217207b0c8751fce978c67a53e7 SHA1 7d9569120787984943be86b9e0e838a43cbb5b29 SHA256 dbd1c61f294ce3ed091809dc9952f6d027dd01c6b7fd9cb71f3046264ebcb02a EBUILD ccp4-6.0.2.ebuild 13248 RMD160 747c3e19277ef49aeda2d42cd8a93597a545775f SHA1 ef54e5d59b6a29ac6d0b06f23e47e274f2c6925b SHA256 f46b1fc972615e04d4f643f33b8b3f5a1df4c19217e221afa621cce6918cb17f -EBUILD ccp4-6.1.3.ebuild 869 RMD160 7dcd5f3a6ee751e79387f6322cd43ec10b54a132 SHA1 edec763d4ed4653e030db809d1c0ffe238249e4e SHA256 7845d2ca9f457f04899a1866218c24fb1da6369f5cfc51747de9895ee79a876e -MISC ChangeLog 4266 RMD160 20392a068b174da7a262f4d3d17bde8c48559aea SHA1 6c492558dde8de0f81aaed2976b0a8727752cf1d SHA256 871a92f3db090cb7ae2c7d618378b95951e46c4d89e2edef281668c6a444e1d7 -MISC metadata.xml 324 RMD160 d3c6fca01ee5c08313bc5e2de49856e76e5543d0 SHA1 99ee02f2d21086d573da8a48ab788f1e8d5e1f25 SHA256 64a4d9df6a76392c7cb32662feb797f0edc8526b119011641169d4611e84333e +EBUILD ccp4-6.1.3.ebuild 858 RMD160 2d7b43dce48ae070e7f297f4dd93e063e69fbaa3 SHA1 069271a426ae6a755a075c46f295cab938eded0c SHA256 8a50241824d62ee37ec3aa3938b8a984289e3c795cd55b9fac13d3ee4bb7ff26 +MISC ChangeLog 4431 RMD160 fd57504cc529f827b8bc406169ba57fe167a10c3 SHA1 0d5a6111c39d676663614edc174bcb090396afcf SHA256 75f5e64fbc8be8e01acc6f1f40dbc3f12726bc033498c70c65d172874f04b9d1 +MISC metadata.xml 311 RMD160 7773ed578c7688537f2cf40b5417f9712fe84d8c SHA1 cd3e212d34f7c968d06bab6a2bc64e223b232b3e SHA256 1c5a8d16813aba13725a331bb6d0ed0d2a3bc4d0942775ceced4dc0a7fe4b653 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.14 (GNU/Linux) -iEYEARECAAYFAktulW4ACgkQgAnW8HDreRb62ACgqvLey5vbj/bP22KCybLEL+Mh -7D0AoK4bVJgTPIRppmaMZg5faebl+vkR -=jX2J +iEYEARECAAYFAkuvXKUACgkQgAnW8HDreRbvGACgtmWVwogfGpUuNaA1mropdfXW +gOgAoKVN1Vp1Mm0C1dfYB7WoSEywEyj3 +=i0d+ -----END PGP SIGNATURE----- -- 2.26.2