New ebuild #309105

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

diff --git a/sci-chemistry/balbes/ChangeLog b/sci-chemistry/balbes/ChangeLog
new file mode 100644 (file)
index 0000000..e55d125
--- /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) <jlec@gentoo.org>
+  +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 (file)
index 0000000..c371dd7
--- /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)
+
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+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 (file)
index 0000000..2af860d
--- /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 (file)
index 0000000..e1d09b7
--- /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 (file)
index 0000000..e1c959f
--- /dev/null
+++ b/sci-chemistry/balbes/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<pkgmetadata>
+       <herd>sci-chemistry</herd>
+<maintainer>
+  <email>jlec@gentoo.org</email>
+</maintainer>
+<longdescription>
+       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.
+</longdescription>
+</pkgmetadata>

diff --git a/sci-chemistry/ccp4/Manifest b/sci-chemistry/ccp4/Manifest
index 78614c025f55e47d89b1332a966b91c4d8c436f3..c9c3361cfd05acd86b714e9a6849ba1a1cedb6db 100644 (file)
--- 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
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