New Addition

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

diff --git a/sci-chemistry/procheck/ChangeLog b/sci-chemistry/procheck/ChangeLog
new file mode 100644 (file)
index 0000000..57e0e2f
--- /dev/null
+++ b/sci-chemistry/procheck/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-chemistry/procheck
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/procheck/ChangeLog,v 1.1 2010/07/18 18:16:27 jlec Exp $
+
+*procheck-3.5.4 (18 Jul 2010)
+
+  18 Jul 2010; Justin Lecher <jlec@gentoo.org> +files/3.5.4-ldflags.patch,
+  +procheck-3.5.4.ebuild, +metadata.xml:
+  New Addition
+

diff --git a/sci-chemistry/procheck/Manifest b/sci-chemistry/procheck/Manifest
new file mode 100644 (file)
index 0000000..7f7e594
--- /dev/null
+++ b/sci-chemistry/procheck/Manifest
@@ -0,0 +1,17 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 3.5.4-ldflags.patch 1649 RMD160 c47aa744cd81ce4601e105712c9fd2735161944d SHA1 02d967425cd85785c66f379270c9e70f2cba1581 SHA256 d46c5f8fbb6d7f6f1fedc522f311ae4c5baa12b9ff47e6d3970312e1b2b34e57
+DIST procheck-3.5.4-README 6585 RMD160 9b813fabdaef8f257b2ef8af6e6ef5a9f3ea1bac SHA1 d9712c404a5e712c37cf449628370fece47c8bd4 SHA256 202d5b4d9ffaebdad19c368e6e6fd8ab54744c511609b1c609ef46c21fa0ffa0
+DIST procheck-3.5.4-manual.tar.gz 517840 RMD160 0c4d79655bfa034b496675dfef20efd6953f4b75 SHA1 adc639d0e7dde0fcd34ee4eddb1fa1004aa2e8d4 SHA256 3c2faa505be05102ccbe23473abdddc1cd4dc87c6b5e74222b7ea5c27b18db5a
+DIST procheck-3.5.4.tar.gz 522013 RMD160 6737d6af80b9a4b5008a80558a0993a8689cd238 SHA1 f4c6ec36689064efe1f1eaa8303decbb3bd0993a SHA256 4923fe5a7b86d5369fd639d0c77cfb866e574f076ec8c52424d746e843a404f4
+EBUILD procheck-3.5.4.ebuild 2109 RMD160 0b7cfd764ee9cf9e4bd0d2200d11657394508fd0 SHA1 7c8161ded35f7cdb93c8d936984d0c6694574f30 SHA256 7ea523ce1c2700665fd5e837034e143e6dccabfab00c395efe237e37fbb492f6
+MISC ChangeLog 378 RMD160 fb658ccaf0c7c2739a39e8f82986bb1e52b330a4 SHA1 18e7df71d02a01eec6e32ceabc0f8527a336b7d0 SHA256 6d5c4c275fda009b646e8922da320b10b9707e51fb9c701e10b98ebfb24a6c0a
+MISC metadata.xml 249 RMD160 789eca813b850a4619f671586826b824098ec47b SHA1 554c0cc8335f6d6410f6f504bf032a7c6de36c89 SHA256 c3f71fe107b700acc3c21923ed360604cfd47ac3181d9ed7605a0472250a8064
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.15 (GNU/Linux)
+
+iEYEARECAAYFAkxDRQAACgkQgAnW8HDreRYYOQCfQG4JCfBRDv6eZRexkF/OLDzw
+j9wAoM6VXpI0fjFcvmBhxkc5BURnV9P2
+=bB/2
+-----END PGP SIGNATURE-----

diff --git a/sci-chemistry/procheck/files/3.5.4-ldflags.patch b/sci-chemistry/procheck/files/3.5.4-ldflags.patch
new file mode 100644 (file)
index 0000000..453aebe
--- /dev/null
+++ b/sci-chemistry/procheck/files/3.5.4-ldflags.patch
@@ -0,0 +1,49 @@
+diff --git a/Makefile b/Makefile
+index c5bb58f..0394b0a 100644
+--- a/Makefile
++++ b/Makefile
+@@ -35,31 +35,31 @@ distrib :
+ # Individual executables
+ # ----------------------
+ anglen : anglen.o
+-      $(F77) $(FOPTS) -o $@ anglen.o
++      $(F77) $(FOPTS) $(LDFLAGS) -o $@ anglen.o
+ clean : clean.o
+-      $(F77) $(FOPTS) -o $@ clean.o
++      $(F77) $(FOPTS) $(LDFLAGS) -o $@ clean.o
+ rmsdev : rmsdev.o
+-      $(F77) $(FOPTS) -o $@ rmsdev.o
++      $(F77) $(FOPTS) $(LDFLAGS) -o $@ rmsdev.o
+ secstr : secstr.o
+-      $(F77) $(FOPTS) -o $@ secstr.o
++      $(F77) $(FOPTS) $(LDFLAGS) -o $@ secstr.o
+ gfac2pdb : gfac2pdb.o ps.o
+-      $(F77) $(FOPTS) -o $@ gfac2pdb.o ps.o
++      $(F77) $(FOPTS) $(LDFLAGS) -o $@ gfac2pdb.o ps.o
+ pplot : pplot.o ps.o
+-      $(F77) $(FOPTS) -o $@ pplot.o ps.o
++      $(F77) $(FOPTS) $(LDFLAGS) -o $@ pplot.o ps.o
+ bplot : bplot.o ps.o
+-      $(F77) $(FOPTS) -o $@ bplot.o ps.o
++      $(F77) $(FOPTS) $(LDFLAGS) -o $@ bplot.o ps.o
+ tplot : tplot.o ps.o
+-      $(F77) $(FOPTS) -o $@ tplot.o ps.o
++      $(F77) $(FOPTS) $(LDFLAGS) -o $@ tplot.o ps.o
+ mplot : mplot.o ps.o
+-      $(F77) $(FOPTS) -o $@ mplot.o ps.o
++      $(F77) $(FOPTS) $(LDFLAGS) -o $@ mplot.o ps.o
+ vplot : vplot.o ps.o
+-      $(F77) $(FOPTS) -o $@ vplot.o ps.o
++      $(F77) $(FOPTS) $(LDFLAGS) -o $@ vplot.o ps.o
+ viol2pdb : viol2pdb.o ps.o
+-      $(F77) $(FOPTS) -o $@ viol2pdb.o ps.o
++      $(F77) $(FOPTS) $(LDFLAGS) -o $@ viol2pdb.o ps.o
+ wirplot : wirplot.o ps.o
+-      $(F77) $(FOPTS) -o $@ wirplot.o ps.o
++      $(F77) $(FOPTS) $(LDFLAGS) -o $@ wirplot.o ps.o
+ nb : nb.c
+-      $(CC) $(COPTS) -o nb nb.c $(CLIBS)
++      $(CC) $(COPTS) $(LDFLAGS) -o nb nb.c $(CLIBS)
+ 
+ # Individual rules for FORTRAN files with .inc files
+ # --------------------------------------------------

diff --git a/sci-chemistry/procheck/metadata.xml b/sci-chemistry/procheck/metadata.xml
new file mode 100644 (file)
index 0000000..8487320
--- /dev/null
+++ b/sci-chemistry/procheck/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+       <herd>sci</herd>
+       <maintainer>
+               <email>jlec@gentoo.org</email>
+               <name>Justin Lecher</name>
+       </maintainer>
+</pkgmetadata>
+

diff --git a/sci-chemistry/procheck/procheck-3.5.4.ebuild b/sci-chemistry/procheck/procheck-3.5.4.ebuild
new file mode 100644 (file)
index 0000000..303bbb7
--- /dev/null
+++ b/sci-chemistry/procheck/procheck-3.5.4.ebuild
@@ -0,0 +1,93 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/procheck/procheck-3.5.4.ebuild,v 1.1 2010/07/18 18:16:27 jlec Exp $
+
+EAPI="3"
+
+inherit eutils fortran toolchain-funcs versionator
+
+DESCRIPTION="Checks the stereochemical quality of a protein structure"
+HOMEPAGE="http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html"
+SRC_URI="
+       http://www.ebi.ac.uk/systems-srv/mp/file-exchange/${PN}.tar.gz?fno=2874 -> ${P}.tar.gz
+       http://www.ebi.ac.uk/systems-srv/mp/file-exchange/README?fno=2566 -> ${P}-README
+       doc? (
+               http://www.ebi.ac.uk/systems-srv/mp/file-exchange/manual.tar.gz?fno=2568 -> ${P}-manual.tar.gz )"
+
+LICENSE="procheck"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc"
+
+RDEPEND="app-shells/tcsh"
+DEPEND="${RDEPEND}"
+
+RESTRICT="fetch"
+
+S="${WORKDIR}/${PN}"
+
+FORTRAN="gfortran g77"
+
+pkg_nofetch() {
+       elog "Please visit http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html"
+       elog "And follow the instruction for downloading."
+       elog "Files should be stored in following way"
+       elog "${PN}.tar.gz  ->  ${DISTDIR}/${P}.tar.gz"
+       elog "README  ->  ${DISTDIR}/${P}-README"
+       if use doc; then
+               elog "manual.tar.gz  ->  ${DISTDIR}/${P}-manual.tar.gz"
+       fi
+}
+
+src_prepare() {
+       epatch "${FILESDIR}"/${PV}-ldflags.patch
+}
+
+src_compile() {
+       emake \
+               F77=${FORTRANC} \
+               CC=$(tc-getCC) \
+               COPTS="${CFLAGS}" \
+               FOPTS="${FFLAGS}" \
+               || die "emake failed"
+}
+
+src_install() {
+       for i in *.scr; do
+               newbin ${i} ${i%.scr} || die
+       done
+
+       exeinto /usr/$(get_libdir)/${PN}/
+       doexe \
+               anglen \
+               clean \
+               rmsdev \
+               secstr \
+               gfac2pdb \
+               pplot \
+               bplot \
+               tplot \
+               mplot \
+               vplot \
+               viol2pdb \
+               wirplot \
+               nb || die
+       dodoc "${DISTDIR}"/${P}-README || die
+
+       insinto /usr/$(get_libdir)/${PN}/
+       doins *.dat *.prm || die
+       newins resdefs.dat resdefs.data || die
+
+       cat >> "${T}"/30${PN} <<- EOF
+       prodir="${EPREFIX}/usr/$(get_libdir)/${PN}/"
+       EOF
+
+       insinto /etx/profile.d/
+       doins "${T}"/30${PN} || die
+
+       if use doc; then
+               pushd "${WORKDIR}"
+                       dohtml -r manual || die
+               popd
+       fi
+}