Part of the RCSB Protein Data Bank tools. Provides the data necessary to run the other applications.

Package-Manager: portage-2.1_pre1

7 files changed, 102 insertions, 0 deletions

diff --git a/sci-libs/cifparse-obj/Manifest b/sci-libs/cifparse-obj/Manifest
new file mode 100644
index 000000000000..555bddf8e468
--- /dev/null
+++ b/sci-libs/cifparse-obj/Manifest
@@ -0,0 +1,5 @@
+MD5 9c1f36b1c5398d2273e7c8a53f03b102 ChangeLog 465
+MD5 84aa38c82119d76c654d332683489b11 cifparse-obj-6.302.ebuild 908
+MD5 88ff9a7be10296fc91b2f04eec9eaab3 files/digest-cifparse-obj-6.302 80
+MD5 445290482fdc500ef2e98a2035590a13 files/respect-flags-and-add-gcc4.patch 10289
+MD5 af1bfbb0777267a03e889b08173f2757 metadata.xml 248
diff --git a/sci-libs/rcsb-data/ChangeLog b/sci-libs/rcsb-data/ChangeLog
new file mode 100644
index 000000000000..4703578f4930
--- /dev/null
+++ b/sci-libs/rcsb-data/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-libs/rcsb-data
+# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/rcsb-data/ChangeLog,v 1.1 2005/12/20 04:08:40 spyderous Exp $
+
+*rcsb-data-1.700 (20 Dec 2005)
+
+  20 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>;
+  +files/respect-bindir.patch, +metadata.xml, +rcsb-data-1.700.ebuild:
+  Part of the RCSB Protein Data Bank tools. Provides the data necessary to run
+  the other applications.
+
diff --git a/sci-libs/rcsb-data/Manifest b/sci-libs/rcsb-data/Manifest
new file mode 100644
index 000000000000..ca9646805501
--- /dev/null
+++ b/sci-libs/rcsb-data/Manifest
@@ -0,0 +1,5 @@
+MD5 f16762bb01625286be6cdb4e8e51d3d9 ChangeLog 476
+MD5 f0539a87f3decb3c2a841511143cabb9 files/digest-rcsb-data-1.700 80
+MD5 008f15f3e5c0253396f3c44e4193cb5b files/respect-bindir.patch 798
+MD5 af1bfbb0777267a03e889b08173f2757 metadata.xml 248
+MD5 fa69d1dd891b772277729d73203af702 rcsb-data-1.700.ebuild 1029
diff --git a/sci-libs/rcsb-data/files/digest-rcsb-data-1.700 b/sci-libs/rcsb-data/files/digest-rcsb-data-1.700
new file mode 100644
index 000000000000..abb82a2a5747
--- /dev/null
+++ b/sci-libs/rcsb-data/files/digest-rcsb-data-1.700
@@ -0,0 +1 @@
+MD5 8023ecb2deb2b4cd6fcc2e8f32e8b21a pdb-extract-v1.700-prod-src.tar.gz 9081548
diff --git a/sci-libs/rcsb-data/files/respect-bindir.patch b/sci-libs/rcsb-data/files/respect-bindir.patch
new file mode 100644
index 000000000000..a7925c489591
--- /dev/null
+++ b/sci-libs/rcsb-data/files/respect-bindir.patch
@@ -0,0 +1,30 @@
+diff -urN pdb-extract-v1.700-prod-src.orig/etc/binary.sh pdb-extract-v1.700-prod-src/etc/binary.sh
+--- pdb-extract-v1.700-prod-src.orig/etc/binary.sh	2005-12-18 23:53:45.000000000 -0800
++++ pdb-extract-v1.700-prod-src/etc/binary.sh	2005-12-18 23:55:49.000000000 -0800
+@@ -6,6 +6,8 @@
+ #
+ #  Assumptions: Script is started from within the etc directory.
+ 
++BINDIR="/usr/bin"
++
+ # Change mode of data directory recursively to allow full access.
+ chmod -R 777 ../data
+  
+@@ -31,7 +33,7 @@
+ 
+ # Create component.odb
+ 
+-./bin/connect -all
++${BINDIR}/connect -all
+ 
+ # Move the result to the binary directory
+ mv component_new.odb data/binary/component.odb
+@@ -44,7 +46,7 @@
+ 
+ 
+ # Start main binary production
+-./bin/binary_main -dic -path .
++${BINDIR}/binary_main -dic -path .
+ 
+ 
+ # Cleanup all files
diff --git a/sci-libs/rcsb-data/metadata.xml b/sci-libs/rcsb-data/metadata.xml
new file mode 100644
index 000000000000..211b8bd0f0a4
--- /dev/null
+++ b/sci-libs/rcsb-data/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+<email>spyderous@gentoo.org</email>
+<name>Donnie Berkholz</name>
+</maintainer>
+</pkgmetadata>
diff --git a/sci-libs/rcsb-data/rcsb-data-1.700.ebuild b/sci-libs/rcsb-data/rcsb-data-1.700.ebuild
new file mode 100644
index 000000000000..316b4f59ee89
--- /dev/null
+++ b/sci-libs/rcsb-data/rcsb-data-1.700.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/rcsb-data/rcsb-data-1.700.ebuild,v 1.1 2005/12/20 04:08:40 spyderous Exp $
+
+inherit eutils
+
+MY_PN="pdb-extract"
+MY_P="${MY_PN}-v${PV}-prod-src"
+DESCRIPTION="Data required to run RCSB PDB applications"
+HOMEPAGE="http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html"
+SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz"
+LICENSE="PDB"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+RDEPEND=""
+DEPEND="${RDEPEND}
+	sci-chemistry/pdb-extract"
+S="${WORKDIR}/${MY_P}"
+
+src_unpack() {
+	unpack ${A}
+	epatch ${FILESDIR}/respect-bindir.patch
+	sed -i \
+		-e "s:^\(BINDIR=\).*:\1${ROOT}usr/bin:g" \
+		${S}/etc/binary.sh
+}
+
+src_compile() {
+	emake binary || die "make binary failed"
+}
+
+src_install() {
+	insinto /usr/lib/rcsb/data/binary
+	doins data/binary/*
+	insinto /usr/lib/rcsb/data/ascii
+	doins data/ascii/*
+
+	echo "RCSBROOT=\"/usr/lib/rcsb\"" > ${T}/env.d
+	newenvd ${T}/env.d 50validation
+}