proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

1 files changed, 56 insertions, 0 deletions

diff --git a/sci-biology/psipred/psipred-3.4.ebuild b/sci-biology/psipred/psipred-3.4.ebuild
new file mode 100644
index 000000000000..95d859b7898d
--- /dev/null
+++ b/sci-biology/psipred/psipred-3.4.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils prefix toolchain-funcs versionator
+
+#MY_P="${PN}$(delete_all_version_separators)"
+MY_P="${PN}${PV}"
+
+DESCRIPTION="Protein Secondary Structure Prediction"
+HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/"
+SRC_URI="
+	http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz
+	test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )"
+
+LICENSE="psipred"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="test"
+
+RDEPEND="
+	app-shells/tcsh
+	sci-biology/ncbi-tools
+	|| ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )"
+DEPEND=""
+
+S="${WORKDIR}"/${PN}
+
+src_prepare() {
+	rm -f bin/*
+	epatch \
+		"${FILESDIR}"/3.1-Makefile.patch \
+		"${FILESDIR}"/3.1-path.patch \
+		"${FILESDIR}"/3.2-fgets.patch
+	eprefixify runpsipred*
+	emake -C src clean
+}
+
+src_compile() {
+	emake -C src CC=$(tc-getCC)
+}
+
+src_install() {
+	emake -C src DESTDIR="${D}" install
+	dobin runpsipred* bin/* BLAST+/runpsipred*
+	insinto /usr/share/${PN}
+	doins -r data
+	dodoc README
+}
+
+pkg_postinst() {
+	elog "Please use the update_blastdb.pl in order to"
+	elog "maintain your own local blastdb"
+}