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

5 files changed, 99 insertions, 0 deletions

diff --git a/sci-biology/profphd/Manifest b/sci-biology/profphd/Manifest
new file mode 100644
index 000000000000..386263860516
--- /dev/null
+++ b/sci-biology/profphd/Manifest
@@ -0,0 +1,2 @@
+DIST profphd-1.0.39.tar.xz 4406776 SHA256 4ff67e7b4dcb5748ee5115f1e7b9de7de6ca1c5a7982971a7147fe4ee5a5d288 SHA512 0ea6a34a8dad8fcd0d8b23e7a7d476e211587bf580389e9f43ed857bab7853cbe5ce698d2a610e9344e9bc95661cf074355310ea02c1a03e6378058ba169b15b WHIRLPOOL 7e149f3e724ae5e727810ace6a1063708c35bb957861e4873c0763e48af5362ea50757d94c592052fec9d6e63767d036a39104a72ba6deb981c1f6023f19464e
+DIST profphd-1.0.40.tar.xz 4491592 SHA256 50c85da552993758df191e3e06910fb221a156a8eaba94badf5a716b04648c5c SHA512 287f1a548030e7978119788dffdf2529e0018cd772bc820e116f79ed10cefd440645424b56415333362098a1ed32f4841d3fd4069adede2a95968f81c63956e3 WHIRLPOOL 4d7ac3cf32607cefc983116fa8fe8e795e92e89590bd612a2180e9fd59ec5c60220b065a2fddf3552aa81a3d02f852a36e08086d0867ac28ded2faf0d31a38ad
diff --git a/sci-biology/profphd/files/profphd-1.0.39-perl.patch b/sci-biology/profphd/files/profphd-1.0.39-perl.patch
new file mode 100644
index 000000000000..10682271601c
--- /dev/null
+++ b/sci-biology/profphd/files/profphd-1.0.39-perl.patch
@@ -0,0 +1,16 @@
+ src/prof/prof | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/prof/prof b/src/prof/prof
+index 4f26024..356442d 100755
+--- a/src/prof/prof
++++ b/src/prof/prof
+@@ -238,7 +238,7 @@ See each keyword for more help.  Most of these are likely to be broken.
+ 
+ alternative connectivity patterns (default=3)
+ 
+-=item 3
++=item C<3>
+ 
+ predict sec + acc + htm
+ 
diff --git a/sci-biology/profphd/metadata.xml b/sci-biology/profphd/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/profphd/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/profphd/profphd-1.0.39.ebuild b/sci-biology/profphd/profphd-1.0.39.ebuild
new file mode 100644
index 000000000000..8deb4f87abae
--- /dev/null
+++ b/sci-biology/profphd/profphd-1.0.39.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="Secondary structure and solvent accessibility predictor"
+HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction"
+SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND="dev-lang/perl"
+RDEPEND="${DEPEND}
+	dev-perl/librg-utils-perl
+	sci-libs/profnet
+	sci-libs/profphd-utils
+"
+
+src_prepare() {
+	sed \
+		-e '/ln -s/s:prof$:profphd:g' \
+		-i src/prof/Makefile || die
+	epatch "${FILESDIR}"/${P}-perl.patch
+}
+
+src_compile() {
+	emake prefix="${EPREFIX}/usr"
+}
+
+src_install() {
+	emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install
+}
diff --git a/sci-biology/profphd/profphd-1.0.40.ebuild b/sci-biology/profphd/profphd-1.0.40.ebuild
new file mode 100644
index 000000000000..518ab5f1e473
--- /dev/null
+++ b/sci-biology/profphd/profphd-1.0.40.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="Secondary structure and solvent accessibility predictor"
+HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction"
+SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND="dev-lang/perl"
+RDEPEND="${DEPEND}
+	dev-perl/librg-utils-perl
+	sci-libs/profnet
+	sci-libs/profphd-utils
+"
+
+src_prepare() {
+	sed \
+		-e '/ln -s/s:prof$:profphd:g' \
+		-i src/prof/Makefile || die
+	epatch "${FILESDIR}"/${PN}-1.0.39-perl.patch
+}
+
+src_compile() {
+	emake prefix="${EPREFIX}/usr"
+}
+
+src_install() {
+	emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install
+}