reinit the tree, so we can have metadata

5 files changed, 106 insertions, 0 deletions

diff --git a/sci-biology/profphd/Manifest b/sci-biology/profphd/Manifest
new file mode 100644
index 000000000000..a1c2c78c4d86
--- /dev/null
+++ b/sci-biology/profphd/Manifest
@@ -0,0 +1,8 @@
+AUX profphd-1.0.39-perl.patch 376 SHA256 3452144a6f1dade6ab5219b757975002b617b04b1da151593e810bbd561be500 SHA512 e4004dbb835560b3a2aa140aea0ed57812ee9dc11dc18fb7b1dbdeee73bacfef3fecfd686f15fa87cde5597ddb322057d67fa61708ba3077c5449f93a0284b8e WHIRLPOOL 5fd5111f9f5075a7533b5af6e72976cab6404f36b3be3558809815553243aaad4e763e7cc1ec8e06c3c841617200c9c7396aa64c4728f6224b4879416de8f3b8
+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
+EBUILD profphd-1.0.39.ebuild 833 SHA256 5eabc85a7d5f82757e1cb0bd01e1e45989018a497ac95b23920ba25fdbea18cf SHA512 a2e15d1bd08ffa70e966001cc1a9787e2ad4c736e4275dee7ea8695ff6b36869c6acc60b6ae3e1fc607f86adff8bd5ae518dac2004f6c3b9657c5a53a732a123 WHIRLPOOL 87b646cf24398916dee0b1dd5625ef2fc09e2820192b88643aa2b1ce3c30d753bd88880d8fedd060479f070b69ce84ebd78362b38a9ebec28039f8fbbc9531f6
+EBUILD profphd-1.0.40.ebuild 841 SHA256 8e3275137c7f8b644f90901b47380f87f767033629b8b870463884c2e3b4e0ca SHA512 c08773dfc516365b2d75cd0f7869f8c1178a17921ebd65e5ea1b78c236449ea818ce3086e63fd43eeb0ed9b4919b48e7f9f9d1e5a148de5a8e63342bf45d2d9d WHIRLPOOL d37116e5e176754bb004583eb0fd9bfc9b93ef7ee515318e89096cbce4c6fc077a0faae0611d69aac4d69c5bd2a550335ed75840f548bb2da6125ae0bc4d5b35
+MISC ChangeLog 2522 SHA256 2b57417f14f49a172bb9a6e1f06cfbf8963d4529af5a7b441640bb91cdcf3356 SHA512 46d4708b0e051161ec27f737a34a93991017d801d4ff8529629ecba6421151cecde05f08638071fd414746082f704c240cf6d2dcb9c42d839195f4e343ce9612 WHIRLPOOL a0a43bfd5b9026e5053ae9cc1c12043d4801dcce42e021ca0498c025bc1c3f474e096495bf567da6e0a9c15e1b9c90f4e946a0d8054045eca846cbd910e1e05b
+MISC ChangeLog-2015 726 SHA256 6b1b7fe7d0c46bcdc7cec211cbaccc8760e115256be3533b14356084cf707b7b SHA512 fa760ad44e8fdfe6c16727e6b2c8820ccbb1d06df9f1a1d6750876ed734fadcbc39fb56d5e3c7098b479500b880e236a8f744c17b257b997a3a06e0fe0ef81e6 WHIRLPOOL 3eb1e886b3d977cbc425e4be86c25d2f1804cfadd66c6ad09bdf6dd023bd0e7afba1807b08d3ee9de64888f6e91c86b48ada852054f6a0a40283fadbd434679a
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
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..959160fe46b1
--- /dev/null
+++ b/sci-biology/profphd/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</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..cacbc13cbdf2
--- /dev/null
+++ b/sci-biology/profphd/profphd-1.0.39.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+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..8e24cebeb5f3
--- /dev/null
+++ b/sci-biology/profphd/profphd-1.0.40.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+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
+}