reinit the tree, so we can have metadata

5 files changed, 106 insertions, 0 deletions

diff --git a/sci-biology/ariadne/Manifest b/sci-biology/ariadne/Manifest
new file mode 100644
index 000000000000..f65f5231299d
--- /dev/null
+++ b/sci-biology/ariadne/Manifest
@@ -0,0 +1,7 @@
+AUX ariadne-1.3-gcc4.patch 207 SHA256 8362c7cc50340129e7c2f76ebf6333b15c59d4a6e01f24b40ba0032370987b0e SHA512 81750d979dbabe25867daba2dd658eeb1a8e1c04560d2fc067ece20dc3e92abaf98aceefd769c79be87bfcfb18902cb2042a3abbf9c47f79ff281a02b0a9d249 WHIRLPOOL f862b3c59938fedc947c5bd2706aac30dfba582f3831bed05bd25d4f0064d2bc961b7073e3c025e7303ae55b612ea7ea548402af02f329edf538b1d802de3363
+AUX ariadne-1.3-implicits.patch 480 SHA256 994186ec3843ab228e00f3c30c96e5830dfe76da91a7ef59d58f75e6ec2536da SHA512 014dddcf7c3c107ecd77acb9d0110c50bf864cfa20959283ae868a74116d333e2a09749291882f12fffaabed34773e52c9cba5d0b7e476d1e8a14a7df5091a84 WHIRLPOOL 1690e687a4e04ceb59207c55a6a0011d28147843fa29120cec9bcf6ab24e31f1daca9406e2b6162dfb4463173b75eb754626366b7a424a7e6a44aaa791023dfb
+DIST ariadne-1.3.tar.Z 69427 SHA256 8b6b0acb6e8d02b1303d94b20906bf2bf1dee3de4eceeb1b927cfba7a96fd00d SHA512 6c803f945bbcf36c08407e907ad716dc7cd01c7bed555777af46a5dc626b56ca3d1de7d16cab82bfa8bd5a91e06f42c590c0489594251405999459459e9c7289 WHIRLPOOL 460d8acf2bb49e097a9544ecc089ca60c3478b64ab4d903bd6ee801eccd62fc560bdccf1454c9f22632081cbf1df35de09a4f81d6c131d3f52f36753bc692927
+EBUILD ariadne-1.3-r3.ebuild 904 SHA256 2b02c45f7d4e66da3684cef162ee77bfa190e68daac3ec63a4ca75544a683811 SHA512 eceba1b9bf54353df40f061deaa6925034d4bf029a735adce713e20a93a014fc921bfe50cd1caf1befce59348d7f15cbb5d4fe52f220534b05d8c1b3592adaf6 WHIRLPOOL 7425e55a035c7ddf741738387f0e71499adf1bfbf6cf7e950b44ddefda4fe36c7d90a66a962602cfbd38acba8077a3965b13a58e5e1564fce3978516a6743103
+MISC ChangeLog 2555 SHA256 40a8883ae9a28fb0016421f602f8552bfbeb2ea870748397eca80ea7318be879 SHA512 bccf46011df1058beabac685cfebb37063f87e88cdcae1cc7b0bcc8a140ae1053c702fb4f72a4276656f89d1ec2ca139b459c23bf750caedd4dcd1bcbba304cd WHIRLPOOL 5024abd3b8608abedef84f70af53479829c24d8e91128a0f10e87d959ed1bc0c1de5972624aa7dc21ba319dff939a7618db1a3ce188286aebef8f084c322fa22
+MISC ChangeLog-2015 2027 SHA256 65cc77f47568411aa45c916571e6dafafa339568ebcb235cc99cf0f7be9d9a6d SHA512 a63f1a231c2096a8bced1076b9a733e06824ed481de950929d3749cd90a77b61254b47efecb426196ec66daf5b25bce068b45d1c38ac04d26e446cc3427d8f5a WHIRLPOOL b00873b5b4bb252e3d8b860cacd030e7db9460b2a2b86880479c9debde6b5fe23b3c5d051685bf53be7b1e7e15caed0fa69ce94682007d26961777c3bb9914f6
+MISC metadata.xml 954 SHA256 aef3dabcfb12e924a2557c41f1e043866b164b90bab8f731347d239c4fb7df0e SHA512 07101ae5c65d25810f0b32e5bef44b2ee078e858e17ee4b1351f444dc95ad746417f3684206c94487c6203bfcdafc5b0c67b17a1fb5fbfd4ba7a74009bfd2743 WHIRLPOOL b41dfc704c477aced682fabc75d70d93376b33e31ca0432fcbcafa2886641b69291cc55ff149f71edbf33f69725d3e0261cdb97269977a9b9412d3910e08f825
diff --git a/sci-biology/ariadne/ariadne-1.3-r3.ebuild b/sci-biology/ariadne/ariadne-1.3-r3.ebuild
new file mode 100644
index 000000000000..0103c6d3648c
--- /dev/null
+++ b/sci-biology/ariadne/ariadne-1.3-r3.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="Protein sequences and profiles comparison"
+HOMEPAGE="http://www.well.ox.ac.uk/ariadne/"
+SRC_URI="http://www.well.ox.ac.uk/${PN}/${P}.tar.Z"
+
+LICENSE="ARIADNE"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND=">=sci-biology/ncbi-tools-0.20041020-r1"
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}/SRC-${PV}
+
+PATCHES=(
+	"${FILESDIR}"/${P}-gcc4.patch
+	"${FILESDIR}"/${P}-implicits.patch
+)
+
+src_prepare() {
+	default
+	sed -i -e "s/\$(CFLAGS)/\$(LDFLAGS) &/" Makefile || die #359045
+	sed -e "s/blosum62/BLOSUM62/" -i prospero.c || die
+}
+
+src_compile() {
+	emake CC="$(tc-getCC)" OPTIMISE="${CFLAGS}"
+}
+
+src_install() {
+	dobin Linux/{ariadne,prospero}
+
+	use static-libs && dolib.a Linux/libseq.a
+
+	insinto /usr/include/${PN}
+	doins Include/*.h
+
+	einstalldocs
+}
diff --git a/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch b/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch
new file mode 100644
index 000000000000..8bda75cb4f3a
--- /dev/null
+++ b/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch
@@ -0,0 +1,10 @@
+--- a/cl.c
++++ b/cl.c
+@@ -658,6 +658,7 @@
+       fclose(fp);
+       if ( ! stat( filename, &buf ) )
+ 	{
++	  char *ctime(), *t;
+ 	  sprintf( date, "%s", ctime(&buf.st_mtime) );
+ 	  t = date;
+ 	  while ( *t )
diff --git a/sci-biology/ariadne/files/ariadne-1.3-implicits.patch b/sci-biology/ariadne/files/ariadne-1.3-implicits.patch
new file mode 100644
index 000000000000..31c442b12265
--- /dev/null
+++ b/sci-biology/ariadne/files/ariadne-1.3-implicits.patch
@@ -0,0 +1,23 @@
+topalign.c:96:5: warning: implicit declaration of function ‘toupper’
+prospero.c:63:3: warning: implicit declaration of function ‘strcpy’
+
+--- SRC-1.3/prospero.c
++++ SRC-1.3/prospero.c
+@@ -26,6 +26,7 @@
+ */
+ 
+ #include<stdio.h>
++#include<string.h>
+ #include<math.h>
+ #include"cl.h"
+ #include"seq_util.h"
+--- SRC-1.3/topalign.c
++++ SRC-1.3/topalign.c
+@@ -26,6 +26,7 @@
+ */
+ 
+ #include<stdio.h>
++#include<ctype.h>
+ #include<math.h>
+ #include"seq_util.h"
+ #include"ariadne.h"
diff --git a/sci-biology/ariadne/metadata.xml b/sci-biology/ariadne/metadata.xml
new file mode 100644
index 000000000000..d0e8e0be55e0
--- /dev/null
+++ b/sci-biology/ariadne/metadata.xml
@@ -0,0 +1,20 @@
+<?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>
+	<longdescription>
+		ARIADNE is a package of two programs, ariadne and prospero, that
+		compare protein sequences and profiles using the Smith-Waterman
+		algorithm, and assesses statistical significance using a new accurate
+		formula, described in Mott, 2000, "Accurate Formula for P-values of
+		gapped local sequence and profile alignments" J. Mol Biol. 300:649-659.
+		The sequence/profile comparison algorithms used in ARIADNE are
+		standard, and are probably not the fastest implementations available.
+		The novel part is the method for determining statistical significance,
+		which will give thresholds of significance that are accurate to within
+		5% 95% of the time.
+	</longdescription>
+</pkgmetadata>