reinit the tree, so we can have metadata

5 files changed, 92 insertions, 0 deletions

diff --git a/sci-biology/recon/Manifest b/sci-biology/recon/Manifest
new file mode 100644
index 000000000000..f560e8f0a55f
--- /dev/null
+++ b/sci-biology/recon/Manifest
@@ -0,0 +1,7 @@
+AUX recon-1.08-buffer-overflow.patch 290 SHA256 da8bfcd418482f8529c9709ece7136939404a2436440729ccff0481246aa97cc SHA512 d903e6a8e4b61e5f91a318313203890242aa9badbf6af69009b5a3ef6351ba6984e00cdaa7aaf744095fd79557c1a5ad96a80119248cddfde9874f4b763df11b WHIRLPOOL 7889625a0d829a877e1cbde608459ab73773bbc91d26d0daf8fd835ae4611f433df9c77bd30d5fa004ef589d2b0cac2fc4797292c5a16174223d7ec4e1cd708c
+AUX recon-1.08-perl-shebangs.patch 420 SHA256 2a7cfab0cf60bf2aeba4b8f93732cbece2570c5fc035a288566692daf4a94467 SHA512 b681a0f911268ab39bc64cc35f4647a71696f3cbc4610f6fb7c061ca70406934ca2f85525578c28530431725ae9399c327a7551eb19dd46552ce5e65b2399a88 WHIRLPOOL cd2e803be5cdefbb7d340970926dee446714f687d84aca95b21c7099104ffaa45d9adcd314137ceefdec2f4621026ea41ff99156f6c8a8c78953f22f0066f6f5
+DIST RECON-1.08.tar.gz 108477 SHA256 699765fa49d18dbfac9f7a82ecd054464b468cb7521abe9c2bd8caccf08ee7d8 SHA512 68672312f31751fa93250bbe337ae57f11dc4b1994c7dd5249dca916012c2df83a03c925cb631709e081c72055ef5bffd0846bc252d8c3c6247ae5ef61b160c9 WHIRLPOOL e9a60353e4f6bbe37883c648a7c8f5d363c780d03a681dd2d6803d2e65a1eb5f9b8fb02a85721636e7a792b53628a00f21d57d1c4066fb8b91b2fb1d4c383763
+EBUILD recon-1.08.ebuild 964 SHA256 f09185a1705fcbec9fa3d809b9aa197ed173ba271f718ad87549f71c30dab7d1 SHA512 39805629341d019e769ff796f9ef12aedaadcc431904a6bd0b6e48b145a3631a1f7ebbccdff6fc23cdaf75e55ee909ea5fc7969b35082fcec0b963e48baf3215 WHIRLPOOL d9cc8f9f8ebca84915f3a2846121794fcf04c18f28f34fc8e8d0bef49e3c914ded6e00d031da8c4a316b5d130157243ead45164001d2060660c3f5a83947a41c
+MISC ChangeLog 2550 SHA256 af2f31194d3b60bf6f4a501218b9e2d8fc117ab587c47a381a5a4d569743394f SHA512 1a50787fb16133e861edac99632d9b24b42b0a8772fe4bbc8cb96ecbbf30864fa1dfacc3ac0af0902e87d8fe2a5a03b53e43f37f9dca4d4989aa547cea48dc8b WHIRLPOOL 13899a0089c87e97e76ca04466451cc90d5eaf23d71156e204123140592e80eb6d80a2b86f568ba8ea203febde4c79502c2f8dea9b49629bc2efb2fe7da12110
+MISC ChangeLog-2015 921 SHA256 681e41db69008ab6d9e89f99e5fd69990aa4c1d3010fceea4174e4d4848dc87b SHA512 8bade18c4824f46d75759628b9cbc0f4e1f23d411416cd4475761173200282ae140b856c9743710d61a7c85897ca6e01ef0000a2de1724c9440af27423284ca3 WHIRLPOOL bb6bfd318652806a56d15632c37ed235b81882d9b4e74df24af59a195de8b53ec99d2dbb62496287cd4ebf1c1a2e43d34d3d6ada9a97e772fa70c4b597fd594c
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/recon/files/recon-1.08-buffer-overflow.patch b/sci-biology/recon/files/recon-1.08-buffer-overflow.patch
new file mode 100644
index 000000000000..e6bf54e7c2f2
--- /dev/null
+++ b/sci-biology/recon/files/recon-1.08-buffer-overflow.patch
@@ -0,0 +1,11 @@
+--- a/src/eledef.c
++++ b/src/eledef.c
+@@ -385,7 +385,7 @@ void ele_def(int method, FILE *frags, float cutoff, EPROT_t **all_epp, int *ecp,
+ 
+ void img_charge(IPROT_t **shadow, int ct, FILE *input) {
+   int i=0, pos=0;
+-  char line[151];
++  char line[256];
+   int scan_flag;
+   MSP_t msp;
+ 
diff --git a/sci-biology/recon/files/recon-1.08-perl-shebangs.patch b/sci-biology/recon/files/recon-1.08-perl-shebangs.patch
new file mode 100644
index 000000000000..769fe4a93c65
--- /dev/null
+++ b/sci-biology/recon/files/recon-1.08-perl-shebangs.patch
@@ -0,0 +1,19 @@
+Make Perl shebangs Prefix friendly
+See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/
+
+--- a/scripts/MSPCollect.pl
++++ b/scripts/MSPCollect.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ if (!@ARGV) {
+     die "usage: MSPCollect BLAST_output_file\n";
+--- a/scripts/recon.pl
++++ b/scripts/recon.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ $path = "";
+ 
diff --git a/sci-biology/recon/metadata.xml b/sci-biology/recon/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/recon/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/recon/recon-1.08.ebuild b/sci-biology/recon/recon-1.08.ebuild
new file mode 100644
index 000000000000..a96403c812be
--- /dev/null
+++ b/sci-biology/recon/recon-1.08.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="Automated de novo identification of repeat families from genomic sequences"
+HOMEPAGE="http://www.repeatmasker.org/RepeatModeler.html"
+SRC_URI="http://www.repeatmasker.org/${P^^}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="examples"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-lang/perl"
+
+S=${WORKDIR}/${P^^}
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.08-buffer-overflow.patch
+	"${FILESDIR}"/${PN}-1.08-perl-shebangs.patch
+)
+
+src_prepare() {
+	default
+	sed -i "s|$path = \"\";|$path = \"${EPREFIX}/usr/libexec/${PN}\";|" scripts/recon.pl || die
+}
+
+src_compile() {
+	emake CC="$(tc-getCC)" CFLAGS="${CFLAGS}" -C src
+}
+
+src_install() {
+	dobin scripts/*
+
+	exeinto /usr/libexec/${PN}
+	doexe src/{edgeredef,eledef,eleredef,famdef,imagespread}
+
+	newdoc {00,}README
+
+	if use examples; then
+		insinto /usr/share/${PN}
+		doins -r Demos
+	fi
+}