sci-biology/recon: Version bump to 1.08

Package-Manager: Portage-2.3.3, Repoman-2.3.1

4 files changed, 79 insertions, 0 deletions

diff --git a/sci-biology/recon/Manifest b/sci-biology/recon/Manifest
index d779bd4735c4..c27ca97b5128 100644
--- a/sci-biology/recon/Manifest
+++ b/sci-biology/recon/Manifest
@@ -1 +1,2 @@
+DIST RECON-1.08.tar.gz 108477 SHA256 699765fa49d18dbfac9f7a82ecd054464b468cb7521abe9c2bd8caccf08ee7d8 SHA512 68672312f31751fa93250bbe337ae57f11dc4b1994c7dd5249dca916012c2df83a03c925cb631709e081c72055ef5bffd0846bc252d8c3c6247ae5ef61b160c9 WHIRLPOOL e9a60353e4f6bbe37883c648a7c8f5d363c780d03a681dd2d6803d2e65a1eb5f9b8fb02a85721636e7a792b53628a00f21d57d1c4066fb8b91b2fb1d4c383763
 DIST RECON1.06.tar.gz 109484 SHA256 6e106adb546952ecdfe7e9c1b56a4a80581383446c63abbe0c61c53af0e67461 SHA512 0df3ecb4b569d087ffce6b4f326f6c8686e78b08864dff09b7441d4f4067e72baf80ecb211366c23f7b49ed123426f612347309ceb5ae052d9bb371070525d32 WHIRLPOOL d1f66533d16bc1b5cb4cc51b35278a25c5cd1b797a4178987a873757f9b8f591527f84d65a0dfd4f8b165c35bf336c94f8c465235a3ebc101992e5af970cccec
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/recon-1.08.ebuild b/sci-biology/recon/recon-1.08.ebuild
new file mode 100644
index 000000000000..8d934d014fd8
--- /dev/null
+++ b/sci-biology/recon/recon-1.08.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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
+}