commit: 960abf9442aca3794235dc9f15e92005e9d0d77d
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 25 16:14:33 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Feb 25 16:14:33 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=960abf94
sci-biology/recon: Version bump to 1.08
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/recon/Manifest | 1 +
.../recon/files/recon-1.08-buffer-overflow.patch | 11 +++++
.../recon/files/recon-1.08-perl-shebangs.patch | 19 +++++++++
sci-biology/recon/recon-1.08.ebuild | 48 ++++++++++++++++++++++
4 files changed, 79 insertions(+)
diff --git a/sci-biology/recon/Manifest b/sci-biology/recon/Manifest
index d779bd4735..c27ca97b51 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 0000000000..e6bf54e7c2
--- /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 0000000000..769fe4a93c
--- /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 0000000000..8d934d014f
--- /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
+}
