diff options
Diffstat (limited to 'sci-biology/recon')
| -rw-r--r-- | sci-biology/recon/Manifest | 7 | ||||
| -rw-r--r-- | sci-biology/recon/files/recon-1.08-buffer-overflow.patch | 11 | ||||
| -rw-r--r-- | sci-biology/recon/files/recon-1.08-perl-shebangs.patch | 19 | ||||
| -rw-r--r-- | sci-biology/recon/metadata.xml | 8 | ||||
| -rw-r--r-- | sci-biology/recon/recon-1.08.ebuild | 47 |
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 +} |