diff options
| -rw-r--r-- | sci-biology/hydra-sv/Manifest | 2 | ||||
| -rw-r--r-- | sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild | 28 | ||||
| -rw-r--r-- | sci-biology/mrfast/Manifest | 5 | ||||
| -rw-r--r-- | sci-biology/mrfast/files/mrfast-2.1.0.3-disc_buffer_overflow.patch | 52 | ||||
| -rw-r--r-- | sci-biology/mrfast/metadata.xml | 9 | ||||
| -rw-r--r-- | sci-biology/mrfast/mrfast-2.1.0.3.ebuild (renamed from sci-biology/mrfast/mrfast-2.1.0.1.ebuild) | 5 |
6 files changed, 99 insertions, 2 deletions
diff --git a/sci-biology/hydra-sv/Manifest b/sci-biology/hydra-sv/Manifest new file mode 100644 index 000000000..9def91162 --- /dev/null +++ b/sci-biology/hydra-sv/Manifest @@ -0,0 +1,2 @@ +DIST Hydra.v0.5.3.tar.gz 228772 RMD160 c926616bc422bad52fcb3c5e205b459e1ed590f8 SHA1 31d180da2b0ec842bd37d943d1a3ee44ae562dbd SHA256 0d03168f1ab6cec69108730c5747d310ff54023294bba67de77a9d3eebdcfacd +EBUILD hydra-sv-0.5.3.ebuild 647 RMD160 01c9d60a577cc7500e4f4e60cac7879b01f46f62 SHA1 63feeb7ac9982e702e48a6cca921cd853facd0b0 SHA256 242250ca2fd057aad6216381cb2fbb355cdce4634ffac149d026f8038472532b diff --git a/sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild b/sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild new file mode 100644 index 000000000..84dd6edcd --- /dev/null +++ b/sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mosaik/mosaik-1.0.1388.ebuild,v 1.1 2010/04/11 17:29:40 weaver Exp $ + +EAPI=4 + +DESCRIPTION="Detection of structural variation breakpoints in unique and duplicated genomic regions" +HOMEPAGE="http://code.google.com/p/hydra-sv/" +SRC_URI="http://hydra-sv.googlecode.com/files/Hydra.v${PV}.tar.gz" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND="" +RDEPEND="" + +S="${WORKDIR}/Hydra-Version-${PV}" + +src_compile() { + emake clean + emake +} + +src_install() { + dobin bin/* scripts/* || die +} diff --git a/sci-biology/mrfast/Manifest b/sci-biology/mrfast/Manifest index 74a1702ec..54d4c61fa 100644 --- a/sci-biology/mrfast/Manifest +++ b/sci-biology/mrfast/Manifest @@ -1,2 +1,3 @@ -DIST mrfast-2.1.0.1.tar.gz 42880 RMD160 957b2c680a31a9784ff532ff69699222e6aee869 SHA1 8c6534e75199081b4cfb5d44570b0e894b58a9d8 SHA256 b0ea57c5d54f4253cc3a7f7c2c2c48d90b701ac9c5c9b7e99fa2c601ce6f8b6a -EBUILD mrfast-2.1.0.1.ebuild 568 RMD160 d9ac7485618c575d069f80e392a71e7e83a19c3c SHA1 5f0c7685acc363ff36842073cc7b35a0cb49c53c SHA256 87f807b56a809ff86868c680cc47617ffa8a70fefe99d38dc623352f55375f87 +AUX mrfast-2.1.0.3-disc_buffer_overflow.patch 2071 RMD160 665c77acae571d3d4cfa3bca4cc2566b16cd8fe6 SHA1 3697d49baa30219bde46c64c6544bceaa349e56c SHA256 9c98bad2e6249da0aaff9b5ea1041c084f670f969151c09135b3ad6cbed38e05 +DIST mrfast-2.1.0.3.tar.gz 42853 RMD160 70a05079efbef01fd41786433cb5ff9c29d87d0c SHA1 8165d5ca855dc0eee32a7e34777a29f978a952e6 SHA256 2e96e908819ef4b982dd749444fe7b7a5198a0d8df1e4edb475394091c398f4a +EBUILD mrfast-2.1.0.3.ebuild 638 RMD160 1840369ae706bbc238e97a17078748140cef3002 SHA1 48305b6a9a7a6aee657f97f8a8aed9c1bcdd787c SHA256 e247742416152251e82d7d00e0f1b4057b4e2d6e10e30a96f3c8579aa61c0521 diff --git a/sci-biology/mrfast/files/mrfast-2.1.0.3-disc_buffer_overflow.patch b/sci-biology/mrfast/files/mrfast-2.1.0.3-disc_buffer_overflow.patch new file mode 100644 index 000000000..bdf5cbb91 --- /dev/null +++ b/sci-biology/mrfast/files/mrfast-2.1.0.3-disc_buffer_overflow.patch @@ -0,0 +1,52 @@ +diff -durr mrfast-2.1.0.3.orig/MrFAST.c mrfast-2.1.0.3/MrFAST.c +--- mrfast-2.1.0.3.orig/MrFAST.c 2011-12-18 17:48:16.431973604 -0500 ++++ mrfast-2.1.0.3/MrFAST.c 2011-12-18 17:55:11.400723582 -0500 +@@ -7358,6 +7358,7 @@ + char fname1[FILE_NAME_LENGTH]; + char fname2[FILE_NAME_LENGTH]; + char l; ++ int l_int; + int loc1, loc2; + int err1, err2; + char dir1, dir2; +@@ -7399,28 +7400,28 @@ + + //tmp = fwrite (&(mi2[k].cigarSize), sizeof(int), 1, out); + +- tmp = fread(&l, sizeof(int), 1, in); +- tmp = fread(cigar1, sizeof(char), l, in); +- cigar1[(int)l]='\0'; ++ tmp = fread(&l_int, sizeof(int), 1, in); ++ tmp = fread(cigar1, sizeof(char), l_int, in); ++ cigar1[l_int]='\0'; + //tmp = fwrite ((mi2[k].cigar), sizeof(char), mi2[k].cigarSize, out); + + //tmp = fwrite (&(mi2[k].mdSize), sizeof(int), 1, out); +- tmp = fread(&l, sizeof(int), 1, in); +- tmp = fread(editString1, sizeof(char), l, in); +- editString1[(int)l]='\0'; ++ tmp = fread(&l_int, sizeof(int), 1, in); ++ tmp = fread(editString1, sizeof(char), l_int, in); ++ editString1[l_int]='\0'; + //tmp = fwrite ((mi2[k].md), sizeof(char), mi2[k].mdSize, out); + + tmp = fread(&loc2, sizeof(int), 1, in); + tmp = fread(&err2, sizeof(int), 1, in); + tmp = fread(&sc2, sizeof(float), 1, in); + +- tmp = fread(&l, sizeof(int), 1, in); +- tmp = fread(cigar2, sizeof(char), l, in); +- cigar2[(int)l]='\0'; ++ tmp = fread(&l_int, sizeof(int), 1, in); ++ tmp = fread(cigar2, sizeof(char), l_int, in); ++ cigar2[l_int]='\0'; + /* FARHAD: l is of type char; and you fread into it with sizeof(char) above; but as sizeof(int) here; are you sure? 1 byte vs. 4 bytes */ +- tmp = fread(&l, sizeof(int), 1, in); +- tmp = fread(editString2, sizeof(char), l, in); +- editString2[(int)l]='\0'; ++ tmp = fread(&l_int, sizeof(int), 1, in); ++ tmp = fread(editString2, sizeof(char), l_int, in); ++ editString2[l_int]='\0'; + + convertMDCigarToMatrix(cigar1, strlen(cigar1), editString1, strlen(editString1), tmp_matrix1); + convertMDCigarToMatrix(cigar2, strlen(cigar2), editString2, strlen(editString2), tmp_matrix2); diff --git a/sci-biology/mrfast/metadata.xml b/sci-biology/mrfast/metadata.xml new file mode 100644 index 000000000..3302123e5 --- /dev/null +++ b/sci-biology/mrfast/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>weaver@gentoo.org</email> + <name>Andrey Kislyuk</name> + </maintainer> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/mrfast/mrfast-2.1.0.1.ebuild b/sci-biology/mrfast/mrfast-2.1.0.3.ebuild index 8f7d38656..b04437fdf 100644 --- a/sci-biology/mrfast/mrfast-2.1.0.1.ebuild +++ b/sci-biology/mrfast/mrfast-2.1.0.3.ebuild @@ -4,6 +4,8 @@ EAPI=4 +inherit base + DESCRIPTION="Micro Read Fast Alignment Search Tool" HOMEPAGE="http://mrfast.sourceforge.net/" SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" @@ -16,7 +18,10 @@ KEYWORDS="~amd64" DEPEND="" RDEPEND="" +PATCHES=("${FILESDIR}"/${P}-*.patch) + src_prepare() { + base_src_prepare sed -i -e 's/CFLAGS =/CFLAGS +=/' -e 's/LDFLAGS =/LDFLAGS +=/' Makefile } |