From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1PwLK7-0001Ay-9Y for garchives@archives.gentoo.org; Sun, 06 Mar 2011 21:17:07 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 987A7E0603; Sun, 6 Mar 2011 21:16:59 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 4CF40E0603 for ; Sun, 6 Mar 2011 21:16:58 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher ADH-CAMELLIA256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 798BC1B409B for ; Sun, 6 Mar 2011 21:16:58 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id 886FF8006A for ; Sun, 6 Mar 2011 21:16:57 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/amos-short/files/, sci-biology/amos-short/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/amos-short/amos-short-0.9.3.ebuild sci-biology/amos-short/files/amos-2.0.8-gcc44.patch sci-biology/amos-short/metadata.xml X-VCS-Directories: sci-biology/amos-short/files/ sci-biology/amos-short/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: baea040e8119bc768ba9f83cd7b82fdaab992c62 Date: Sun, 6 Mar 2011 21:16:57 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: X-Archives-Hash: e3af2bae6bc253538dd677d6aed89a98 commit: baea040e8119bc768ba9f83cd7b82fdaab992c62 Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Sun Mar 6 12:33:52 2011 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sun Mar 6 12:33:52 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3Dbaea040e sci-biology/amos-short: new package (Portage version: 2.1.9.28/git/Linux i686, unsigned Manifest commit) --- sci-biology/amos-short/amos-short-0.9.3.ebuild | 34 ++++++ .../amos-short/files/amos-2.0.8-gcc44.patch | 117 ++++++++++++++= ++++++ sci-biology/amos-short/metadata.xml | 9 ++ 3 files changed, 160 insertions(+), 0 deletions(-) diff --git a/sci-biology/amos-short/amos-short-0.9.3.ebuild b/sci-biology= /amos-short/amos-short-0.9.3.ebuild new file mode 100644 index 0000000..484a4c3 --- /dev/null +++ b/sci-biology/amos-short/amos-short-0.9.3.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3D"3" + +inherit eutils + +DESCRIPTION=3D"A Modular, Open-Source whole genome assembler with defaul= ts for short reads" +HOMEPAGE=3D"http://amos.sourceforge.net/" +SRC_URI=3D"http://sourceforge.net/projects/amos/files/short_read_assembl= y/0.9.3/AMOS-short.tgz" +#SRC_URI=3D"mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE=3D"GPL-2" +SLOT=3D"0" +IUSE=3D"" +KEYWORDS=3D"~amd64 ~x86" + +DEPEND=3D"" +RDEPEND=3D"${DEPEND}" + +S=3D"${WORKDIR}"/AMOS + +src_prepare() { + epatch "${FILESDIR}"/amos-2.0.8-gcc44.patch +} + +src_compile() { + emake -j1 || die "emake failed" +} + +src_install() { + emake DESTDIR=3D"${D}" install || die "emake install failed" +} diff --git a/sci-biology/amos-short/files/amos-2.0.8-gcc44.patch b/sci-bi= ology/amos-short/files/amos-2.0.8-gcc44.patch new file mode 100644 index 0000000..00a37be --- /dev/null +++ b/sci-biology/amos-short/files/amos-2.0.8-gcc44.patch @@ -0,0 +1,117 @@ +diff -ur amos-2.0.8.orig/src/Align/align.cc amos-2.0.8/src/Align/align.c= c +--- amos-2.0.8.orig/src/Align/align.cc 2008-03-19 16:07:24.000000000 +02= 00 ++++ amos-2.0.8/src/Align/align.cc 2009-07-30 19:40:51.000000000 +0300 +@@ -247,7 +247,7 @@ + // Add incr_val to the after count in this Vote_t for ch . +=20 + { +- char * p; ++ const char * p; +=20 + p =3D strchr (ALPHABET, tolower (ch)); + if (p =3D=3D NULL) +@@ -285,7 +285,7 @@ + // count for a blank. +=20 + { +- char * p; ++ const char * p; +=20 + p =3D strchr (ALPHABET, tolower (ch)); + if (p =3D=3D NULL) +@@ -357,7 +357,7 @@ +=20 + { + int i; +- char * p; ++ const char * p; +=20 + for (i =3D 0; i <=3D ALPHABET_SIZE; i ++) + here [i] =3D after [i] =3D 0; +diff -ur amos-2.0.8.orig/src/Align/align_poly.cc amos-2.0.8/src/Align/al= ign_poly.cc +--- amos-2.0.8.orig/src/Align/align_poly.cc 2006-03-30 05:03:12.00000000= 0 +0300 ++++ amos-2.0.8/src/Align/align_poly.cc 2009-07-30 19:43:44.000000000 +03= 00 +@@ -247,7 +247,7 @@ + // Add 1 to the after count in this Vote_t for ch . +=20 + { +- char * p; ++ const char * p; +=20 + p =3D strchr (ALPHABET, tolower (ch)); + if (p =3D=3D NULL) +@@ -285,7 +285,7 @@ + // count for a blank. +=20 + { +- char * p; ++ const char * p; +=20 + p =3D strchr (ALPHABET, tolower (ch)); + if (p =3D=3D NULL) +@@ -357,7 +357,7 @@ +=20 + { + int i; +- char * p; ++ const char * p; +=20 + for (i =3D 0; i <=3D ALPHABET_SIZE; i ++) + here [i] =3D after [i] =3D 0; +diff -ur amos-2.0.8.orig/src/AMOS/IDMap_AMOS.cc amos-2.0.8/src/AMOS/IDMa= p_AMOS.cc +--- amos-2.0.8.orig/src/AMOS/IDMap_AMOS.cc 2006-11-21 17:45:46.000000000= +0200 ++++ amos-2.0.8/src/AMOS/IDMap_AMOS.cc 2009-07-30 19:30:03.000000000 +030= 0 +@@ -10,6 +10,7 @@ + #include "IDMap_AMOS.hh" + #include + #include ++#include + #include + using namespace AMOS; + using namespace std; +diff -ur amos-2.0.8.orig/src/AMOS/Message_AMOS.cc amos-2.0.8/src/AMOS/Me= ssage_AMOS.cc +--- amos-2.0.8.orig/src/AMOS/Message_AMOS.cc 2005-01-07 23:53:05.0000000= 00 +0200 ++++ amos-2.0.8/src/AMOS/Message_AMOS.cc 2009-07-30 19:32:21.000000000 +0= 300 +@@ -7,6 +7,8 @@ + //! + ///////////////////////////////////////////////////////////////////////= ///////// +=20 ++#include ++ + #include "Message_AMOS.hh" + using namespace AMOS; + using namespace std; +diff -ur amos-2.0.8.orig/src/Common/amp.cc amos-2.0.8/src/Common/amp.cc +--- amos-2.0.8.orig/src/Common/amp.cc 2006-10-25 16:56:41.000000000 +030= 0 ++++ amos-2.0.8/src/Common/amp.cc 2009-07-30 19:33:59.000000000 +0300 +@@ -1,6 +1,7 @@ + #include "amp.hh" + #include + #include ++#include + #include + #include + using namespace std; +diff -ur amos-2.0.8.orig/src/Foundation/FileSystem.cc amos-2.0.8/src/Fou= ndation/FileSystem.cc +--- amos-2.0.8.orig/src/Foundation/FileSystem.cc 2005-07-09 00:52:03.000= 000000 +0300 ++++ amos-2.0.8/src/Foundation/FileSystem.cc 2009-07-30 19:35:48.00000000= 0 +0300 +@@ -55,7 +55,7 @@ + { + // Check to see if path was given +=20 +- char * end_of_path =3D strrchr(filename, PATH_DELIMINATOR); ++ const char * end_of_path =3D strrchr(filename, PATH_DELIMINATOR); + =20 + if (end_of_path) + { +diff -ur amos-2.0.8.orig/src/Foundation/Options.cc amos-2.0.8/src/Founda= tion/Options.cc +--- amos-2.0.8.orig/src/Foundation/Options.cc 2008-06-22 18:19:07.000000= 000 +0300 ++++ amos-2.0.8/src/Foundation/Options.cc 2009-07-30 19:37:40.000000000 += 0300 +@@ -26,6 +26,7 @@ + */ +=20 + #include "Options.hh" ++#include + #include +=20 + //! Constructor takes command line options in standard argc, argv forma= t diff --git a/sci-biology/amos-short/metadata.xml b/sci-biology/amos-short= /metadata.xml new file mode 100644 index 0000000..07b5255 --- /dev/null +++ b/sci-biology/amos-short/metadata.xml @@ -0,0 +1,9 @@ + + + + sci-biology + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + +