Attachment 162406 Details for Bug 203334 – new patch

[patch] new patch

gmap.diff (text/plain), 3.86 KB, created by Guido Falsi on 2015-10-24 07:40:25 UTC

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Creator: Guido Falsi

Created: 2015-10-24 07:40:25 UTC

Size: 3.86 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 400058)
>+++ Makefile	(working copy)
>@@ -2,16 +2,32 @@
> # $FreeBSD$
> 
> PORTNAME=	gmap
>-PORTVERSION=	2006.04.21
>-PORTREVISION=	1
>+PORTVERSION=	2015.09.21
> CATEGORIES=	biology
> MASTER_SITES=	http://research-pub.gene.com/gmap/src/
>-DISTNAME=	${PORTNAME}-${PORTVERSION:C|\.|-|g}
>+DISTNAME=	${PORTNAME}-gsnap-${PORTVERSION:C|\.|-|g}
> 
> MAINTAINER=	rpz@cse.wustl.edu
> COMMENT=	Genomic Mapping and Alignment Program for mRNA and EST Sequences
> 
>+LICENSE=	GMAP
>+LICENSE_NAME=	GMAP License
>+LICENSE_FILE=	${WRKSRC}/COPYING
>+LICENSE_PERMS=	dist-mirror pkg-mirror auto-accept
>+
> USES=		gmake perl5
> GNU_CONFIGURE=	yes
> 
>+WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION:C|\.|-|g}
>+
>+OPTIONS_DEFINE=	SIMD
>+
>+SIMD_CONFIGURE_OFF=	--disable-builtin-popcount --disable-simd
>+
>+# shebang_fix operates during patch.
>+# These scripts are created during configure.
>+post-configure:
>+	${REINPLACE_CMD} -e 's|/usr/bin/perl|${PERL}|g' \
>+		${WRKSRC}/Makefile ${WRKSRC}/util/*.pl
>+
> .include <bsd.port.mk>
>Index: distinfo
>===================================================================
>--- distinfo	(revision 400058)
>+++ distinfo	(working copy)
>@@ -1,2 +1,2 @@
>-SHA256 (gmap-2006-04-21.tar.gz) = e635884c07d57e9a79e6e6744587dc1459dd0895eb40d6ca4b61f9827e332984
>-SIZE (gmap-2006-04-21.tar.gz) = 1282409
>+SHA256 (gmap-gsnap-2015-09-21.tar.gz) = af78237ee9b90ba4416872b3509536060749c3622bbcaadec10e2dcc01301d9c
>+SIZE (gmap-gsnap-2015-09-21.tar.gz) = 4168019
>Index: files/patch-configure
>===================================================================
>--- files/patch-configure	(revision 400058)
>+++ files/patch-configure	(nonexistent)
>@@ -1,11 +0,0 @@
>---- configure.orig	Mon Sep 25 21:06:11 2006
>-+++ configure	Mon Sep 25 21:05:13 2006
>-@@ -3365,7 +3365,7 @@
>- else
>-   answer=""
>- fi;
>--if test x"$answer" == x; then
>-+if test x"$answer" = x; then
>- 
>-   EXP_VAR=GMAPDB
>-   FROM_VAR='${prefix}/share'
>
>Property changes on: files/patch-configure
>___________________________________________________________________
>Deleted: fbsd:nokeywords
>## -1 +0,0 ##
>-yes
>\ No newline at end of property
>Deleted: svn:eol-style
>## -1 +0,0 ##
>-native
>\ No newline at end of property
>Deleted: svn:mime-type
>## -1 +0,0 ##
>-text/plain
>\ No newline at end of property
>Index: pkg-message
>===================================================================
>--- pkg-message	(nonexistent)
>+++ pkg-message	(working copy)
>@@ -0,0 +1,7 @@
>+NOTE:
>+
>+The default configuration for the gmap port disables all optimizations
>+to maintain compatibility with the widest range of systems.
>+
>+To get a binary optimized for your system please deinstall gmap and
>+build from ports using "make config" to enable the SIMD option.
>
>Property changes on: pkg-message
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: pkg-plist
>===================================================================
>--- pkg-plist	(revision 400058)
>+++ pkg-plist	(working copy)
>@@ -1,12 +1,35 @@
>+bin/atoiindex
>+bin/cmetindex
>+bin/dbsnp_iit
>+bin/ensembl_genes
>+bin/fa_coords
>+bin/get-genome
>+bin/gff3_genes
>+bin/gff3_introns
>+bin/gff3_splicesites
> bin/gmap
>-bin/get-genome
>+bin/gmap_build
>+bin/gmap_compress
>+bin/gmap_process
>+bin/gmap_reassemble
>+bin/gmap_uncompress
> bin/gmapindex
>+bin/gmapl
>+bin/gsnap
>+bin/gsnapl
>+bin/gtf_genes
>+bin/gtf_introns
>+bin/gtf_splicesites
>+bin/gvf_iit
>+bin/iit_dump
>+bin/iit_get
> bin/iit_store
>-bin/iit_get
>-bin/iit_dump
>-bin/gmap_compress
>-bin/gmap_uncompress
>-bin/gmap_process
>-bin/gmap_setup
> bin/md_coords
>-bin/fa_coords
>+bin/psl_genes
>+bin/psl_introns
>+bin/psl_splicesites
>+bin/sam_sort
>+bin/snpindex
>+bin/uniqscan
>+bin/uniqscanl
>+bin/vcf_iit

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Attachments on bug 203334: 161380 | 162401 | 162406