Attachment 161380 Details for Bug 203334 – Unified diff

Unified diff

gmap-diff.txt (text/plain), 3.27 KB, created by Jason W. Bacon on 2015-09-25 13:55:38 UTC

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Creator: Jason W. Bacon

Created: 2015-09-25 13:55:38 UTC

Size: 3.27 KB

patch

obsolete

>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/gmap/Makefile /usr/wip/biology/gmap/Makefile
>--- /usr/ports/biology/gmap/Makefile	2014-09-05 04:25:45.000000000 -0500
>+++ /usr/wip/biology/gmap/Makefile	2015-09-25 08:28:07.000000000 -0500
>@@ -1,17 +1,29 @@
> # Created by: Bob Zimmermann <rpz@cse.wustl.edu>
>-# $FreeBSD: head/biology/gmap/Makefile 367328 2014-09-05 09:25:45Z antoine $
>+# $FreeBSD: head/biology/gmap/Makefile 340722 2014-01-22 17:00:46Z mat $
> 
> 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}
>+
>+# shebang_fix operates during patch.
>+# These scripts are created during configure.
>+post-configure:
>+	${REINPLACE_CMD} -e 's|/usr/bin/perl|${PERL}|g' \
>+		${WRKSRC}/Makefile ${WRKSRC}/util/*.pl
>+
> .include <bsd.port.mk>
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/gmap/distinfo /usr/wip/biology/gmap/distinfo
>--- /usr/ports/biology/gmap/distinfo	2014-01-22 09:30:13.000000000 -0600
>+++ /usr/wip/biology/gmap/distinfo	2015-09-24 20:35:55.000000000 -0500
>@@ -1,2 +1,2 @@
>-SHA256 (gmap-2006-04-21.tar.gz) = e635884c07d57e9a79e6e6744587dc1459dd0895eb40d6ca4b61f9827e332984
>-SIZE (gmap-2006-04-21.tar.gz) = 1282409
>+SHA256 (gmap-gsnap-2015-09-21.tar.gz) = af78237ee9b90ba4416872b3509536060749c3622bbcaadec10e2dcc01301d9c
>+SIZE (gmap-gsnap-2015-09-21.tar.gz) = 4168019
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/gmap/files/patch-configure /usr/wip/biology/gmap/files/patch-configure
>--- /usr/ports/biology/gmap/files/patch-configure	2014-01-22 11:40:44.000000000 -0600
>+++ /usr/wip/biology/gmap/files/patch-configure	1969-12-31 18:00:00.000000000 -0600
>@@ -1,11 +0,0 @@
>---- configure.orig	Mon Sep 25 21:06:11 2006
>-+++ configure	Mon Sep 25 21:05:13 2006
>-@@ -3365,7 +3365,7 @@
>- else
>-   answer=""
>- fi;
>--if test x"$answer" == x; then
>-+if test x"$answer" = x; then
>- 
>-   EXP_VAR=GMAPDB
>-   FROM_VAR='${prefix}/share'
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/gmap/pkg-plist /usr/wip/biology/gmap/pkg-plist
>--- /usr/ports/biology/gmap/pkg-plist	2014-01-22 09:16:56.000000000 -0600
>+++ /usr/wip/biology/gmap/pkg-plist	2015-09-24 20:40:48.000000000 -0500
>@@ -1,12 +1,35 @@
>-bin/gmap
>+bin/atoiindex
>+bin/cmetindex
>+bin/dbsnp_iit
>+bin/ensembl_genes
>+bin/fa_coords
> bin/get-genome
>-bin/gmapindex
>-bin/iit_store
>-bin/iit_get
>-bin/iit_dump
>+bin/gff3_genes
>+bin/gff3_introns
>+bin/gff3_splicesites
>+bin/gmap
>+bin/gmap_build
> bin/gmap_compress
>-bin/gmap_uncompress
> bin/gmap_process
>-bin/gmap_setup
>+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/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