Attachment 144093 Details for Bug 191336 – svn diff for biology/consed

[patch] svn diff for biology/consed

consed.diff (text/plain), 158.10 KB, created by Motomichi Matsuzaki on 2014-06-24 11:20:29 UTC

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Creator: Motomichi Matsuzaki

Created: 2014-06-24 11:20:29 UTC

Size: 158.10 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 359067)
>+++ Makefile	(working copy)
>@@ -2,19 +2,21 @@
> # $FreeBSD$
> 
> PORTNAME=	consed
>-PORTVERSION=	16.0
>+PORTVERSION=	27.0
> CATEGORIES=	biology
> MASTER_SITES=	http://www.phrap.org/consed/distributions/${PORTVERSION}/
> DISTNAME=	${PORTNAME}_linux
>-EXTRACT_SUFX=	.tar.Z
> 
> MAINTAINER=	mzaki@m.u-tokyo.ac.jp
> COMMENT=	Graphical tool for editing Phrap assemblies
> 
> RUN_DEPENDS=	phred:${PORTSDIR}/biology/phred \
>-		phrap:${PORTSDIR}/biology/phrap \
>-		phd2fasta:${PORTSDIR}/biology/phd2fasta
>+		phrap:${PORTSDIR}/biology/phrap
> 
>+CONFLICTS_INSTALL=	phd2fasta-[0-9]*
>+
>+SUB_FILES=	pkg-message
>+
> USES=		perl5
> USE_LINUX=	yes
> USE_LINUX_APPS=	xorglibs
>@@ -26,84 +28,12 @@
> .endif
> 
> NO_WRKSUBDIR=	yes
>+NO_BUILD=	yes
> 
>-BUILD_WRKSRC=	${WRKSRC}/misc/mktrace
>-ALL_TARGET=	mktrace
>-
>-BINARIES=	consed mktrace sffinfo sff2scf
>-CONTRIBS=	ace2OligosWithComments.perl ace2fof \
>-		aceContigs2Phds.perl acestatus.pl export_cons \
>-		mergeAces.perl recover_consensus_tags revert_fof
>-SCRIPTS=	ace2Fasta.perl ace2Oligos.perl addReads2Consed.perl \
>-		amplifyTranscripts.perl catPhdFiles.perl \
>-		countEditedBases.perl determineReadTypes.perl fasta2Phd.perl \
>-		findSequenceMatchesForConsed.perl lib2Phd.perl \
>-		orderPrimerPairs.perl phd2Ace.perl phredPhrap removeReads \
>-		revertToUneditedRead tagRepeats.perl transferConsensusTags.perl
>-.for f in ${BINARIES} ${CONTRIBS} ${SCRIPTS}
>-PLIST_FILES+=	bin/${f}
>-.endfor
>-
>-DATADIR=	${PREFIX}/lib/screenLibs
>-DATAFILES=	primerCloneScreen.seq primerSubcloneScreen.seq \
>-		repeats.fasta singleVectorForRestrictionDigest.fasta
>-NULLFILES=	vector.seq
>-.for f in ${DATAFILES} ${NULLFILES}
>-PORTDATA+=	${f}.dist
>-.endfor
>-PORTDOCS=	README.txt
>-
>-NO_STAGE=	yes
>-
>-OPTIONS_DEFINE=	DOCS EXAMPLES
>-
>-.include <bsd.port.options.mk>
>-
>-.if ${PORT_OPTIONS:MEXAMPLES}
>-EXAMPLES=	standard autofinish assembly_view polyphred
>-PLIST=		${PKGDIR}/pkg-plist.examples
>-.endif
>-
>-post-build:
>-	(cd ${WRKSRC}/misc/454; ${CC} ${CFLAGS} sffinfo.c -o sffinfo)
>-	(cd ${WRKSRC}/misc/454; ${CC} ${CFLAGS} sff2scf.c -o sff2scf)
>-
> do-install:
>-	@${INSTALL_PROGRAM} ${WRKSRC}/consed_linux2.4 ${PREFIX}/bin/consed
>-	@${INSTALL_PROGRAM} ${BUILD_WRKSRC}/mktrace ${PREFIX}/bin/
>-	@${INSTALL_PROGRAM} ${WRKSRC}/misc/454/sffinfo ${PREFIX}/bin/
>-	@${INSTALL_PROGRAM} ${WRKSRC}/misc/454/sff2scf ${PREFIX}/bin/
>-.for f in ${BINARIES}
>-	@${CHMOD} a-r ${PREFIX}/bin/${f}
>-.endfor
>-.for f in ${CONTRIBS}
>-	@${INSTALL_SCRIPT} ${WRKSRC}/contributions/${f} ${PREFIX}/bin/
>-.endfor
>-.for f in ${SCRIPTS}
>-	@${INSTALL_SCRIPT} ${WRKSRC}/scripts/${f} ${PREFIX}/bin/
>-.endfor
>-	@${MKDIR} ${DATADIR}
>-.for f in ${DATAFILES}
>-	@${INSTALL_DATA} ${WRKSRC}/misc/${f} ${DATADIR}/${f}.dist
>-.endfor
>-.for f in ${NULLFILES}
>-	@${INSTALL_DATA} /dev/null ${DATADIR}/${f}.dist
>-.endfor
>-.if ${PORT_OPTIONS:MEXAMPLES}
>-	@${MKDIR} ${EXAMPLESDIR}
>-.for dir in ${EXAMPLES}
>-	@${CP} -R ${WRKSRC}/${dir} ${EXAMPLESDIR}
>-.endfor
>-.endif
>-.if ${PORT_OPTIONS:MDOCS}
>-	@${MKDIR} ${DOCSDIR}
>-.for f in ${PORTDOCS}
>-	@${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR}
>-.endfor
>-.endif
>-.if ! ${PORT_OPTIONS:MEXAMPLES}
>-	@${ECHO_CMD} "Examples were not installed. You can define WITH_EXAMPLES=yes to install them."
>-.endif
>-	@${ECHO_CMD} "You must set the CONSED_HOME environment variable to '${PREFIX}'"
>+	${MKDIR} ${STAGEDIR}${DATADIR}
>+	${LN} -sf ../../bin ${STAGEDIR}${DATADIR}/bin
>+	(cd ${WRKSRC}; ${ENV} CC=${CC} ./installConsed.perl consed_linux32bit ${STAGEDIR}${DATADIR})
>+	${LN} -sf ../../../etc/PhredPar/phredpar.dat ${STAGEDIR}${DATADIR}/lib/phredpar.dat
> 
> .include <bsd.port.mk>
>Index: distinfo
>===================================================================
>--- distinfo	(revision 359067)
>+++ distinfo	(working copy)
>@@ -1,2 +1,2 @@
>-SHA256 (consed_linux.tar.Z) = ac9ce155ce46f7200accaa033c9b1ea1d8c071c68c2a82ab5f4b623d9ff6b117
>-SIZE (consed_linux.tar.Z) = 27555099
>+SHA256 (consed_linux.tar.gz) = 8038d2b94078ba918e97785fc7497252139029281000f1c54ff9dd1ec70e05fc
>+SIZE (consed_linux.tar.gz) = 34390726
>Index: files/patch-installConsed.perl
>===================================================================
>--- files/patch-installConsed.perl	(revision 0)
>+++ files/patch-installConsed.perl	(working copy)
>@@ -0,0 +1,51 @@
>+--- installConsed.perl.orig	2014-02-12 05:28:45.000000000 +0900
>++++ installConsed.perl	2014-06-24 16:57:29.000000000 +0900
>+@@ -9,7 +9,7 @@
>+ # and this must be empty and must allow write access
>+ 
>+ # edit this if you are using a different compiler than gcc
>+-$CC = "gcc";
>++$CC = $ENV{'CC'};
>+ 
>+ $szVersion = "25.0";
>+ 
>+@@ -78,9 +78,9 @@
>+ $szHowToStartOver = "if you have had an error in the midst of this script, you have a problem because some things have been done and others not done.  The cleanest solution is to go back to where nothing is done.  To do that, type:\nrm -rf $szConsedHome/bin\nrm -rf $szConsedHome/lib\nrm -rf $szConsedHome/examples";
>+ 
>+ 
>+-if ( -e "$szConsedHome/bin" ) {
>+-   die "$szConsedHome/bin already exists\n$szHowToStartOver\n";
>+-}
>++#if ( -e "$szConsedHome/bin" ) {
>++#   die "$szConsedHome/bin already exists\n$szHowToStartOver\n";
>++#}
>+ 
>+ if ( -e "$szConsedHome/lib" ) {
>+    die "$szConsedHome/lib already exists\n$szHowToStartOver\n";
>+@@ -91,7 +91,7 @@
>+ }
>+ 
>+ 
>+-&doCommand( "mkdir $szConsedHome/bin" );
>++#&doCommand( "mkdir $szConsedHome/bin" );
>+ &doCommand( "mkdir -p $szConsedHome/lib/screenLibs" );
>+ &doCommand( "mkdir $szConsedHome/examples" );
>+ &doCommand( "cp $szConsedExecutable $szConsedHome/bin" );
>+@@ -101,7 +101,7 @@
>+ print "done\n";
>+ &doCommand( "cp README.txt $szConsedHome" );
>+ 
>+-&doCommand( "chmod -R a+w $szConsedHome/examples/*" );
>++#&doCommand( "chmod -R a+w $szConsedHome/examples/*" );
>+ 
>+ &doCommand( "cp $szDownloadDirectory/scripts/* $szConsedHome/bin" );
>+ 
>+@@ -112,7 +112,7 @@
>+ @aScreenLibs = split(' ', $szScreenLibs );
>+ foreach $szScreenFile ( @aScreenLibs ) {
>+    print "about to cp $szDownloadDirectory/misc/$szScreenFile $szConsedHome/lib/screenLibs\n";
>+-   &doCommand( "cp $szDownloadDirectory/misc/$szScreenFile $szConsedHome/lib/screenLibs" );
>++   &doCommand( "cp $szDownloadDirectory/misc/$szScreenFile $szConsedHome/lib/screenLibs/$szScreenFile.sample" );
>+ }
>+ 
>+ 
>
>Property changes on: files/patch-installConsed.perl
>___________________________________________________________________
>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: files/patch-scripts_addReads2Consed.perl
>===================================================================
>--- files/patch-scripts_addReads2Consed.perl	(revision 359067)
>+++ files/patch-scripts_addReads2Consed.perl	(working copy)
>@@ -1,11 +0,0 @@
>---- scripts/addReads2Consed.perl.orig	2007-09-26 04:02:19.000000000 +0900
>-+++ scripts/addReads2Consed.perl	2007-12-11 17:27:20.000000000 +0900
>-@@ -71,7 +71,7 @@
>- $szVectorFile = $szConsedHome . "/lib/screenLibs/vector.seq";
>- 
>- # change this to reflect wherever you put the phred parameter file
>--$szPhredParameterFile = $szConsedHome . "/lib/phredpar.dat";
>-+$szPhredParameterFile = $szConsedHome . "/etc/PhredPar/phredpar.dat";
>- #$szPhredParameterFile = "/usr/local/common/lib/PhredPar/phredpar.dat";
>- #$szPhredParameterFile = "/usr/local/etc/PhredPar/phredpar.dat";
>- 
>Index: files/patch-scripts_determineReadTypes.perl
>===================================================================
>--- files/patch-scripts_determineReadTypes.perl	(revision 359067)
>+++ files/patch-scripts_determineReadTypes.perl	(working copy)
>@@ -1,11 +0,0 @@
>---- scripts/determineReadTypes.perl.orig	Tue Aug 31 03:14:13 2004
>-+++ scripts/determineReadTypes.perl	Wed Jul 13 17:00:22 2005
>-@@ -177,7 +177,7 @@
>- # you can remove or comment out this line when you are satisfied with
>- # your customized version of this file.
>- 
>--die "You must edit determineReadTypes.perl--please read README.txt that came with consed.  Look under INSTALLING CONSED.  Also look at the comments at the beginning of determineReadTypes.perl  Then, and only then, comment out the line in determineReadTypes.perl that begins with \"die\" and has this error message\n by putting a # in front of that line";
>-+#die "You must edit determineReadTypes.perl--please read README.txt that came with consed.  Look under INSTALLING CONSED.  Also look at the comments at the beginning of determineReadTypes.perl  Then, and only then, comment out the line in determineReadTypes.perl that begins with \"die\" and has this error message\n by putting a # in front of that line";
>- 
>- $szVersion = "001205";
>- 
>Index: files/patch-scripts_phredPhrap
>===================================================================
>--- files/patch-scripts_phredPhrap	(revision 359067)
>+++ files/patch-scripts_phredPhrap	(working copy)
>@@ -1,36 +1,11 @@
>---- scripts/phredPhrap.orig	2007-09-26 04:02:20.000000000 +0900
>-+++ scripts/phredPhrap	2007-12-11 17:32:27.000000000 +0900
>-@@ -101,7 +101,7 @@
>+--- scripts/phredPhrap.orig	2014-02-12 05:28:45.000000000 +0900
>++++ scripts/phredPhrap	2014-06-22 03:07:33.000000000 +0900
>+@@ -217,7 +217,7 @@
>+ #$solexaDirPath = "../solexa_dir";
>+ #$sffDirPath = "../sff_dir";
>  
>- 
>- # change this to reflect wherever you put the phredpar.dat file
>--$szPhredParameterFile = $szConsedHome . "/lib/phredpar.dat";
>-+$szPhredParameterFile = $szConsedHome . "/etc/PhredPar/phredpar.dat";
>- #$szPhredParameterFile = "/usr/local/common/lib/PhredPar/phredpar.dat";
>- #$szPhredParameterFile = "/usr/local/etc/PhredPar/phredpar.dat";
>- 
>-@@ -207,7 +207,7 @@
>- $chromatDirPath = "../chromat_dir";
>- $phdDirPath = "../phd_dir";
>- 
> -$niceExe = "/bin/nice";
> +$niceExe = "/usr/bin/nice";
>  $mvExe = "/bin/mv";
>  $lsExe = "/bin/ls";
>  $pwdExe = "/bin/pwd";
>-@@ -568,11 +568,11 @@
>- 
>- # only uncomment the following 4 lines when you have customized 
>- # determineReadTypes.perl
>--#print "\n\n--------------------------------------------------------\n";
>--#print "Now running determineReadTypes.perl...\n";
>--#print "--------------------------------------------------------\n\n\n";
>-+print "\n\n--------------------------------------------------------\n";
>-+print "Now running determineReadTypes.perl...\n";
>-+print "--------------------------------------------------------\n\n\n";
>- 
>--#!system( "$determineReadTypes" ) || die "some problem running determineReadTypes.perl $!\n";
>-+!system( "$determineReadTypes" ) || die "some problem running determineReadTypes.perl $!\n";
>- 
>- 
>- print "\n\n--------------------------------------------------------\n";
>Index: files/pkg-message.in
>===================================================================
>--- files/pkg-message.in	(revision 0)
>+++ files/pkg-message.in	(working copy)
>@@ -0,0 +1,12 @@
>+-----------------------------------------------------------------------------
>+CONSED installation directory: %%PREFIX%%/share/consed
>+
>+  You must do either of following (see section 4.5 of README.txt):
>+  1) set CONSED_HOME environment variable to the location above
>+  2) make /usr/local/genome be a symlink targeting to the location above
>+
>+Example files are installed not as world writable, which README.txt assumes.
>+So you must copy the files to anywhere you have writable permissions.
>+
>+Now you can follow README.txt from section 4.12
>+-----------------------------------------------------------------------------
>
>Property changes on: files/pkg-message.in
>___________________________________________________________________
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>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
>Index: pkg-plist
>===================================================================
>--- pkg-plist	(revision 0)
>+++ pkg-plist	(working copy)
>@@ -0,0 +1,1215 @@
>+bin/ace2Fasta.perl
>+bin/ace2Oligos.perl
>+bin/ace2OligosWithComments.perl
>+bin/ace2fof
>+bin/aceContigs2Phds.perl
>+bin/acestatus.pl
>+bin/add454Reads.perl
>+bin/addReads2Consed.perl
>+bin/addSangerReads.perl
>+bin/addSolexaReads.perl
>+bin/alignRNA2Genomic.perl
>+bin/alignSolexaReads2Refs.perl
>+bin/amplifyTranscripts.perl
>+bin/bam2Ace.perl
>+bin/cons.perl
>+bin/consed
>+@mode 111
>+bin/consed_linux32bit
>+@mode
>+bin/countEditedBases.perl
>+bin/determineReadTypes.perl
>+bin/export_cons
>+bin/fasta2Ace.perl
>+bin/fasta2Phd.perl
>+bin/fasta2PhdBall.perl
>+bin/fastq2Phrap.perl
>+bin/filter454Reads.perl
>+bin/findSequenceMatchesForConsed.perl
>+bin/fixContigEnd.perl
>+bin/lib2Phd.perl
>+bin/makePhdBall.perl
>+bin/makeRegionsFile.perl
>+bin/mergeAces.perl
>+bin/mktrace
>+bin/orderPrimerPairs.perl
>+bin/phd2Ace.perl
>+bin/phd2fasta
>+bin/phredPhrap
>+bin/phredPhrap.orig
>+bin/phredPhrapWithPhdBalls
>+bin/recover_consensus_tags
>+bin/removeReads
>+bin/revertToUneditedRead
>+bin/revert_fof
>+bin/selectOneRegion.perl
>+bin/selectRegions.perl
>+bin/sff2phd.perl
>+bin/sff2phd_Samborskyy
>+bin/sff2scf
>+bin/sff2scfAndPhd
>+bin/sffinfo
>+bin/tagRepeats.perl
>+bin/testSocket.perl
>+bin/transferConsensusTags.perl
>+%%DATADIR%%/README.txt
>+%%DATADIR%%/bin
>+%%DATADIR%%/examples/454_newbler/edit_dir/454Contigs.ace.1
>+%%DATADIR%%/examples/454_newbler/edit_dir/454Contigs.ace.1.091026.110917.fasta
>+%%DATADIR%%/examples/454_newbler/edit_dir/454Contigs.ace.1.aview
>+%%DATADIR%%/examples/454_newbler/phdball_dir/phd.ball.1
>+%%DATADIR%%/examples/454_newbler/sff_dir/pairedreads.sff
>+%%DATADIR%%/examples/align454reads/edit_dir/reference.fa
>+%%DATADIR%%/examples/align454reads/edit_dir/sff.fof
>+%%DATADIR%%/examples/align454reads/sff_dir/newreads.sff
>+%%DATADIR%%/examples/align454reads/sff_dir/reads.sff
>+%%DATADIR%%/examples/align454reads_answer/edit_dir/reference.ace
>+%%DATADIR%%/examples/align454reads_answer/edit_dir/reference.ace.1
>+%%DATADIR%%/examples/align454reads_answer/edit_dir/reference.fa
>+%%DATADIR%%/examples/align454reads_answer/edit_dir/sff.fof
>+%%DATADIR%%/examples/align454reads_answer/phdball_dir/phd.ball.1
>+%%DATADIR%%/examples/align454reads_answer/phdball_dir/phd.ball.2
>+%%DATADIR%%/examples/align454reads_answer/phdball_dir/phd.ball.3
>+%%DATADIR%%/examples/align454reads_answer/sff_dir/newreads.sff
>+%%DATADIR%%/examples/align454reads_answer/sff_dir/reads.sff
>+%%DATADIR%%/examples/assembly_view/edit_dir/.consedrc_mini
>+%%DATADIR%%/examples/assembly_view/edit_dir/assembly_view.030319.170348.fasta
>+%%DATADIR%%/examples/assembly_view/edit_dir/assembly_view.030319.170348.fasta.log
>+%%DATADIR%%/examples/assembly_view/edit_dir/assembly_view.fasta.screen.ace.1
>+%%DATADIR%%/examples/assembly_view/edit_dir/assembly_view.fasta.screen.ace.1.aview
>+%%DATADIR%%/examples/assembly_view/edit_dir/doNotShowInAssemblyView.fof
>+%%DATADIR%%/examples/assembly_view/edit_dir/fragSizes.txt
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q102.x1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q124.x1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q124.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q126.x1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q126.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q131.x1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q131.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q134.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q144.x1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q144.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q148.x1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q148.x1r1p24_e150.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q148.x1u1_e133.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q148.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q149.x1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q149.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q156.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q161.x1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q161.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q192.x1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q192.x1r1p30_e173.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q192.x1r1p33_e178.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q192.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q203.x1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q203.x1r2p46_e234.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q203.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q206.x1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q206.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q207.x1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q207.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q210.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q211.x1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q212.x1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q212.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q215.x1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q215.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q232.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q243.x1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q243.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q247.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q265.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q267.x1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q267.y1.phd.1
>+%%DATADIR%%/examples/assembly_view/phd_dir/djs736a1_fp02q270.x1.phd.1
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>
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>___________________________________________________________________
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>Index: pkg-plist.examples
>===================================================================
>--- pkg-plist.examples	(revision 359067)
>+++ pkg-plist.examples	(working copy)
>@@ -1,990 +0,0 @@
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>-share/examples/consed/assembly_view/edit_dir/.consedrc_mini
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>-share/examples/consed/polyphred/poly_dir/va-23.x.poly
>-share/examples/consed/standard/chromat_dir/djs74-1180.s1
>-share/examples/consed/standard/chromat_dir/djs74-1432.s1
>-share/examples/consed/standard/chromat_dir/djs74-1532.s1
>-share/examples/consed/standard/chromat_dir/djs74-1802.s1
>-share/examples/consed/standard/chromat_dir/djs74-1803.s1
>-share/examples/consed/standard/chromat_dir/djs74-1861.s1
>-share/examples/consed/standard/chromat_dir/djs74-1871.s1
>-share/examples/consed/standard/chromat_dir/djs74-2231.s1
>-share/examples/consed/standard/chromat_dir/djs74-2350.s1
>-share/examples/consed/standard/chromat_dir/djs74-2361.s1
>-share/examples/consed/standard/chromat_dir/djs74-237.s1
>-share/examples/consed/standard/chromat_dir/djs74-2516.s1
>-share/examples/consed/standard/chromat_dir/djs74-2664.s1
>-share/examples/consed/standard/chromat_dir/djs74-2679.s1
>-share/examples/consed/standard/chromat_dir/djs74-2689.s1
>-share/examples/consed/standard/chromat_dir/djs74-2931.s1
>-share/examples/consed/standard/chromat_dir/djs74-3174.s1
>-share/examples/consed/standard/chromat_dir/djs74-423.s1
>-share/examples/consed/standard/chromat_dir/djs74-561.s1
>-share/examples/consed/standard/chromat_dir/djs74-564.s1
>-share/examples/consed/standard/chromat_dir/djs74-690.x1
>-share/examples/consed/standard/chromat_dir/djs74-824.s1
>-share/examples/consed/standard/chromat_dir/djs74-932.s1
>-share/examples/consed/standard/chromat_dir/djs74-996.s2
>-share/examples/consed/standard/chromats_to_add/djs74-1455.s1
>-share/examples/consed/standard/chromats_to_add/djs74-1465.s1
>-share/examples/consed/standard/chromats_to_add/djs74-2282.s1
>-share/examples/consed/standard/chromats_to_add/djs74-2712.s1
>-share/examples/consed/standard/chromats_to_add/djs74-2861.s1
>-share/examples/consed/standard/chromats_to_add/djs74-536.s2
>-share/examples/consed/standard/chromats_to_add/djs74-568.s1
>-share/examples/consed/standard/chromats_to_add/djs74-649.x1
>-share/examples/consed/standard/chromats_to_add/djs74-867.s1
>-share/examples/consed/standard/edit_dir/custom_navigation.nav
>-share/examples/consed/standard/edit_dir/fragSizes.txt
>-share/examples/consed/standard/edit_dir/reads_to_add.fof
>-share/examples/consed/standard/edit_dir/reads_to_remove.fof
>-share/examples/consed/standard/edit_dir/standard.030328.142354.fasta
>-share/examples/consed/standard/edit_dir/standard.030328.142354.fasta.log
>-share/examples/consed/standard/edit_dir/standard.contigs
>-share/examples/consed/standard/edit_dir/standard.contigs.log
>-share/examples/consed/standard/edit_dir/standard.fasta
>-share/examples/consed/standard/edit_dir/standard.fasta.log
>-share/examples/consed/standard/edit_dir/standard.fasta.screen
>-share/examples/consed/standard/edit_dir/standard.fasta.screen.ace.1
>-share/examples/consed/standard/edit_dir/standard.fasta.screen.ace.1.aview
>-share/examples/consed/standard/edit_dir/standard.fasta.screen.contigs
>-share/examples/consed/standard/edit_dir/standard.fasta.screen.contigs.qual
>-share/examples/consed/standard/edit_dir/standard.fasta.screen.log
>-share/examples/consed/standard/edit_dir/standard.fasta.screen.problems
>-share/examples/consed/standard/edit_dir/standard.fasta.screen.problems.qual
>-share/examples/consed/standard/edit_dir/standard.fasta.screen.qual
>-share/examples/consed/standard/edit_dir/standard.fasta.screen.singlets
>-share/examples/consed/standard/edit_dir/standard.fasta.screen.view
>-share/examples/consed/standard/edit_dir/standard.newtags
>-share/examples/consed/standard/edit_dir/standard.phrap.out
>-share/examples/consed/standard/edit_dir/standard.screen.out
>-share/examples/consed/standard/edit_dir/standardNewChromats.fof
>-share/examples/consed/standard/edit_dir/standard_to_alu.cross
>-share/examples/consed/standard/phd_dir/djs74-1180.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-1432.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-1532.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-1802.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-1803.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-1861.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-1871.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-2231.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-2350.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-2361.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-237.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-2516.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-2664.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-2679.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-2689.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-2931.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-3174.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-423.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-423.s1.phd.2
>-share/examples/consed/standard/phd_dir/djs74-561.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-564.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-690.x1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-824.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-932.s1.phd.1
>-share/examples/consed/standard/phd_dir/djs74-996.s2.phd.1
>-@dirrm share/examples/consed/assembly_view/chromat_dir
>-@dirrm share/examples/consed/assembly_view/edit_dir
>-@dirrm share/examples/consed/assembly_view/phd_dir
>-@dirrm share/examples/consed/assembly_view
>-@dirrm share/examples/consed/autofinish/chromat_dir
>-@dirrm share/examples/consed/autofinish/edit_dir
>-@dirrm share/examples/consed/autofinish/phd_dir
>-@dirrm share/examples/consed/autofinish
>-@dirrm share/examples/consed/polyphred/chromat_dir
>-@dirrm share/examples/consed/polyphred/edit_dir
>-@dirrm share/examples/consed/polyphred/phd_dir
>-@dirrm share/examples/consed/polyphred/poly_dir
>-@dirrm share/examples/consed/polyphred
>-@dirrm share/examples/consed/standard/chromat_dir
>-@dirrm share/examples/consed/standard/chromats_to_add
>-@dirrm share/examples/consed/standard/edit_dir
>-@dirrm share/examples/consed/standard/phd_dir
>-@dirrm share/examples/consed/standard
>-@dirrm share/examples/consed

Flags:

mzaki: maintainer-approval+

Actions: View | Diff

Attachments on bug 191336: 144093 | 144094 | 144095