From owner-freebsd-ports-bugs@FreeBSD.ORG Tue Dec 11 11:20:01 2007 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 94F9E16A418 for ; Tue, 11 Dec 2007 11:20:01 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:4f8:fff6::28]) by mx1.freebsd.org (Postfix) with ESMTP id 80AD113C4D1 for ; Tue, 11 Dec 2007 11:20:01 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.14.2/8.14.2) with ESMTP id lBBBK1Jo045661 for ; Tue, 11 Dec 2007 11:20:01 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.2/8.14.1/Submit) id lBBBK1oK045660; Tue, 11 Dec 2007 11:20:01 GMT (envelope-from gnats) Resent-Date: Tue, 11 Dec 2007 11:20:01 GMT Resent-Message-Id: <200712111120.lBBBK1oK045660@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Motomichi Matsuzaki Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id D656516A41A for ; Tue, 11 Dec 2007 11:11:56 +0000 (UTC) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (www.freebsd.org [IPv6:2001:4f8:fff6::21]) by mx1.freebsd.org (Postfix) with ESMTP id D19F413C474 for ; Tue, 11 Dec 2007 11:11:56 +0000 (UTC) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (localhost [127.0.0.1]) by www.freebsd.org (8.14.2/8.14.2) with ESMTP id lBBBBrJg041553 for ; Tue, 11 Dec 2007 11:11:53 GMT (envelope-from nobody@www.freebsd.org) Received: (from nobody@localhost) by www.freebsd.org (8.14.2/8.14.1/Submit) id lBBBBrYj041552; Tue, 11 Dec 2007 11:11:53 GMT (envelope-from nobody) Message-Id: <200712111111.lBBBBrYj041552@www.freebsd.org> Date: Tue, 11 Dec 2007 11:11:53 GMT From: Motomichi Matsuzaki To: freebsd-gnats-submit@FreeBSD.org X-Send-Pr-Version: www-3.1 Cc: Subject: ports/118548: New port: biology/consed viewing and editing workbench for sequence assembly X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 11 Dec 2007 11:20:01 -0000 >Number: 118548 >Category: ports >Synopsis: New port: biology/consed viewing and editing workbench for sequence assembly >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Tue Dec 11 11:20:01 UTC 2007 >Closed-Date: >Last-Modified: >Originator: Motomichi Matsuzaki >Release: >Organization: >Environment: >Description: Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. >How-To-Repeat: >Fix: Patch attached with submission follows: # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # biology/consed # biology/consed/files # biology/consed/files/patch-scripts::phredPhrap # biology/consed/files/patch-misc::mktrace.c # biology/consed/files/patch-scripts::addReads2Consed.perl # biology/consed/files/patch-scripts::determineReadTypes.perl # biology/consed/Makefile # biology/consed/pkg-plist.examples # biology/consed/pkg-descr # biology/consed/distinfo # biology/phd2fasta # biology/phd2fasta/files # biology/phd2fasta/files/patch-Makefile # biology/phd2fasta/Makefile # biology/phd2fasta/distinfo # biology/phd2fasta/pkg-descr # biology/phrap # biology/phrap/Makefile # biology/phrap/distinfo # biology/phrap/pkg-descr # biology/phrap/files # biology/phrap/files/patch-makefile # biology/phred # biology/phred/Makefile # biology/phred/distinfo # biology/phred/files # biology/phred/files/patch-Makefile # biology/phred/pkg-descr # echo c - biology/consed mkdir -p biology/consed > /dev/null 2>&1 echo c - biology/consed/files mkdir -p biology/consed/files > /dev/null 2>&1 echo x - biology/consed/files/patch-scripts::phredPhrap sed 's/^X//' >biology/consed/files/patch-scripts::phredPhrap << 'END-of-biology/consed/files/patch-scripts::phredPhrap' X--- scripts/phredPhrap.orig 2007-09-26 04:02:20.000000000 +0900 X+++ scripts/phredPhrap 2007-12-11 17:32:27.000000000 +0900 X@@ -101,7 +101,7 @@ X X X # change this to reflect wherever you put the phredpar.dat file X-$szPhredParameterFile = $szConsedHome . "/lib/phredpar.dat"; X+$szPhredParameterFile = $szConsedHome . "/etc/PhredPar/phredpar.dat"; X #$szPhredParameterFile = "/usr/local/common/lib/PhredPar/phredpar.dat"; X #$szPhredParameterFile = "/usr/local/etc/PhredPar/phredpar.dat"; X X@@ -207,7 +207,7 @@ X $chromatDirPath = "../chromat_dir"; X $phdDirPath = "../phd_dir"; X X-$niceExe = "/bin/nice"; X+$niceExe = "/usr/bin/nice"; X $mvExe = "/bin/mv"; X $lsExe = "/bin/ls"; X $pwdExe = "/bin/pwd"; X@@ -568,11 +568,11 @@ X X # only uncomment the following 4 lines when you have customized X # determineReadTypes.perl X-#print "\n\n--------------------------------------------------------\n"; X-#print "Now running determineReadTypes.perl...\n"; X-#print "--------------------------------------------------------\n\n\n"; X+print "\n\n--------------------------------------------------------\n"; X+print "Now running determineReadTypes.perl...\n"; X+print "--------------------------------------------------------\n\n\n"; X X-#!system( "$determineReadTypes" ) || die "some problem running determineReadTypes.perl $!\n"; X+!system( "$determineReadTypes" ) || die "some problem running determineReadTypes.perl $!\n"; X X X print "\n\n--------------------------------------------------------\n"; END-of-biology/consed/files/patch-scripts::phredPhrap echo x - biology/consed/files/patch-misc::mktrace.c sed 's/^X//' >biology/consed/files/patch-misc::mktrace.c << 'END-of-biology/consed/files/patch-misc::mktrace.c' X--- misc/mktrace/mktrace.c.orig Tue Aug 31 03:14:17 2004 X+++ misc/mktrace/mktrace.c Wed Jul 13 16:31:28 2005 X@@ -70,9 +70,9 @@ X else X { X printf( "enter FASTA filename: " ); X- gets( ifnm ); X+ fgets( ifnm, sizeof(ifnm), stdin ); X printf( "enter output filename: " ); X- gets( ofnm ); X+ fgets( ofnm, sizeof(ofnm), stdin ); X } X X /* END-of-biology/consed/files/patch-misc::mktrace.c echo x - biology/consed/files/patch-scripts::addReads2Consed.perl sed 's/^X//' >biology/consed/files/patch-scripts::addReads2Consed.perl << 'END-of-biology/consed/files/patch-scripts::addReads2Consed.perl' X--- scripts/addReads2Consed.perl.orig 2007-09-26 04:02:19.000000000 +0900 X+++ scripts/addReads2Consed.perl 2007-12-11 17:27:20.000000000 +0900 X@@ -71,7 +71,7 @@ X $szVectorFile = $szConsedHome . "/lib/screenLibs/vector.seq"; X X # change this to reflect wherever you put the phred parameter file X-$szPhredParameterFile = $szConsedHome . "/lib/phredpar.dat"; X+$szPhredParameterFile = $szConsedHome . "/etc/PhredPar/phredpar.dat"; X #$szPhredParameterFile = "/usr/local/common/lib/PhredPar/phredpar.dat"; X #$szPhredParameterFile = "/usr/local/etc/PhredPar/phredpar.dat"; X END-of-biology/consed/files/patch-scripts::addReads2Consed.perl echo x - biology/consed/files/patch-scripts::determineReadTypes.perl sed 's/^X//' >biology/consed/files/patch-scripts::determineReadTypes.perl << 'END-of-biology/consed/files/patch-scripts::determineReadTypes.perl' X--- scripts/determineReadTypes.perl.orig Tue Aug 31 03:14:13 2004 X+++ scripts/determineReadTypes.perl Wed Jul 13 17:00:22 2005 X@@ -177,7 +177,7 @@ X # you can remove or comment out this line when you are satisfied with X # your customized version of this file. X X-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"; X+#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"; X X $szVersion = "001205"; X END-of-biology/consed/files/patch-scripts::determineReadTypes.perl echo x - biology/consed/Makefile sed 's/^X//' >biology/consed/Makefile << 'END-of-biology/consed/Makefile' X# New ports collection makefile for: phred X# Date created: 8 July 2005 X# Whom: Motomichi Matsuzaki X# X# $FreeBSD$ X# X XPORTNAME= consed XPORTVERSION= 16.0 XCATEGORIES= biology XMASTER_SITES= http://www.phrap.org/consed/distributions/${PORTVERSION}/ XDISTNAME= ${PORTNAME}_linux XEXTRACT_SUFX= .tar.Z X XMAINTAINER= mzaki@biol.s.u-tokyo.ac.jp XCOMMENT= A graphical tool for editing Phrap assemblies X XRUN_DEPENDS= phred:${PORTSDIR}/biology/phred \ X phrap:${PORTSDIR}/biology/phrap \ X phd2fasta:${PORTSDIR}/biology/phd2fasta X XUSE_PERL5= yes XUSE_LINUX= yes XUSE_XLIB= yes XONLY_FOR_ARCHS= i386 amd64 X XRESTRICTED= Redistribution is not permitted in any form. You must request access permission via e-mail to get the tarball. Free for academic use. X XNO_WRKSUBDIR= yes X XBUILD_WRKSRC= ${WRKSRC}/misc/mktrace XALL_TARGET= mktrace X XBINARIES= consed mktrace sffinfo sff2scf XCONTRIBS= ace2OligosWithComments.perl ace2fof \ X aceContigs2Phds.perl acestatus.pl export_cons \ X mergeAces.perl recover_consensus_tags revert_fof XSCRIPTS= ace2Fasta.perl ace2Oligos.perl addReads2Consed.perl \ X amplifyTranscripts.perl catPhdFiles.perl \ X countEditedBases.perl determineReadTypes.perl fasta2Phd.perl \ X findSequenceMatchesForConsed.perl lib2Phd.perl \ X orderPrimerPairs.perl phd2Ace.perl phredPhrap removeReads \ X revertToUneditedRead tagRepeats.perl transferConsensusTags.perl X.for file in ${BINARIES} ${CONTRIBS} ${SCRIPTS} XPLIST_FILES+= bin/${file} X.endfor X XDATADIR= ${PREFIX}/lib/screenLibs XDATAFILES= primerCloneScreen.seq primerSubcloneScreen.seq \ X repeats.fasta singleVectorForRestrictionDigest.fasta XNULLFILES= vector.seq X.for file in ${DATAFILES} ${NULLFILES} XPORTDATA+= ${file}.dist X.endfor XPORTDOCS= README.txt X X.if defined(WITH_EXAMPLES) XEXAMPLES= standard autofinish assembly_view polyphred XPLIST= ${PKGDIR}/pkg-plist.examples X.endif X Xpost-build: X (cd ${WRKSRC}/misc/454; ${CC} ${CFLAGS} sffinfo.c -o sffinfo) X (cd ${WRKSRC}/misc/454; ${CC} ${CFLAGS} sff2scf.c -o sff2scf) X Xdo-install: X @${INSTALL_PROGRAM} ${WRKSRC}/consed_linux2.4 ${PREFIX}/bin/consed X @${INSTALL_PROGRAM} ${BUILD_WRKSRC}/mktrace ${PREFIX}/bin/ X @${INSTALL_PROGRAM} ${WRKSRC}/misc/454/sffinfo ${PREFIX}/bin/ X @${INSTALL_PROGRAM} ${WRKSRC}/misc/454/sff2scf ${PREFIX}/bin/ X.for file in ${BINARIES} X @${CHMOD} a-r ${PREFIX}/bin/${file} X.endfor X.for file in ${CONTRIBS} X @${INSTALL_SCRIPT} ${WRKSRC}/contributions/${file} ${PREFIX}/bin/ X.endfor X.for file in ${SCRIPTS} X @${INSTALL_SCRIPT} ${WRKSRC}/scripts/${file} ${PREFIX}/bin/ X.endfor X @${MKDIR} ${DATADIR} X.for file in ${DATAFILES} X @${INSTALL_DATA} ${WRKSRC}/misc/${file} ${DATADIR}/${file}.dist X.endfor X.for file in ${NULLFILES} X @${INSTALL_DATA} /dev/null ${DATADIR}/${file}.dist X.endfor X.if !defined(NOPORTEXAMPLES) X @${MKDIR} ${EXAMPLESDIR} X.for dir in ${EXAMPLES} X @${CP} -R ${WRKSRC}/${dir} ${EXAMPLESDIR} X.endfor X.endif X.if !defined(NOPORTDOCS) X @${MKDIR} ${DOCSDIR} X.for file in ${PORTDOCS} X @${INSTALL_DATA} ${WRKSRC}/${file} ${DOCSDIR} X.endfor X.endif X.if !defined(WITH_EXAMPLES) X @${ECHO_CMD} "Examples were not installed. You can define WITH_EXAMPLES=yes to install them." X.endif X @${ECHO_CMD} "You must set the CONSED_HOME environment variable to '${PREFIX}'" X X.include END-of-biology/consed/Makefile echo x - biology/consed/pkg-plist.examples sed 's/^X//' >biology/consed/pkg-plist.examples << 'END-of-biology/consed/pkg-plist.examples' Xshare/examples/consed/assembly_view/edit_dir/.consedrc Xshare/examples/consed/assembly_view/edit_dir/.consedrc_mini Xshare/examples/consed/assembly_view/edit_dir/assembly_view.030319.170348.fasta Xshare/examples/consed/assembly_view/edit_dir/assembly_view.030319.170348.fasta.log Xshare/examples/consed/assembly_view/edit_dir/assembly_view.fasta.screen.ace.1 Xshare/examples/consed/assembly_view/edit_dir/assembly_view.fasta.screen.ace.1.aview Xshare/examples/consed/assembly_view/edit_dir/doNotShowInAssemblyView.fof Xshare/examples/consed/assembly_view/edit_dir/fragSizes.txt Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q102.x1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q124.x1.phd.1 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Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q149.y1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q156.y1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q161.x1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q161.y1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q192.x1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q192.x1r1p30_e173.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q192.x1r1p33_e178.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q192.y1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q203.x1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q203.x1r2p46_e234.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q203.y1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q206.x1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q206.y1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q207.x1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q207.y1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q210.y1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q211.x1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q212.x1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q212.y1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q215.x1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q215.y1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q232.y1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q243.x1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q243.y1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q247.y1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q265.y1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q267.x1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q267.y1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q270.x1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q270.y1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q277.x1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q277.y1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q279.x1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q282.x1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q282.y1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q287.x1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q287.y1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q293.x1.phd.1 Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q293.y1.phd.1 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Xshare/examples/consed/standard/edit_dir/standard.contigs Xshare/examples/consed/standard/edit_dir/standard.contigs.log Xshare/examples/consed/standard/edit_dir/standard.fasta Xshare/examples/consed/standard/edit_dir/standard.fasta.log Xshare/examples/consed/standard/edit_dir/standard.fasta.screen Xshare/examples/consed/standard/edit_dir/standard.fasta.screen.ace.1 Xshare/examples/consed/standard/edit_dir/standard.fasta.screen.ace.1.aview Xshare/examples/consed/standard/edit_dir/standard.fasta.screen.contigs Xshare/examples/consed/standard/edit_dir/standard.fasta.screen.contigs.qual Xshare/examples/consed/standard/edit_dir/standard.fasta.screen.log Xshare/examples/consed/standard/edit_dir/standard.fasta.screen.problems Xshare/examples/consed/standard/edit_dir/standard.fasta.screen.problems.qual Xshare/examples/consed/standard/edit_dir/standard.fasta.screen.qual Xshare/examples/consed/standard/edit_dir/standard.fasta.screen.singlets Xshare/examples/consed/standard/edit_dir/standard.fasta.screen.view Xshare/examples/consed/standard/edit_dir/standard.newtags Xshare/examples/consed/standard/edit_dir/standard.phrap.out Xshare/examples/consed/standard/edit_dir/standard.screen.out Xshare/examples/consed/standard/edit_dir/standardNewChromats.fof Xshare/examples/consed/standard/edit_dir/standard_to_alu.cross Xshare/examples/consed/standard/phd_dir/djs74-1180.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-1432.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-1532.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-1802.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-1803.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-1861.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-1871.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-2231.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-2350.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-2361.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-237.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-2516.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-2664.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-2679.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-2689.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-2931.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-3174.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-423.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-423.s1.phd.2 Xshare/examples/consed/standard/phd_dir/djs74-561.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-564.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-690.x1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-824.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-932.s1.phd.1 Xshare/examples/consed/standard/phd_dir/djs74-996.s2.phd.1 X@dirrm share/examples/consed/assembly_view/chromat_dir X@dirrm share/examples/consed/assembly_view/edit_dir X@dirrm share/examples/consed/assembly_view/phd_dir X@dirrm share/examples/consed/assembly_view X@dirrm share/examples/consed/autofinish/chromat_dir X@dirrm share/examples/consed/autofinish/edit_dir X@dirrm share/examples/consed/autofinish/phd_dir X@dirrm share/examples/consed/autofinish X@dirrm share/examples/consed/polyphred/chromat_dir X@dirrm share/examples/consed/polyphred/edit_dir X@dirrm share/examples/consed/polyphred/phd_dir X@dirrm share/examples/consed/polyphred/poly_dir X@dirrm share/examples/consed/polyphred X@dirrm share/examples/consed/standard/chromat_dir X@dirrm share/examples/consed/standard/chromats_to_add X@dirrm share/examples/consed/standard/edit_dir X@dirrm share/examples/consed/standard/phd_dir X@dirrm share/examples/consed/standard X@dirrm share/examples/consed END-of-biology/consed/pkg-plist.examples echo x - biology/consed/pkg-descr sed 's/^X//' >biology/consed/pkg-descr << 'END-of-biology/consed/pkg-descr' XConsed is a tool for viewing and editing sequence assemblies made by phrap, Xand includes Autofinish which will automatically choose finishing reads. X XWWW: http://www.phrap.org/consed/consed.html END-of-biology/consed/pkg-descr echo x - biology/consed/distinfo sed 's/^X//' >biology/consed/distinfo << 'END-of-biology/consed/distinfo' XMD5 (consed_linux.tar.Z) = 35d508cfc308128ab85b04c65d968efd XSHA256 (consed_linux.tar.Z) = ac9ce155ce46f7200accaa033c9b1ea1d8c071c68c2a82ab5f4b623d9ff6b117 XSIZE (consed_linux.tar.Z) = 27555099 END-of-biology/consed/distinfo echo c - biology/phd2fasta mkdir -p biology/phd2fasta > /dev/null 2>&1 echo c - biology/phd2fasta/files mkdir -p biology/phd2fasta/files > /dev/null 2>&1 echo x - biology/phd2fasta/files/patch-Makefile sed 's/^X//' >biology/phd2fasta/files/patch-Makefile << 'END-of-biology/phd2fasta/files/patch-Makefile' X--- Makefile.orig 2002-08-09 05:30:48.000000000 +0900 X+++ Makefile 2007-12-06 19:02:31.000000000 +0900 X@@ -1,5 +1,5 @@ X-CC=cc X-CFLAGS=-O -w X+CC?=cc X+CFLAGS+=-w X CLIB=-lm X X OBJ= phd2fasta.o \ END-of-biology/phd2fasta/files/patch-Makefile echo x - biology/phd2fasta/Makefile sed 's/^X//' >biology/phd2fasta/Makefile << 'END-of-biology/phd2fasta/Makefile' X# New ports collection makefile for: phd2fasta X# Date created: 6 December 2007 X# Whom: Motomichi Matsuzaki X# X# $FreeBSD$ X# X XPORTNAME= phd2fasta XPORTVERSION= 0.990622.f XCATEGORIES= biology XMASTER_SITES= # put the tarball manually XDISTFILES= phd2fasta-acd-dist.tar.Z X XMAINTAINER= mzaki@biol.s.u-tokyo.ac.jp XCOMMENT= A converter from output files of Phred/Consed to FASTA files X XRESTRICTED= Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use. X XNO_WRKSUBDIR= yes X XALL_TARGET= phd2fasta X XBINMODE= 0111 # avoid copying binaries as required by the agreement XBINARIES= phd2fasta XPLIST_FILES= bin/phd2fasta X XPORTDOCS= PHD2FASTA.DOC X X.include X X.for file in ${DISTFILES} X.if !exists(${DISTDIR}/${file}) XIGNORE= you must request the source code \(${file}\) via e-mail, place it manually in ${DISTDIR}, and then try it again X.endif X.endfor X Xdo-install: X.for file in ${BINARIES} X @${INSTALL_PROGRAM} ${WRKSRC}/${file} ${PREFIX}/bin/ X.endfor X.if !defined(NOPORTDOCS) X @${MKDIR} ${DOCSDIR} X.for file in ${PORTDOCS} X @${INSTALL_DATA} ${WRKSRC}/${file} ${DOCSDIR} X.endfor X.endif X X.include END-of-biology/phd2fasta/Makefile echo x - biology/phd2fasta/distinfo sed 's/^X//' >biology/phd2fasta/distinfo << 'END-of-biology/phd2fasta/distinfo' XMD5 (phd2fasta-acd-dist.tar.Z) = d72a5b20925d45ca87b353e20f3c673c XSHA256 (phd2fasta-acd-dist.tar.Z) = e73e190a9721e8f459e8589bd448114cf670054240439dec2c8cde8d9f97c6a0 XSIZE (phd2fasta-acd-dist.tar.Z) = 58431 END-of-biology/phd2fasta/distinfo echo x - biology/phd2fasta/pkg-descr sed 's/^X//' >biology/phd2fasta/pkg-descr << 'END-of-biology/phd2fasta/pkg-descr' XPhred and consed write sequence and quality value information in X'phd' output files. A phd file contains information in a header, Xthe called bases, the base quality values, and the base call trace Xlocations. Phd2fasta reads phd files and writes sequence and quality Xvalue FASTA files, which phrap and cross_match need as input. X(Consed needs phd files in order to obtain the base call locations.) X XWWW: http://www.phrap.org/phredphrapconsed.html END-of-biology/phd2fasta/pkg-descr echo c - biology/phrap mkdir -p biology/phrap > /dev/null 2>&1 echo x - biology/phrap/Makefile sed 's/^X//' >biology/phrap/Makefile << 'END-of-biology/phrap/Makefile' X# New ports collection makefile for: phrap X# Date created: 21 June 2005 X# Whom: Motomichi Matsuzaki X# X# $FreeBSD$ X# X XPORTNAME= phrap XPORTVERSION= 0.990329 XCATEGORIES= biology XMASTER_SITES= # put the tarball manually XDISTFILES= distrib.tar.Z XDIST_SUBDIR= ${PORTNAME} X XMAINTAINER= ports@FreeBSD.org XCOMMENT= Phrap is a program for assembling shotgun DNA sequence data X XRESTRICTED= Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use. X XNO_WRKSUBDIR= yes X XMAKEFILE= makefile XALL_TARGET= all manyreads X XBINARIES= cluster cross_match cross_match.manyreads loco \ X phrap phrap.longreads phrap.manyreads swat XSCRIPTS= phrapview X.for file in ${BINARIES} ${SCRIPTS} XPLIST_FILES+= bin/${file} X.endfor X XPORTDATA= BLOSUM50 BLOSUM62 PAM250 mat50 mat70 penalty2 vector.seq XPORTDOCS= general.doc phrap.doc swat.doc X X.include X X.for file in ${DISTFILES} X.if !exists(${DISTDIR}/${DIST_SUBDIR}/${file}) XIGNORE= you must request the source code \(${DISTFILES}\) via e-mail, place it manually in ${DISTDIR}/${DIST_SUBDIR}, and then try it again X.endif X.endfor X Xdo-install: X.for file in ${BINARIES} X @${INSTALL_PROGRAM} ${WRKSRC}/${file} ${PREFIX}/bin/ X @${CHMOD} a-r ${PREFIX}/bin/${file} # as required by the agreement X.endfor X.for file in ${SCRIPTS} X @${INSTALL_SCRIPT} ${WRKSRC}/${file} ${PREFIX}/bin/ X.endfor X @${MKDIR} ${DATADIR} X.for file in ${PORTDATA} X @${INSTALL_DATA} ${WRKSRC}/${file} ${DATADIR} X.endfor X.if !defined(NOPORTDOCS) X @${MKDIR} ${DOCSDIR} X.for file in ${PORTDOCS} X @${INSTALL_DATA} ${WRKSRC}/${file} ${DOCSDIR} X.endfor X.endif X X.include END-of-biology/phrap/Makefile echo x - biology/phrap/distinfo sed 's/^X//' >biology/phrap/distinfo << 'END-of-biology/phrap/distinfo' XMD5 (phrap/distrib.tar.Z) = 35175595801cafd22ec348fb9dba0ce4 XSHA256 (phrap/distrib.tar.Z) = e0be79818e3a8ca17391f42cc0ffbaf1a63299c8845a0b9ac3aaeb3cac641fcc XSIZE (phrap/distrib.tar.Z) = 366163 END-of-biology/phrap/distinfo echo x - biology/phrap/pkg-descr sed 's/^X//' >biology/phrap/pkg-descr << 'END-of-biology/phrap/pkg-descr' XPhrap is a program for assembling shotgun DNA sequence data. XAmong other features, it allows use of the entire read and not just the Xtrimmed high quality part, it uses a combination of user-supplied and Xinternally computed data quality information to improve assembly accuracy Xin the presence of repeats, it constructs the contig sequence as a mosaic Xof the highest quality read segments rather than a consensus, it provides Xextensive assembly information to assist in trouble-shooting assembly Xproblems, and it handles large datasets. X XThis package also contains Swat and Cross_match. XSwat is a program for searching one or more DNA or protein query sequences Xagainst a sequence database, using (an efficient implementation of) the XSmith-Waterman-Gotoh algorithm. XCross_Match is a general-purpose utility based on Swat for comparing any Xtwo sets of DNA sequences, and it can be used to: X* produce vector-masked versions of a set of reads X* compare a set of cDNA sequences to a set of cosmids X* compare contigs found by two altanative assembly procedures to each other X* compare phrap contigs to the final edited cosmid sequence. X XWWW: http://www.phrap.org/phredphrapconsed.html END-of-biology/phrap/pkg-descr echo c - biology/phrap/files mkdir -p biology/phrap/files > /dev/null 2>&1 echo x - biology/phrap/files/patch-makefile sed 's/^X//' >biology/phrap/files/patch-makefile << 'END-of-biology/phrap/files/patch-makefile' X--- makefile.orig 1999-03-11 15:13:20.000000000 +0900 X+++ makefile 2007-12-11 13:19:39.000000000 +0900 X@@ -23,8 +23,8 @@ X #*****************************************************************************/ X X # Makefile for swat, phrap, cross_match, phrapview; also swprobs (currently inactivated) X-CC= cc X-CFLAGS= -O2 X+CC?= cc X+#CFLAGS= -O2 X LFLAGS= -lm X X SWATOBJS= swat.o weibull.o X@@ -55,11 +55,11 @@ X X manyreads: X touch swat.h; X- make CFLAGS="-O2 -DMANYREADS" phrap cross_match; X+ make CFLAGS="$(CFLAGS) -DMANYREADS" phrap cross_match; X mv phrap phrap.manyreads; X mv cross_match cross_match.manyreads; X touch swat.h; X- make CFLAGS="-O2 -DLONGREADS" phrap; X+ make CFLAGS="$(CFLAGS) -DLONGREADS" phrap; X mv phrap phrap.longreads; X touch swat.h; X make phrap cross_match; END-of-biology/phrap/files/patch-makefile echo c - biology/phred mkdir -p biology/phred > /dev/null 2>&1 echo x - biology/phred/Makefile sed 's/^X//' >biology/phred/Makefile << 'END-of-biology/phred/Makefile' X# New ports collection makefile for: phred X# Date created: 6 December 2007 X# Whom: Motomichi Matsuzaki X# X# $FreeBSD$ X# X XPORTNAME= phred XPORTVERSION= 0.020425.c XCATEGORIES= biology XMASTER_SITES= # put the tarball manually XDISTNAME= ${PORTNAME}-dist-${PORTVERSION:S/0.//}-acd XEXTRACT_SUFX= .tar.Z X XMAINTAINER= mzaki@biol.s.u-tokyo.ac.jp XCOMMENT= base calling and quality value assignment on DNA sequencing X XRESTRICTED= Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use. X XNO_WRKSUBDIR= yes X XALL_TARGET= phred daev X XBINMODE= 0111 # avoid copying binaries as required by the agreement XBINARIES= phred daev X.for file in ${BINARIES} XPLIST_FILES+= bin/${file} X.endfor X XDATADIR= ${PREFIX}/etc/PhredPar XDATAFILES= phredpar.dat X.for file in ${DATAFILES} XPORTDATA+= ${file}.dist X.endfor X XPORTDOCS= NEWS PHRED.DOC DAEV.DOC X X.include X X.for file in ${DISTFILES} X.if !exists(${DISTDIR}/${file}) XIGNORE= you must request the source code \(${file}\) via e-mail, place it manually in ${DISTDIR}, and then try it again X.endif X.endfor X Xdo-install: X.for file in ${BINARIES} X @${INSTALL_PROGRAM} ${WRKSRC}/${file} ${PREFIX}/bin/ X.endfor X @${MKDIR} ${DATADIR} X.for file in ${DATAFILES} X @${INSTALL_DATA} ${WRKSRC}/${file} ${DATADIR}/${file}.dist X.endfor X.if !defined(NOPORTDOCS) X @${MKDIR} ${DOCSDIR} X.for file in ${PORTDOCS} X @${INSTALL_DATA} ${WRKSRC}/${file} ${DOCSDIR} X.endfor X.endif X @${ECHO} "---------------------------------------------------------------------------" X @${ECHO} "You must set PHRED_PARAMETER_FILE environment variable." X @${ECHO} "" X @${ECHO} "The default parameter file in the distribution is located at:" X @${ECHO} " ${DATADIR}/phredpar.dat.dist" X @${ECHO} "---------------------------------------------------------------------------" X X.include END-of-biology/phred/Makefile echo x - biology/phred/distinfo sed 's/^X//' >biology/phred/distinfo << 'END-of-biology/phred/distinfo' XMD5 (phred-dist-020425.c-acd.tar.Z) = f6f86e14b6283d4797a5872a8d44a358 XSHA256 (phred-dist-020425.c-acd.tar.Z) = c7a7773447376c024212b680e1ce1e52c30ad8e18dee317ba863bc10db94f6c9 XSIZE (phred-dist-020425.c-acd.tar.Z) = 547645 END-of-biology/phred/distinfo echo c - biology/phred/files mkdir -p biology/phred/files > /dev/null 2>&1 echo x - biology/phred/files/patch-Makefile sed 's/^X//' >biology/phred/files/patch-Makefile << 'END-of-biology/phred/files/patch-Makefile' X--- Makefile.orig 2002-07-27 07:22:10.000000000 +0900 X+++ Makefile 2007-12-06 16:41:35.000000000 +0900 X@@ -12,8 +12,8 @@ X X # UNIX specific definitions (default) X # X-CC= cc X-CFLAGS= -O -DANSI_C $(LXFLAGS) X+CC?= cc X+CFLAGS+= -DANSI_C $(LXFLAGS) X CLIB= -lm X X # Windows 'nmake' specific definitions END-of-biology/phred/files/patch-Makefile echo x - biology/phred/pkg-descr sed 's/^X//' >biology/phred/pkg-descr << 'END-of-biology/phred/pkg-descr' XPhred reads DNA sequencer trace data, calls bases, assigns quality values Xto the bases, and writes the base calls and quality values to output files. X XTrace data is read from chromatogram files in the SCF, ABI, and EST formats, Xeven if they were compressed using gzip, bzip2, or UNIX compress. XQuality values are written to FASTA format files or PHD files, which can be Xused by the Phrap sequence assembly program in order to increase the accuracy Xof the assembled sequence. X XBase calling and quality value accuracies tested for: X ABI models 373, 377, and 3700 X Molecular Dynamics MegaBACE X LI-COR 4000 X XBase calling accuracies tested for: X ABI model 3100 X Beckman CEQ X XIt contains also a data evaluation program called 'daev'. XSee DAEV.DOC for more information. X XYou must obtain the tarball via e-mail to build. See the web site below. X XWWW: http://www.phrap.org/phredphrapconsed.html END-of-biology/phred/pkg-descr exit >Release-Note: >Audit-Trail: >Unformatted: