Date: Tue, 11 Dec 2007 11:11:53 GMT From: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/118548: New port: biology/consed viewing and editing workbench for sequence assembly Message-ID: <200712111111.lBBBBrYj041552@www.freebsd.org> Resent-Message-ID: <200712111120.lBBBK1oK045660@freefall.freebsd.org>
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>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 <mzaki@biol.s.u-tokyo.ac.jp>
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 <bsd.port.mk>
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
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q124.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q126.x1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q126.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q131.x1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q131.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q134.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q144.x1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q144.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q148.x1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q148.x1r1p24_e150.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q148.x1u1_e133.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q148.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q149.x1.phd.1
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
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q305.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q307.x1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q307.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q322.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q351.x1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q351.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q352.x1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q352.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q362.x1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q362.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q363.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q370.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q378.x1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q378.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q379.x1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q379.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q381.x1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q381.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q403.x1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q403.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q405.x1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q405.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q407.x1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q407.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q409.x1.phd.1
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Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q415.x1.phd.1
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Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q441.x1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q441.y1.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q444.x1.phd.1
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Xshare/examples/consed/assembly_view/phd_dir/djs736a1_fp02q452.x1.phd.1
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Xshare/examples/consed/assembly_view/phd_dir/djs736a2_fp04q282.y2.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a2_fp04q286.x2.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a2_fp04q286.y2.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a2_fp04q291.y2.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a2_fp04q293.x2.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a2_fp04q293.y2.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a2_fp04q294.y2.phd.1
Xshare/examples/consed/assembly_view/phd_dir/djs736a2_fp04q296.y2.phd.1
Xshare/examples/consed/autofinish/edit_dir/.consedrc.bu
Xshare/examples/consed/autofinish/edit_dir/autoPCRAmplify.fof
Xshare/examples/consed/autofinish/edit_dir/autoPCRAmplify.txt
Xshare/examples/consed/autofinish/edit_dir/autoPCRAmplify2.txt
Xshare/examples/consed/autofinish/edit_dir/autofinish.contigs
Xshare/examples/consed/autofinish/edit_dir/autofinish.contigs.log
Xshare/examples/consed/autofinish/edit_dir/autofinish.fasta
Xshare/examples/consed/autofinish/edit_dir/autofinish.fasta.log
Xshare/examples/consed/autofinish/edit_dir/autofinish.fasta.screen
Xshare/examples/consed/autofinish/edit_dir/autofinish.fasta.screen.ace.1
Xshare/examples/consed/autofinish/edit_dir/autofinish.fasta.screen.contigs
Xshare/examples/consed/autofinish/edit_dir/autofinish.fasta.screen.contigs.qual
Xshare/examples/consed/autofinish/edit_dir/autofinish.fasta.screen.log
Xshare/examples/consed/autofinish/edit_dir/autofinish.fasta.screen.problems
Xshare/examples/consed/autofinish/edit_dir/autofinish.fasta.screen.problems.qual
Xshare/examples/consed/autofinish/edit_dir/autofinish.fasta.screen.qual
Xshare/examples/consed/autofinish/edit_dir/autofinish.fasta.screen.singlets
Xshare/examples/consed/autofinish/edit_dir/autofinish.fasta.screen.view
Xshare/examples/consed/autofinish/edit_dir/autofinish.fof
Xshare/examples/consed/autofinish/edit_dir/autofinish.newtags
Xshare/examples/consed/autofinish/edit_dir/autofinishNewChromats.fof
Xshare/examples/consed/autofinish/edit_dir/autofinish_to_alu.cross
Xshare/examples/consed/autofinish/edit_dir/librariesInfo.txt_hide
Xshare/examples/consed/autofinish/phd_dir/djs228_1013.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_1029.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_1033.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_1034.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_1051.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_1094.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_1141.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_1153.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_1211.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_1248.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_1273.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_1331.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_1336.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_1343.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_1418.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_1422.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_168.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_1680.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_1740.s1.phd.1
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Xshare/examples/consed/autofinish/phd_dir/djs228_1803.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_1919.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_1929.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2019.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2078.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2083.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2116.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2151.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2222.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2273.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2282.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2338.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2346.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2390.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2417.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2436.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2529.s2.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2632.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2659.s1.phd.1
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Xshare/examples/consed/autofinish/phd_dir/djs228_2714.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2751.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2813.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2854.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2862.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2894.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2912.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2933.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_2949.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_3085.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_3196.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_331.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_426.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_433.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_434.s3.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_441.s3.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_474.s2.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_481.s2.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_523.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_539.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_560.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_671.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_671.s2.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_715.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_844.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_891.s1.phd.1
Xshare/examples/consed/autofinish/phd_dir/djs228_892.s1.phd.1
Xshare/examples/consed/polyphred/chromat_dir/ca-21.s
Xshare/examples/consed/polyphred/chromat_dir/ca-22.r
Xshare/examples/consed/polyphred/chromat_dir/ca-22.s
Xshare/examples/consed/polyphred/chromat_dir/ca-23.s
Xshare/examples/consed/polyphred/chromat_dir/ca-9.r
Xshare/examples/consed/polyphred/chromat_dir/ca-9.s
Xshare/examples/consed/polyphred/chromat_dir/va-1.x
Xshare/examples/consed/polyphred/chromat_dir/va-13.x
Xshare/examples/consed/polyphred/chromat_dir/va-16.x
Xshare/examples/consed/polyphred/chromat_dir/va-23.x
Xshare/examples/consed/polyphred/edit_dir/core
Xshare/examples/consed/polyphred/edit_dir/example2.contigs
Xshare/examples/consed/polyphred/edit_dir/example2.contigs.log
Xshare/examples/consed/polyphred/edit_dir/example2.fasta
Xshare/examples/consed/polyphred/edit_dir/example2.fasta.log
Xshare/examples/consed/polyphred/edit_dir/example2.fasta.screen
Xshare/examples/consed/polyphred/edit_dir/example2.fasta.screen.ace.1
Xshare/examples/consed/polyphred/edit_dir/example2.fasta.screen.contigs
Xshare/examples/consed/polyphred/edit_dir/example2.fasta.screen.contigs.qual
Xshare/examples/consed/polyphred/edit_dir/example2.fasta.screen.log
Xshare/examples/consed/polyphred/edit_dir/example2.fasta.screen.polyphred.out
Xshare/examples/consed/polyphred/edit_dir/example2.fasta.screen.qual
Xshare/examples/consed/polyphred/edit_dir/example2.fasta.screen.singlets
Xshare/examples/consed/polyphred/edit_dir/example2.fasta.screen.view
Xshare/examples/consed/polyphred/edit_dir/example2.newtags
Xshare/examples/consed/polyphred/edit_dir/example2.phrap.out
Xshare/examples/consed/polyphred/edit_dir/example2.screen.out
Xshare/examples/consed/polyphred/edit_dir/example2_to_alu.cross
Xshare/examples/consed/polyphred/edit_dir/phd.fof
Xshare/examples/consed/polyphred/edit_dir/problem_reads
Xshare/examples/consed/polyphred/edit_dir/problem_reads.qual
Xshare/examples/consed/polyphred/phd_dir/ca-21.s.phd.1
Xshare/examples/consed/polyphred/phd_dir/ca-22.r.phd.1
Xshare/examples/consed/polyphred/phd_dir/ca-22.s.phd.1
Xshare/examples/consed/polyphred/phd_dir/ca-23.s.phd.1
Xshare/examples/consed/polyphred/phd_dir/ca-9.r.phd.1
Xshare/examples/consed/polyphred/phd_dir/ca-9.s.phd.1
Xshare/examples/consed/polyphred/phd_dir/va-1.x.phd.1
Xshare/examples/consed/polyphred/phd_dir/va-13.x.phd.1
Xshare/examples/consed/polyphred/phd_dir/va-16.x.phd.1
Xshare/examples/consed/polyphred/phd_dir/va-23.x.phd.1
Xshare/examples/consed/polyphred/poly_dir/ca-21.s.poly
Xshare/examples/consed/polyphred/poly_dir/ca-22.r.poly
Xshare/examples/consed/polyphred/poly_dir/ca-22.s.poly
Xshare/examples/consed/polyphred/poly_dir/ca-23.s.poly
Xshare/examples/consed/polyphred/poly_dir/ca-9.r.poly
Xshare/examples/consed/polyphred/poly_dir/ca-9.s.poly
Xshare/examples/consed/polyphred/poly_dir/va-1.x.poly
Xshare/examples/consed/polyphred/poly_dir/va-13.x.poly
Xshare/examples/consed/polyphred/poly_dir/va-16.x.poly
Xshare/examples/consed/polyphred/poly_dir/va-23.x.poly
Xshare/examples/consed/standard/chromat_dir/djs74-1180.s1
Xshare/examples/consed/standard/chromat_dir/djs74-1432.s1
Xshare/examples/consed/standard/chromat_dir/djs74-1532.s1
Xshare/examples/consed/standard/chromat_dir/djs74-1802.s1
Xshare/examples/consed/standard/chromat_dir/djs74-1803.s1
Xshare/examples/consed/standard/chromat_dir/djs74-1861.s1
Xshare/examples/consed/standard/chromat_dir/djs74-1871.s1
Xshare/examples/consed/standard/chromat_dir/djs74-2231.s1
Xshare/examples/consed/standard/chromat_dir/djs74-2350.s1
Xshare/examples/consed/standard/chromat_dir/djs74-2361.s1
Xshare/examples/consed/standard/chromat_dir/djs74-237.s1
Xshare/examples/consed/standard/chromat_dir/djs74-2516.s1
Xshare/examples/consed/standard/chromat_dir/djs74-2664.s1
Xshare/examples/consed/standard/chromat_dir/djs74-2679.s1
Xshare/examples/consed/standard/chromat_dir/djs74-2689.s1
Xshare/examples/consed/standard/chromat_dir/djs74-2931.s1
Xshare/examples/consed/standard/chromat_dir/djs74-3174.s1
Xshare/examples/consed/standard/chromat_dir/djs74-423.s1
Xshare/examples/consed/standard/chromat_dir/djs74-561.s1
Xshare/examples/consed/standard/chromat_dir/djs74-564.s1
Xshare/examples/consed/standard/chromat_dir/djs74-690.x1
Xshare/examples/consed/standard/chromat_dir/djs74-824.s1
Xshare/examples/consed/standard/chromat_dir/djs74-932.s1
Xshare/examples/consed/standard/chromat_dir/djs74-996.s2
Xshare/examples/consed/standard/chromats_to_add/djs74-1455.s1
Xshare/examples/consed/standard/chromats_to_add/djs74-1465.s1
Xshare/examples/consed/standard/chromats_to_add/djs74-2282.s1
Xshare/examples/consed/standard/chromats_to_add/djs74-2712.s1
Xshare/examples/consed/standard/chromats_to_add/djs74-2861.s1
Xshare/examples/consed/standard/chromats_to_add/djs74-536.s2
Xshare/examples/consed/standard/chromats_to_add/djs74-568.s1
Xshare/examples/consed/standard/chromats_to_add/djs74-649.x1
Xshare/examples/consed/standard/chromats_to_add/djs74-867.s1
Xshare/examples/consed/standard/edit_dir/custom_navigation.nav
Xshare/examples/consed/standard/edit_dir/fragSizes.txt
Xshare/examples/consed/standard/edit_dir/reads_to_add.fof
Xshare/examples/consed/standard/edit_dir/reads_to_remove.fof
Xshare/examples/consed/standard/edit_dir/standard.030328.142354.fasta
Xshare/examples/consed/standard/edit_dir/standard.030328.142354.fasta.log
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 <mzaki@biol.s.u-tokyo.ac.jp>
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 <bsd.port.pre.mk>
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 <bsd.port.post.mk>
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 <mzaki@biol.s.u-tokyo.ac.jp>
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 <bsd.port.pre.mk>
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 <bsd.port.post.mk>
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 <mzaki@biol.s.u-tokyo.ac.jp>
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 <bsd.port.pre.mk>
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 <bsd.port.post.mk>
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
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