diff options
| author | pi <pi@FreeBSD.org> | 2014-08-24 02:04:58 +0800 |
|---|---|---|
| committer | pi <pi@FreeBSD.org> | 2014-08-24 02:04:58 +0800 |
| commit | 0d4dc2e5c8aa52558141f0a47ae160333cf66a79 (patch) | |
| tree | 23e972a9950cc8d2fbf2c0128d929e3655a093ab | |
| parent | 1bdcb7adc25e2a9b462e12dcf04efbefa2bdc259 (diff) | |
| download | freebsd-ports-gnome-0d4dc2e5c8aa52558141f0a47ae160333cf66a79.tar.gz freebsd-ports-gnome-0d4dc2e5c8aa52558141f0a47ae160333cf66a79.tar.zst freebsd-ports-gnome-0d4dc2e5c8aa52558141f0a47ae160333cf66a79.zip | |
update ports:
biology/phrab
biology/phred
biology/consed
Although these programs are licensed freely for academic and nonprofit
purposes, users have to contact the authors to obtain the tarballs.
PR: 191336
Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer)
31 files changed, 735 insertions, 1187 deletions
diff --git a/biology/consed/Makefile b/biology/consed/Makefile index 4debb50ee96d..971c930d5e15 100644 --- a/biology/consed/Makefile +++ b/biology/consed/Makefile @@ -2,22 +2,68 @@ # $FreeBSD$ PORTNAME= consed -PORTVERSION= 16.0 +PORTVERSION= 27.0 CATEGORIES= biology -MASTER_SITES= http://www.phrap.org/consed/distributions/${PORTVERSION}/ +# MASTER_SITES= http://www.phrap.org/consed/distributions/${PORTVERSION}/ +MASTER_SITES= http://bozeman.mbt.washington.edu/consed/distributions/${PORTVERSION}/ DISTNAME= ${PORTNAME}_linux MAINTAINER= mzaki@m.u-tokyo.ac.jp COMMENT= Graphical tool for editing Phrap assemblies RUN_DEPENDS= phred:${PORTSDIR}/biology/phred \ - phrap:${PORTSDIR}/biology/phrap \ - phd2fasta:${PORTSDIR}/biology/phd2fasta + phrap:${PORTSDIR}/biology/phrap -USES= perl5 tar:Z +CONFLICTS_INSTALL= phd2fasta-[0-9]* + +SUB_FILES= pkg-message + +USES= perl5 shebangfix USE_LINUX= yes USE_LINUX_APPS= xorglibs ONLY_FOR_ARCHS= i386 amd64 +MYSHEBANG= bin/ace2Fasta.perl \ + bin/tagRepeats.perl \ + bin/selectRegions.perl \ + bin/selectOneRegion.perl \ + bin/revertToUneditedRead \ + bin/removeReads \ + bin/phredPhrap.orig \ + bin/phredPhrap \ + bin/phd2Ace.perl \ + bin/orderPrimerPairs.perl \ + bin/makeRegionsFile.perl \ + bin/makePhdBall.perl \ + bin/lib2Phd.perl \ + bin/fixContigEnd.perl \ + bin/findSequenceMatchesForConsed.perl \ + bin/revert_fof \ + bin/filter454Reads.perl \ + bin/fastq2Phrap.perl \ + bin/fasta2PhdBall.perl \ + bin/fasta2Phd.perl \ + bin/fasta2Ace.perl \ + bin/determineReadTypes.perl \ + bin/countEditedBases.perl \ + bin/bam2Ace.perl \ + bin/amplifyTranscripts.perl \ + bin/alignSolexaReads2Refs.perl \ + bin/alignRNA2Genomic.perl \ + bin/addSolexaReads.perl \ + bin/addSangerReads.perl \ + bin/addReads2Consed.perl \ + bin/add454Reads.perl \ + bin/ace2Oligos.perl \ + bin/transferConsensusTags.perl \ + bin/ace2fof \ + bin/ace2OligosWithComments.perl \ + bin/sff2phd.perl \ + bin/recover_consensus_tags \ + bin/phredPhrapWithPhdBalls \ + bin/cons.perl \ + bin/acestatus.pl \ + bin/aceContigs2Phds.perl \ + bin/sff2phd_Samborskyy RESTRICTED= Redistribution is not permitted in any form. You must request access permission via e-mail to get the tarball. Free for academic use. .if defined(PACKAGE_BUILDING) @@ -25,84 +71,13 @@ IGNORE= distribution files must be obtained via the authors .endif NO_WRKSUBDIR= 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} ${CFLAGS} sff2scf.c -o sff2scf) +NO_BUILD= yes do-install: - @${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 + cd ${STAGEDIR}${PREFIX} && ${ECHO_CMD} ${MYSHEBANG} | ${XARGS} ${SED} -i '' ${_SHEBANG_REINPLACE_ARGS} .include <bsd.port.mk> diff --git a/biology/consed/distinfo b/biology/consed/distinfo index 6c2724276ef8..828556d8cd5e 100644 --- a/biology/consed/distinfo +++ b/biology/consed/distinfo @@ -1,2 +1,2 @@ -SHA256 (consed_linux.tar.Z) = ac9ce155ce46f7200accaa033c9b1ea1d8c071c68c2a82ab5f4b623d9ff6b117 -SIZE (consed_linux.tar.Z) = 27555099 +SHA256 (consed_linux.tar.gz) = 8038d2b94078ba918e97785fc7497252139029281000f1c54ff9dd1ec70e05fc +SIZE (consed_linux.tar.gz) = 34390726 diff --git a/biology/consed/files/patch-installConsed.perl b/biology/consed/files/patch-installConsed.perl new file mode 100644 index 000000000000..057ea5d13a90 --- /dev/null +++ b/biology/consed/files/patch-installConsed.perl @@ -0,0 +1,57 @@ +--- installConsed.perl.orig 2014-02-11 21:28:45.000000000 +0100 ++++ installConsed.perl 2014-08-23 19:27:23.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/local/bin/perl -w + + # installConsed.perl + +@@ -9,7 +9,7 @@ + # and this must be empty and must allow write access + + # edit this if you are using a different compiler than gcc +-$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" ); + } + + diff --git a/biology/consed/files/patch-scripts_addReads2Consed.perl b/biology/consed/files/patch-scripts_addReads2Consed.perl deleted file mode 100644 index 094a7028a701..000000000000 --- a/biology/consed/files/patch-scripts_addReads2Consed.perl +++ /dev/null @@ -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"; - diff --git a/biology/consed/files/patch-scripts_determineReadTypes.perl b/biology/consed/files/patch-scripts_determineReadTypes.perl deleted file mode 100644 index 70405b43cca2..000000000000 --- a/biology/consed/files/patch-scripts_determineReadTypes.perl +++ /dev/null @@ -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"; - - $szVersion = "001205"; - diff --git a/biology/consed/files/patch-scripts_phredPhrap b/biology/consed/files/patch-scripts_phredPhrap index 5ac28e3d808a..b0543e7b5ed6 100644 --- a/biology/consed/files/patch-scripts_phredPhrap +++ b/biology/consed/files/patch-scripts_phredPhrap @@ -1,36 +1,11 @@ ---- scripts/phredPhrap.orig 2007-09-26 04:02:20.000000000 +0900 -+++ scripts/phredPhrap 2007-12-11 17:32:27.000000000 +0900 -@@ -101,7 +101,7 @@ - - - # change this to reflect wherever you put the phredpar.dat file --$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"; - $phdDirPath = "../phd_dir"; +--- scripts/phredPhrap.orig 2014-02-12 05:28:45.000000000 +0900 ++++ scripts/phredPhrap 2014-06-22 03:07:33.000000000 +0900 +@@ -217,7 +217,7 @@ + #$solexaDirPath = "../solexa_dir"; + #$sffDirPath = "../sff_dir"; -$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"; diff --git a/biology/consed/files/pkg-message.in b/biology/consed/files/pkg-message.in new file mode 100644 index 000000000000..a82e3e3dfa80 --- /dev/null +++ b/biology/consed/files/pkg-message.in @@ -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 +----------------------------------------------------------------------------- diff --git a/biology/consed/pkg-plist.examples b/biology/consed/pkg-plist.examples deleted file mode 100644 index 5fc178a1cb63..000000000000 --- a/biology/consed/pkg-plist.examples +++ /dev/null @@ -1,990 +0,0 @@ -share/examples/consed/assembly_view/edit_dir/.consedrc -share/examples/consed/assembly_view/edit_dir/.consedrc_mini -share/examples/consed/assembly_view/edit_dir/assembly_view.030319.170348.fasta -share/examples/consed/assembly_view/edit_dir/assembly_view.030319.170348.fasta.log -share/examples/consed/assembly_view/edit_dir/assembly_view.fasta.screen.ace.1 -share/examples/consed/assembly_view/edit_dir/assembly_view.fasta.screen.ace.1.aview -share/examples/consed/assembly_view/edit_dir/doNotShowInAssemblyView.fof -share/examples/consed/assembly_view/edit_dir/fragSizes.txt -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q102.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q124.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q124.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q126.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q126.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q131.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q131.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q134.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q144.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q144.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q148.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q148.x1r1p24_e150.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q148.x1u1_e133.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q148.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q149.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q149.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q156.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q161.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q161.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q192.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q192.x1r1p30_e173.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q192.x1r1p33_e178.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q192.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q203.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q203.x1r2p46_e234.phd.1 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-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q243.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q247.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q265.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q267.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q267.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q270.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q270.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q277.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q277.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q279.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q282.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q282.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q287.x1.phd.1 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-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 diff --git a/biology/phrap/Makefile b/biology/phrap/Makefile index 6fa03617ccc1..de2be50a3c56 100644 --- a/biology/phrap/Makefile +++ b/biology/phrap/Makefile @@ -1,11 +1,10 @@ -# Created by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> # $FreeBSD$ PORTNAME= phrap -PORTVERSION= 0.990329 +PORTVERSION= 1.090518 CATEGORIES= biology MASTER_SITES= # put the tarball manually -DISTFILES= distrib.tar.Z +DISTFILES= distrib.tar.gz DIST_SUBDIR= ${PORTNAME} MAINTAINER= mzaki@m.u-tokyo.ac.jp @@ -19,19 +18,14 @@ IGNORE= distribution files must be obtained via the authors NO_WRKSUBDIR= yes MAKEFILE= makefile -ALL_TARGET= all manyreads +ALL_TARGET= all -BINARIES= cluster cross_match cross_match.manyreads loco \ - phrap phrap.longreads phrap.manyreads swat +BINARIES= calf_merge pcluster cross_match loco phrap swat SCRIPTS= phrapview -.for f in ${BINARIES} ${SCRIPTS} -PLIST_FILES+= bin/${f} -.endfor -PORTDATA= BLOSUM50 BLOSUM62 PAM250 mat50 mat70 penalty2 vector.seq +PORTDATA= BLOSUM50 BLOSUM62 PAM250 mat50 mat70 mb_matrix penalty2 vector.seq PORTDOCS= general.doc phrap.doc swat.doc -NO_STAGE= yes .include <bsd.port.pre.mk> .for f in ${DISTFILES} @@ -42,21 +36,18 @@ IGNORE= you must request the source code \(${DISTFILES}\) via e-mail, place it m do-install: .for f in ${BINARIES} - @${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin/ - @${CHMOD} a-r ${PREFIX}/bin/${f} # as required by the agreement + @${INSTALL_PROGRAM} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin/ .endfor .for f in ${SCRIPTS} - @${INSTALL_SCRIPT} ${WRKSRC}/${f} ${PREFIX}/bin/ + @${INSTALL_SCRIPT} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin/ .endfor - @${MKDIR} ${DATADIR} + @${MKDIR} ${STAGEDIR}${DATADIR} .for f in ${PORTDATA} - @${INSTALL_DATA} ${WRKSRC}/${f} ${DATADIR} + @${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DATADIR} .endfor -.if ${PORT_OPTIONS:MDOCS} - @${MKDIR} ${DOCSDIR} + @${MKDIR} ${STAGEDIR}${DOCSDIR} .for f in ${PORTDOCS} - @${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR} + @${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DOCSDIR} .endfor -.endif .include <bsd.port.post.mk> diff --git a/biology/phrap/distinfo b/biology/phrap/distinfo index 3d39a84a04c2..78f1935d26e9 100644 --- a/biology/phrap/distinfo +++ b/biology/phrap/distinfo @@ -1,2 +1,3 @@ -SHA256 (phrap/distrib.tar.Z) = e0be79818e3a8ca17391f42cc0ffbaf1a63299c8845a0b9ac3aaeb3cac641fcc -SIZE (phrap/distrib.tar.Z) = 366163 +MD5 (phrap/distrib.tar.gz) = 93ef3d1cca4d1a70ed16511d30a355ab +SHA256 (phrap/distrib.tar.gz) = 81f50c4410e8604cdefcc34ef6dc7b037be3bb45b94c439611a5590c1cf83665 +SIZE (phrap/distrib.tar.gz) = 333159 diff --git a/biology/phrap/files/patch-alignments.c b/biology/phrap/files/patch-alignments.c new file mode 100644 index 000000000000..986799024563 --- /dev/null +++ b/biology/phrap/files/patch-alignments.c @@ -0,0 +1,10 @@ +--- ./alignments.c.orig 2009-04-18 23:07:41.000000000 +0200 ++++ ./alignments.c 2014-08-02 12:39:30.000000000 +0200 +@@ -591,6 +591,7 @@ + return adj_score; + } + ++void + print_alignment(profile) + Profile *profile; + { diff --git a/biology/phrap/files/patch-analyze_splices.c b/biology/phrap/files/patch-analyze_splices.c new file mode 100644 index 000000000000..bb3f5fe42475 --- /dev/null +++ b/biology/phrap/files/patch-analyze_splices.c @@ -0,0 +1,88 @@ +--- ./analyze_splices.c.orig 2008-08-31 03:37:44.000000000 +0200 ++++ ./analyze_splices.c 2014-08-02 12:39:30.000000000 +0200 +@@ -146,6 +146,13 @@ + char *exon_seq; + double base_llr, intron_coeff; + ++void find_left_sites(Aligned_pair *, Cand_pair *, char *, char *); ++void find_right_sites(Aligned_pair *, Cand_pair *, char *, char *); ++void increment_splice_site(unsigned char *, unsigned char *, ++ Aligned_pair *, int, int, int, unsigned char *, int); ++void scan(Splice_site *, Aligned_pair *, unsigned char *, ++ int, int, int, int); ++ + set_splice_params() + { + int i, j; +@@ -186,6 +193,7 @@ + cases of large missing exons: want to make sure this part of read doesn't match somewhere else, instead + */ + ++void + append_cand_splice(strand, left_splice_site, right_splice_site, overlap, intron_length, left_pair, right_pair) + int strand, overlap, intron_length; + Splice_site *left_splice_site, *right_splice_site; +@@ -512,6 +520,7 @@ + return penalty; + } + ++void + check_best_site(pair, side, cand_pair) + Aligned_pair *pair; + int side; +@@ -560,6 +569,7 @@ + + int extend[3]; + ++void + find_left_sites(pair, cand_pair, seq1, seq2) + Aligned_pair *pair; + Cand_pair *cand_pair; +@@ -651,6 +661,7 @@ + + } + ++void + find_right_sites(pair, cand_pair, seq1, seq2) + Aligned_pair *pair; + Cand_pair *cand_pair; +@@ -816,6 +827,7 @@ + This doesn't really address multiple testing issue; + */ + ++void + increment_splice_site(seq1, seq2, pair, strand, side, loc, seq, type) + Aligned_pair *pair; + int strand, side, loc, type; +@@ -922,6 +934,7 @@ + + /* input: splice_site, c_len, pair, seq1, exon_seq, genome_overhang, cdna_overhang, base_llr, intron_coeff, max_i */ + ++void + scan(splice_site, pair, seq1, genome_overhang, cdna_overhang, max_i, test_len) + Splice_site *splice_site; + Aligned_pair *pair; +@@ -1098,6 +1111,7 @@ + return n_matches; + } + ++void + check_max_length(length) + int length; + { +@@ -1118,6 +1132,7 @@ + max_length = length; + } + ++void + filter_matches(i_ptr, n_p, pair_pointers, print_flag) + int i_ptr, n_p, print_flag; + Aligned_pair **pair_pointers; +@@ -1276,6 +1291,7 @@ + return seg_equiv1->start - seg_equiv2->start; + } + ++void + analyze_multiple(i_ptr, n_p, pair_pointers, print_flag) + int i_ptr, n_p, print_flag; + Aligned_pair **pair_pointers; diff --git a/biology/phrap/files/patch-anomalies.c b/biology/phrap/files/patch-anomalies.c new file mode 100644 index 000000000000..508d4cd9de69 --- /dev/null +++ b/biology/phrap/files/patch-anomalies.c @@ -0,0 +1,19 @@ +--- ./anomalies.c.orig 2008-11-10 06:02:00.000000000 +0100 ++++ ./anomalies.c 2014-08-02 12:39:30.000000000 +0200 +@@ -28,6 +28,8 @@ + extern Parameters *parameters; + extern int num_pairs, t_num_entries; + ++void visit_cand_pairs_dups(int, Cand_pair *); ++ + #define MAX_CHIMERA_GAP 30 /* maximum gap between distinct confirmed segments for + putative chimeras */ + compare_pair_entries(pair_1, pair_2) +@@ -830,6 +832,7 @@ + notify(" Done\n"); + } + ++void + visit_cand_pairs_dups(entry1, pair) + int entry1; + Cand_pair *pair; diff --git a/biology/phrap/files/patch-calf_utils.c b/biology/phrap/files/patch-calf_utils.c new file mode 100644 index 000000000000..9a09fb4d1c49 --- /dev/null +++ b/biology/phrap/files/patch-calf_utils.c @@ -0,0 +1,19 @@ +--- ./calf_utils.c.orig 2008-11-04 23:21:50.000000000 +0100 ++++ ./calf_utils.c 2014-08-02 12:39:30.000000000 +0200 +@@ -28,6 +28,8 @@ + + extern void *malloc(), *realloc(); + ++void read_type_3(File_stat *, int); ++ + append_file_stat(file_name) + char *file_name; + { +@@ -110,6 +112,7 @@ + get_record_header(file_stat); + } + ++void + read_type_3(file_stat, new_rec_flag) + File_stat *file_stat; + int new_rec_flag; diff --git a/biology/phrap/files/patch-call_subs.c b/biology/phrap/files/patch-call_subs.c new file mode 100644 index 000000000000..8ee1379afc28 --- /dev/null +++ b/biology/phrap/files/patch-call_subs.c @@ -0,0 +1,19 @@ +--- ./call_subs.c.orig 1999-01-17 00:42:56.000000000 +0100 ++++ ./call_subs.c 2014-08-02 12:39:30.000000000 +0200 +@@ -26,15 +26,13 @@ + + extern Parameters *parameters; + ++void + call_write_exp_files(n_sing, n_contigs, contig_ptrs) + int n_sing, n_contigs; + Contig **contig_ptrs; + { + #if defined(GCPHRAP) + write_exp_files(n_sing, n_contigs, contig_ptrs); +- return; +-#else +- return; + #endif + } + diff --git a/biology/phrap/files/patch-cand_pairs.c b/biology/phrap/files/patch-cand_pairs.c new file mode 100644 index 000000000000..6765364b7544 --- /dev/null +++ b/biology/phrap/files/patch-cand_pairs.c @@ -0,0 +1,18 @@ +--- ./cand_pairs.c.orig 2008-08-31 03:02:56.000000000 +0200 ++++ ./cand_pairs.c 2014-08-02 12:39:30.000000000 +0200 +@@ -38,6 +38,7 @@ + + static int num_cand_pairs, num_dups, num_repeat_rejected_pairs; + ++void + cluster_pairs(entry1, entry2, start1, start2, reverse, rev_store_flag) + int entry1, entry2, start1, start2; + int reverse, rev_store_flag; +@@ -74,6 +75,7 @@ + set_equiv_class(entry, final_class); + } + ++void + make_new_cand_pair(entry1, entry2, start1, start2, reverse, rev_store_flag) + int entry1, entry2, start1, start2; + int reverse, rev_store_flag; diff --git a/biology/phrap/files/patch-contigs.c b/biology/phrap/files/patch-contigs.c new file mode 100644 index 000000000000..a2f99c774dc9 --- /dev/null +++ b/biology/phrap/files/patch-contigs.c @@ -0,0 +1,10 @@ +--- ./contigs.c.orig 2008-11-11 22:56:27.000000000 +0100 ++++ ./contigs.c 2014-08-02 12:39:30.000000000 +0200 +@@ -2115,6 +2115,7 @@ + contig1->base_segment = previous_base_segment; + } + ++void + write_contigs() + { + char *our_alloc(); diff --git a/biology/phrap/files/patch-db.c b/biology/phrap/files/patch-db.c new file mode 100644 index 000000000000..ae100313b440 --- /dev/null +++ b/biology/phrap/files/patch-db.c @@ -0,0 +1,19 @@ +--- ./db.c.orig 2009-04-21 18:10:09.000000000 +0200 ++++ ./db.c 2014-08-02 12:39:30.000000000 +0200 +@@ -38,6 +38,8 @@ + int qseq_trans[256]; + int t_num_entries; + ++void size_conflict(SEQ_AREA,long int,char *); ++ + typedef long int POS; + static POS id_pos, descrip_pos, seq_pos, seq_length; + /* N.B. following needed by Bonfield code, so original "static" designation has +@@ -571,6 +573,7 @@ + (unsigned long int)db->seq_area_size, (unsigned long int)db->id_area_size, (unsigned long int)db->descrip_area_size); + } + ++void + size_conflict(size1, size2, label) + SEQ_AREA size1; + long int size2; diff --git a/biology/phrap/files/patch-makefile b/biology/phrap/files/patch-makefile index 7fccdb3846a1..2a83cd9e1e44 100644 --- a/biology/phrap/files/patch-makefile +++ b/biology/phrap/files/patch-makefile @@ -1,9 +1,9 @@ ---- makefile.orig 1999-03-11 15:13:20.000000000 +0900 -+++ makefile 2007-12-11 13:19:39.000000000 +0900 -@@ -23,8 +23,8 @@ - #*****************************************************************************/ - +--- ./makefile.orig 2009-06-02 17:45:34.000000000 +0200 ++++ ./makefile 2014-08-02 12:43:45.000000000 +0200 +@@ -25,8 +25,8 @@ # Makefile for swat, phrap, cross_match, phrapview; also swprobs (currently inactivated) + #CC= icc + #CFLAGS= -O2 -wd266,880 -CC= cc -CFLAGS= -O2 +CC?= cc @@ -11,17 +11,24 @@ LFLAGS= -lm SWATOBJS= swat.o weibull.o -@@ -55,11 +55,11 @@ +@@ -55,7 +55,7 @@ + + CALFOBJS= calf_merge.o calf_utils.o + +-all: swat phrap cross_match phrapview cluster loco calf_merge ++all: swat phrap cross_match phrapview pcluster loco calf_merge + + #manyreads: + # touch swat.h; +@@ -131,9 +131,9 @@ + $(CC) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS) + chmod o-r gccross_match + +-cluster: makefile $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) ++pcluster: makefile $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) + $(CC) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LFLAGS) +- chmod o-r cluster ++ chmod o-r pcluster - manyreads: - touch swat.h; -- make CFLAGS="-O2 -DMANYREADS" phrap cross_match; -+ make CFLAGS="$(CFLAGS) -DMANYREADS" phrap cross_match; - mv phrap phrap.manyreads; - mv cross_match cross_match.manyreads; - touch swat.h; -- make CFLAGS="-O2 -DLONGREADS" phrap; -+ make CFLAGS="$(CFLAGS) -DLONGREADS" phrap; - mv phrap phrap.longreads; - touch swat.h; - make phrap cross_match; + loco: makefile $(LOCOOBJS) $(SWOBJS) + $(CC) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LFLAGS) diff --git a/biology/phrap/files/patch-names.c b/biology/phrap/files/patch-names.c new file mode 100644 index 000000000000..4b6ef3dd9526 --- /dev/null +++ b/biology/phrap/files/patch-names.c @@ -0,0 +1,19 @@ +--- ./names.c.orig 2007-11-06 23:03:53.000000000 +0100 ++++ ./names.c 2014-08-02 12:39:30.000000000 +0200 +@@ -30,6 +30,8 @@ + + #define MAX_SUBCLONE_HIST 101 + ++void print_contig_chains(); ++ + set_delims() + { + subclone_delim = parameters->subclone_delim; +@@ -1014,6 +1016,7 @@ + + /* greedy algorithm for finding chains of contigs */ + /* NEED TO LOOK SYSTEMATICALLY FOR CIRCULAR CHAINS, AND BREAK THEM */ ++void + print_contig_chains() + { + Link *link; diff --git a/biology/phrap/files/patch-nodes.c b/biology/phrap/files/patch-nodes.c new file mode 100644 index 000000000000..50af42003571 --- /dev/null +++ b/biology/phrap/files/patch-nodes.c @@ -0,0 +1,19 @@ +--- ./nodes.c.orig 2008-08-31 03:44:15.000000000 +0200 ++++ ./nodes.c 2014-08-02 12:39:30.000000000 +0200 +@@ -31,6 +31,8 @@ + extern Parameters *parameters; /* exported */ + extern double *scaled_err_probs; + int *contig_graph_weights; ++ ++void nr_tarjan(int); + + set_contig_graph_weights() + { +@@ -679,6 +681,7 @@ + curr_state->calling_point = calling_point; + } + ++void + nr_tarjan(k) + int k; + { diff --git a/biology/phrap/files/patch-pairs.c b/biology/phrap/files/patch-pairs.c new file mode 100644 index 000000000000..d81b915fda34 --- /dev/null +++ b/biology/phrap/files/patch-pairs.c @@ -0,0 +1,91 @@ +--- ./pairs.c.orig 2009-04-23 00:12:20.000000000 +0200 ++++ ./pairs.c 2014-08-02 12:39:30.000000000 +0200 +@@ -37,6 +37,16 @@ + int single_domain; + double mask_frac; + ++void revise_qd_scores(Query_domain *); ++void visit_cand_pairs_scores( Cand_pair *); ++void merge_qds(Database *, int); ++void init_qd_trims(Query_domain *); ++void test_qd1_merges(Query_domain *, Query_domain *); ++void test_qd2_merges(Query_domain *, Query_domain *); ++void compare_query_domains(Query_domain *, Query_domain *); ++void print_score_list(int, Query_domain *); ++void print_pair(Aligned_pair *, FILE *, int); ++ + set_domain_vars() + { + single_domain = parameters->masklevel == 0 || parameters->masklevel == 101; +@@ -697,6 +707,7 @@ + */ + } + ++void + visit_cand_pairs_scores(cand_pair) + Cand_pair *cand_pair; + { +@@ -1423,6 +1434,7 @@ + + int trim_flag; + ++void + merge_qds(db, t_f) + Database *db; + int t_f; +@@ -1463,6 +1475,7 @@ + } + } + ++void + init_qd_trims(query_domain) + Query_domain *query_domain; + { +@@ -1476,6 +1489,7 @@ + init_qd_trims(query_domain->child[1]); + } + ++void + test_qd1_merges(query_domain1, query_domain2) + Query_domain *query_domain1, *query_domain2; + { +@@ -1486,6 +1500,7 @@ + test_qd1_merges(query_domain1->child[1], query_domain2); + } + ++void + test_qd2_merges(query_domain1, query_domain2) + Query_domain *query_domain1, *query_domain2; + { +@@ -1533,6 +1548,7 @@ + } + } + ++void + compare_query_domains(query_domain1, query_domain2) + Query_domain *query_domain1, *query_domain2; + { +@@ -1570,6 +1586,7 @@ + } + } + ++void + print_score_list(entry, query_domain) + int entry; + Query_domain *query_domain; +@@ -1732,6 +1749,7 @@ + } + } + ++void + print_pair(pair, fp, no_zero) + Aligned_pair *pair; + FILE *fp; +@@ -4125,6 +4143,7 @@ + notify("done"); + } + ++void + revise_qd_scores(query_domain) + Query_domain *query_domain; + { diff --git a/biology/phrap/files/patch-qual.c b/biology/phrap/files/patch-qual.c new file mode 100644 index 000000000000..5c7627f1eb3a --- /dev/null +++ b/biology/phrap/files/patch-qual.c @@ -0,0 +1,82 @@ +--- ./qual.c.orig 2008-11-12 17:45:48.000000000 +0100 ++++ ./qual.c 2014-08-02 12:39:30.000000000 +0200 +@@ -44,6 +44,12 @@ + static int mismatch_LLR[256]; + double *scaled_err_probs; /* used for finding high-quality segments */ + ++void read_qual(Database *); ++void rescale_qual(Database *); ++void incr_diff_hist(unsigned char *, unsigned char *, ++ int, int, int, int, ++ int, int, int, int ); ++ + init_qual_arrays() + { + int i; +@@ -580,6 +586,7 @@ + } + + /* read in quality data */ ++void + read_qual(db) + Database *db; + { +@@ -876,6 +883,7 @@ + } + + /* NOT CORRECT WITH COMPRESSED QUAL */ ++void + rescale_qual(db) + Database *db; + { +@@ -1153,6 +1161,10 @@ + int conf_count[2], conf_max_score, conf_max_margin; /* # confirming reads */ + } Diffsegnode; + ++void append_diffdata(Diffsegnode *); ++void append_diffsegnode(Diffsegnode *, int, int, int, int, Diffsegnode *); ++void write_diffsegnode(Diffsegnode *); ++ + int data_type, data_length, data_qual, data_reverse, data_score, data_margin; + unsigned char *data_seq; + +@@ -1400,6 +1412,7 @@ + = n_align[i] = n_unalign[i] = n_p_unalign[i] = 0; + } + ++void + incr_diff_hist(seq, diff, length1, length2, start1, start2, end1, end2, reverse, ignore_ends) + unsigned char *seq; + unsigned char *diff; +@@ -1543,6 +1556,7 @@ + int node_index; + extern unsigned char area_comp_mat[]; + ++void + append_diffdata(diffsegnode) + Diffsegnode *diffsegnode; + { +@@ -1607,6 +1621,7 @@ + diffdata->count[!data_reverse] = 0; + } + ++void + append_diffsegnode(node, entry, seg_start, seg_end, conf_flag, data_node) + Diffsegnode *node, *data_node; /* latter is 0 if reading from global vars */ + int entry, seg_start, seg_end, conf_flag; +@@ -1724,6 +1739,7 @@ + strcpy(cdb, "CDSILRdi"); + } + ++void + write_diffsegnode(node) + Diffsegnode *node; + { +@@ -1800,6 +1816,7 @@ + write_diffsegnode(node->child[1]); + } + ++void + write_diffsegnodes() + { + int i; diff --git a/biology/phrap/files/patch-readin.c b/biology/phrap/files/patch-readin.c new file mode 100644 index 000000000000..0e30d7872bd6 --- /dev/null +++ b/biology/phrap/files/patch-readin.c @@ -0,0 +1,10 @@ +--- ./readin.c.orig 2008-11-11 20:33:41.000000000 +0100 ++++ ./readin.c 2014-08-02 12:39:30.000000000 +0200 +@@ -31,6 +31,7 @@ + /* read in sequence files, initialize array of aligned read info, and log file of ancillary information, + and find pairwise matches */ + ++void + readin_and_match() + { + File *file; diff --git a/biology/phrap/files/patch-segments.c b/biology/phrap/files/patch-segments.c new file mode 100644 index 000000000000..950899da7b15 --- /dev/null +++ b/biology/phrap/files/patch-segments.c @@ -0,0 +1,18 @@ +--- ./segments.c.orig 2008-07-30 19:14:13.000000000 +0200 ++++ ./segments.c 2014-08-02 12:39:30.000000000 +0200 +@@ -112,6 +112,7 @@ + return head; + } + ++void + print_segments(head, index, complement) + Segment *head; + int index; +@@ -128,6 +129,7 @@ + } + } + ++void + old_print_segments(head, index1, index2, offset, rel_orient) + Segment *head; + int index1, index2, offset; diff --git a/biology/phrap/files/patch-tig_node.c b/biology/phrap/files/patch-tig_node.c new file mode 100644 index 000000000000..d2506b8beeda --- /dev/null +++ b/biology/phrap/files/patch-tig_node.c @@ -0,0 +1,18 @@ +--- ./tig_node.c.orig 2007-11-06 23:02:49.000000000 +0100 ++++ ./tig_node.c 2014-08-02 12:39:30.000000000 +0200 +@@ -138,6 +138,7 @@ + tig_node->best_stack_length[0] = tig_node->best_stack_length[1] = 0; + } + ++void + alloc_edge(contig, orientation, pair, reverse) + Contig *contig; + int orientation, reverse; +@@ -176,6 +177,7 @@ + tig_node->edges[orientation] = edge; + } + ++void + find_best_paths(gap_cutoff, LLR_reject_cutoff, LLR_join_cutoff) + int gap_cutoff, LLR_reject_cutoff, LLR_join_cutoff; + { diff --git a/biology/phrap/files/patch-weibull.c b/biology/phrap/files/patch-weibull.c new file mode 100644 index 000000000000..1e8de65cb2b6 --- /dev/null +++ b/biology/phrap/files/patch-weibull.c @@ -0,0 +1,18 @@ +--- ./weibull.c.orig 2008-07-29 20:06:24.000000000 +0200 ++++ ./weibull.c 2014-08-02 12:39:30.000000000 +0200 +@@ -77,6 +77,7 @@ + z_cutoff = Z_CUTOFF; + } + ++void + update_hist(score_entry, z_flag) + Score_entry *score_entry; + int z_flag; +@@ -103,6 +104,7 @@ + score2_sums[length] += score * score; + } + ++void + prune_hist(score_entry) + Score_entry *score_entry; + { diff --git a/biology/phrap/files/patch-words.c b/biology/phrap/files/patch-words.c new file mode 100644 index 000000000000..ed36f2bee041 --- /dev/null +++ b/biology/phrap/files/patch-words.c @@ -0,0 +1,64 @@ +--- ./words.c.orig 2009-04-22 20:48:22.000000000 +0200 ++++ ./words.c 2014-08-02 12:39:30.000000000 +0200 +@@ -59,6 +59,12 @@ + static unsigned char *long_word_array; + static int n_skips[3]; + ++void print_word_counts(); ++void set_lower_upper(); ++void set_index_words(int,int,int); ++void find_external_word_matches(int, unsigned char *); ++void quicksort(SEQ_AREA, SEQ_AREA, int, int, SEQ_AREA *); ++void new_lookup_words(unsigned char *, int, SEQ_AREA, SEQ_AREA, int, int); + + typedef struct sw_edge { + int curr0, curr1, curr2; +@@ -323,6 +329,7 @@ + + /* only used when DNA_flag == 2 */ + ++void + set_lower_upper() + { + unsigned int word_int, word_reduced, last_word_reduced; +@@ -540,6 +547,7 @@ + /* + other input: total_length, num_entries, complexity_flag, alphabet_size, residues, minmatch, nlogn_diff, mod_value, index_shift */ + ++void + set_index_words(pass, trans_type, index_type) + int pass, trans_type, index_type; + { +@@ -1070,7 +1078,7 @@ + refinement in Sedgwick, but using bookkeeping of matching leading parts + of words in a block to substantially improve + efficiency) */ +- ++void + quicksort(left, right, k_start, maxcheck, seq_offsets) + SEQ_AREA left, right; + int k_start, maxcheck; +@@ -1532,6 +1540,7 @@ + + */ + ++void + find_external_word_matches(e1, seq) + int e1; + unsigned char *seq; +@@ -1776,6 +1785,7 @@ + int known_match_size, target_match_size, offset1, sub_check, reuse; + extern int num_pairs; + ++void + new_lookup_words(seq1, trans_type, sa_l_lower, sa_u_upper, ss_displace, n_lc) + int trans_type, ss_displace, n_lc; + SEQ_AREA sa_l_lower, sa_u_upper; +@@ -2850,6 +2860,7 @@ + for (i = 0; i < 5; i++) num_merge_words[i] = 0; + } + ++void + print_word_counts() + { + int i; diff --git a/biology/phrap/pkg-plist b/biology/phrap/pkg-plist new file mode 100644 index 000000000000..e1faf40459ee --- /dev/null +++ b/biology/phrap/pkg-plist @@ -0,0 +1,9 @@ +@mode 111 +bin/calf_merge +bin/pcluster +bin/cross_match +bin/loco +bin/phrap +bin/phrapview +bin/swat +@mode diff --git a/biology/phred/Makefile b/biology/phred/Makefile index 61027fcfe259..06f673b57574 100644 --- a/biology/phred/Makefile +++ b/biology/phred/Makefile @@ -11,6 +11,8 @@ EXTRACT_SUFX= .tar.Z MAINTAINER= mzaki@m.u-tokyo.ac.jp COMMENT= Base calling and quality value assignment on DNA sequencing +SUB_FILES= pkg-message + RESTRICTED= Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use. .if defined(PACKAGE_BUILDING) IGNORE= distribution files must be obtained via the authors @@ -20,21 +22,13 @@ NO_WRKSUBDIR= yes ALL_TARGET= phred daev -BINMODE= 0111 # avoid copying binaries as required by the agreement BINARIES= phred daev -.for f in ${BINARIES} -PLIST_FILES+= bin/${f} -.endfor DATADIR= ${PREFIX}/etc/PhredPar DATAFILES= phredpar.dat -.for f in ${DATAFILES} -PORTDATA+= ${f}.dist -.endfor PORTDOCS= NEWS PHRED.DOC DAEV.DOC -NO_STAGE= yes .include <bsd.port.pre.mk> .for f in ${DISTFILES} @@ -45,23 +39,15 @@ IGNORE= you must request the source code \(${f}\) via e-mail, place it manually do-install: .for f in ${BINARIES} - @${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin/ + @${INSTALL_PROGRAM} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin/ .endfor - @${MKDIR} ${DATADIR} + @${MKDIR} ${STAGEDIR}${DATADIR} .for f in ${DATAFILES} - @${INSTALL_DATA} ${WRKSRC}/${f} ${DATADIR}/${f}.dist + @${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DATADIR}/${f}.sample .endfor -.if ${PORT_OPTIONS:MDOCS} - @${MKDIR} ${DOCSDIR} + @${MKDIR} ${STAGEDIR}${DOCSDIR} .for f in ${PORTDOCS} - @${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR} + @${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DOCSDIR} .endfor -.endif - @${ECHO} "---------------------------------------------------------------------------" - @${ECHO} "You must set PHRED_PARAMETER_FILE environment variable." - @${ECHO} "" - @${ECHO} "The default parameter file in the distribution is located at:" - @${ECHO} " ${DATADIR}/phredpar.dat.dist" - @${ECHO} "---------------------------------------------------------------------------" .include <bsd.port.post.mk> diff --git a/biology/phred/files/pkg-message.in b/biology/phred/files/pkg-message.in new file mode 100644 index 000000000000..04ae9ab3ef43 --- /dev/null +++ b/biology/phred/files/pkg-message.in @@ -0,0 +1,6 @@ +----------------------------------------------------------------------------- +You must set PHRED_PARAMETER_FILE environment variable. + +The default parameter file in the distribution is located at: +%%DATADIR%%/phredpar.dat +----------------------------------------------------------------------------- |