diff options
| author | Kurt Jaeger <pi@FreeBSD.org> | 2014-08-23 18:04:58 +0000 |
|---|---|---|
| committer | Kurt Jaeger <pi@FreeBSD.org> | 2014-08-23 18:04:58 +0000 |
| commit | 690da7ea383f1f7ba029563658b17f1a2544007b (patch) | |
| tree | 23e972a9950cc8d2fbf2c0128d929e3655a093ab /biology/consed | |
| parent | 652bbb78d901c4cafc5ebcb47f5de9e22c3bee34 (diff) | |
| download | ports-690da7ea383f1f7ba029563658b17f1a2544007b.tar.gz ports-690da7ea383f1f7ba029563658b17f1a2544007b.zip | |
Notes
Diffstat (limited to 'biology/consed')
| -rw-r--r-- | biology/consed/Makefile | 139 | ||||
| -rw-r--r-- | biology/consed/distinfo | 4 | ||||
| -rw-r--r-- | biology/consed/files/patch-installConsed.perl | 57 | ||||
| -rw-r--r-- | biology/consed/files/patch-scripts_addReads2Consed.perl | 11 | ||||
| -rw-r--r-- | biology/consed/files/patch-scripts_determineReadTypes.perl | 11 | ||||
| -rw-r--r-- | biology/consed/files/patch-scripts_phredPhrap | 35 | ||||
| -rw-r--r-- | biology/consed/files/pkg-message.in | 12 | ||||
| -rw-r--r-- | biology/consed/pkg-plist.examples | 990 |
8 files changed, 133 insertions, 1126 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 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q203.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q206.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q206.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q207.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q207.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q210.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q211.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q212.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q212.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q215.x1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q215.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q232.y1.phd.1 -share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q243.x1.phd.1 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