Date: Mon, 19 Dec 2016 15:54:29 +0000 (UTC) From: Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r428940 - in head/biology/p5-BioPerl: . files Message-ID: <201612191554.uBJFsTPa041415@repo.freebsd.org>
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Author: sunpoet Date: Mon Dec 19 15:54:29 2016 New Revision: 428940 URL: https://svnweb.freebsd.org/changeset/ports/428940 Log: - Update to 1.007001 - Update *_DEPENDS - Use TEST_DEPENDS: Test::Most and URI::Escape are test-only dependencies - Use PORTDATA, PORTDOCS and PORTEXAMPLES Changes: http://search.cpan.org/dist/BioPerl/Changes Modified: head/biology/p5-BioPerl/Makefile head/biology/p5-BioPerl/distinfo head/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm head/biology/p5-BioPerl/files/patch-Build.PL head/biology/p5-BioPerl/pkg-descr head/biology/p5-BioPerl/pkg-plist Modified: head/biology/p5-BioPerl/Makefile ============================================================================== --- head/biology/p5-BioPerl/Makefile Mon Dec 19 15:54:24 2016 (r428939) +++ head/biology/p5-BioPerl/Makefile Mon Dec 19 15:54:29 2016 (r428940) @@ -2,8 +2,7 @@ # $FreeBSD$ PORTNAME= BioPerl -PORTVERSION= 1.6.924 -PORTREVISION= 5 +PORTVERSION= 1.007001 CATEGORIES= biology perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:CJFIELDS @@ -17,50 +16,52 @@ LICENSE_COMB= dual BUILD_DEPENDS= p5-Algorithm-Munkres>=0:math/p5-Algorithm-Munkres \ p5-Array-Compare>=0:misc/p5-Array-Compare \ - p5-Class-AutoClass>=0:devel/p5-Class-AutoClass \ p5-Clone>=0:devel/p5-Clone \ p5-Convert-Binary-C>=0:converters/p5-Convert-Binary-C \ p5-DBD-mysql>=0:databases/p5-DBD-mysql \ - p5-Data-Stag>=0:devel/p5-Data-Stag \ + p5-DBI>=0:databases/p5-DBI \ + p5-Data-Stag>=0.11:devel/p5-Data-Stag \ p5-Error>=0:lang/p5-Error \ p5-GD>=0:graphics/p5-GD \ - p5-GD-SVG>=0:graphics/p5-GD-SVG \ - p5-Graph>=0:math/p5-Graph \ + p5-Graph>=0.50:math/p5-Graph \ p5-GraphViz>=0:graphics/p5-GraphViz \ - p5-HTML-Parser>=0:www/p5-HTML-Parser \ - p5-HTML-TableExtract>=2:www/p5-HTML-TableExtract \ + p5-HTML-Parser>=3:www/p5-HTML-Parser \ + p5-HTML-TableExtract>=0:www/p5-HTML-TableExtract \ + p5-HTTP-Message>=0:www/p5-HTTP-Message \ p5-IO-String>=0:devel/p5-IO-String \ p5-IO-stringy>=0:devel/p5-IO-stringy \ - p5-Math-Random>=0:math/p5-Math-Random \ + p5-Inline-C>=0.67:devel/p5-Inline-C \ + p5-List-MoreUtils>=0:lang/p5-List-MoreUtils \ p5-PostScript>=0:print/p5-PostScript \ - p5-SOAP-Lite>=0:net/p5-SOAP-Lite \ - p5-SVG>=0:textproc/p5-SVG \ - p5-SVG-Graph>=0:graphics/p5-SVG-Graph \ + p5-SVG>=2.26:textproc/p5-SVG \ + p5-SVG-Graph>=0.01:graphics/p5-SVG-Graph \ p5-Set-Scalar>=0:devel/p5-Set-Scalar \ - p5-Sort-Naturally>=1:textproc/p5-Sort-Naturally \ + p5-Sort-Naturally>=0:textproc/p5-Sort-Naturally \ p5-Spreadsheet-ParseExcel>=0:textproc/p5-Spreadsheet-ParseExcel \ - p5-Test-Most>=0:devel/p5-Test-Most \ - p5-Text-Shellwords>=0:textproc/p5-Text-Shellwords \ - p5-Text-Tabs+Wrap>=0:textproc/p5-Text-Tabs+Wrap \ - p5-URI>=0:net/p5-URI \ p5-XML-DOM>=0:textproc/p5-XML-DOM \ p5-XML-DOM-XPath>=0:textproc/p5-XML-DOM-XPath \ p5-XML-LibXML>=0:textproc/p5-XML-LibXML \ p5-XML-Parser>=0:textproc/p5-XML-Parser \ - p5-XML-SAX>=0:textproc/p5-XML-SAX \ + p5-XML-SAX>=0.15:textproc/p5-XML-SAX \ p5-XML-SAX-Writer>=0:textproc/p5-XML-SAX-Writer \ - p5-XML-Simple>=2:textproc/p5-XML-Simple \ + p5-XML-Simple>=0:textproc/p5-XML-Simple \ p5-XML-Twig>=0:textproc/p5-XML-Twig \ - p5-XML-Writer>=0:textproc/p5-XML-Writer \ + p5-XML-Writer>=0.400:textproc/p5-XML-Writer \ p5-YAML>=0:textproc/p5-YAML \ p5-libwww>=0:www/p5-libwww \ p5-libxml>=0:textproc/p5-libxml RUN_DEPENDS:= ${BUILD_DEPENDS} +TEST_DEPENDS= p5-Test-Most>=0:devel/p5-Test-Most \ + p5-URI>=0:net/p5-URI USES= perl5 USE_PERL5= modbuild NO_ARCH= yes +PORTDATA= * +PORTDOCS= * +PORTEXAMPLES= * + OPTIONS_DEFINE= DOCS EXAMPLES PGTEST SQLITETEST PGTEST_DESC= Test PostGreSQL SQLITETEST_DESC= Test SQLite @@ -70,7 +71,7 @@ SQLITETEST_RUN_DEPENDS= p5-DBD-SQLite>=1 SQLITETEST_BUILD_DEPENDS= p5-DBD-SQLite>=1:databases/p5-DBD-SQLite post-patch: - @${FIND} ${WRKSRC}/examples ${WRKSRC}/doc -name "*.pl" -o -name "*.cgi" \ + @${FIND} ${WRKSRC}/examples ${WRKSRC}/deobfuscator -name "*.pl" -o -name "*.cgi" \ -o -name "*.PL" | ${XARGS} ${REINPLACE_CMD} -i '' -Ee \ '1s|(/usr)?/bin/perl|${PERL}|' @@ -80,13 +81,20 @@ post-install: post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} -.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE MANIFEST README - ${INSTALL_MAN} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR} +.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL.md MANIFEST README.md + ${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR} .endfor - ${CP} -R ${WRKSRC}/doc ${STAGEDIR}${DOCSDIR} + ${CP} -R ${WRKSRC}/deobfuscator ${STAGEDIR}${DOCSDIR} post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${CP} -R ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR} -.include <bsd.port.mk> +.include <bsd.port.pre.mk> + +.if ${PERL_LEVEL} >= 502200 +BUILD_DEPENDS+= p5-CGI>=0:www/p5-CGI +RUN_DEPENDS+= p5-CGI>=0:www/p5-CGI +.endif + +.include <bsd.port.post.mk> Modified: head/biology/p5-BioPerl/distinfo ============================================================================== --- head/biology/p5-BioPerl/distinfo Mon Dec 19 15:54:24 2016 (r428939) +++ head/biology/p5-BioPerl/distinfo Mon Dec 19 15:54:29 2016 (r428940) @@ -1,2 +1,3 @@ -SHA256 (BioPerl-1.6.924.tar.gz) = 616a7546bb3c58504de27304a0f6cb904e18b6bbcdb6a4ec8454f2bd37bb76d0 -SIZE (BioPerl-1.6.924.tar.gz) = 12623118 +TIMESTAMP = 1479828383 +SHA256 (BioPerl-1.007001.tar.gz) = 9da1dbcd10452f53194c98c6cc2f604a59124507dcc1e6a8440565f44dd07b40 +SIZE (BioPerl-1.007001.tar.gz) = 12486953 Modified: head/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm ============================================================================== --- head/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm Mon Dec 19 15:54:24 2016 (r428939) +++ head/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm Mon Dec 19 15:54:29 2016 (r428940) @@ -1,5 +1,5 @@ ---- Bio/Root/Build.pm.orig 2014-07-10 22:13:23.000000000 +0200 -+++ Bio/Root/Build.pm 2014-07-24 11:55:59.000000000 +0200 +--- Bio/Root/Build.pm.orig 2014-07-10 20:13:23 UTC ++++ Bio/Root/Build.pm @@ -83,49 +83,9 @@ } } Modified: head/biology/p5-BioPerl/files/patch-Build.PL ============================================================================== --- head/biology/p5-BioPerl/files/patch-Build.PL Mon Dec 19 15:54:24 2016 (r428939) +++ head/biology/p5-BioPerl/files/patch-Build.PL Mon Dec 19 15:54:29 2016 (r428940) @@ -1,70 +1,79 @@ ---- Build.PL.orig 2009-09-30 00:33:45.000000000 +0800 -+++ Build.PL 2009-12-01 10:25:51.000000000 +0800 -@@ -187,7 +187,6 @@ - }, +--- Build.PL.orig 2016-11-06 03:59:41 UTC ++++ Build.PL +@@ -226,7 +226,6 @@ my $build = Bio::Root::Build->new( - build_requires => { -- 'CPAN' => 1.81, - 'Module::Build' => 0.2805, - 'Test::Harness' => 2.62, - 'Test::Most' => 0, -@@ -376,86 +375,8 @@ + build_requires => { + 'Module::Build' => 0.42, +- 'CPAN' => 1.81, + 'Test::Harness' => 2.62, + 'Test::Most' => 0, + 'URI::Escape' => 0 +@@ -413,101 +412,8 @@ sub test_biodbgff { sub prompt_for_biodb { my $accept = shift; -- my $proceed = $accept ? 0 : $build->y_n("Do you want to run the Bio::DB::GFF or ". -- "Bio::DB::SeqFeature::Store live database tests? ". -- "y/n", 'n'); +- my $proceed = $accept ? 0 : $build->y_n( +- "Do you want to run the Bio::DB::GFF or " +- . "Bio::DB::SeqFeature::Store live database tests? " . "y/n", +- 'n' +- ); - - if ($proceed) { - my @driver_choices; -- foreach my $poss ('SQLite', 'mysql', 'Pg', 'Oracle') { -- if (grep {/$poss/i} @drivers) { +- foreach my $poss ( 'SQLite', 'mysql', 'Pg', 'Oracle' ) { +- if ( grep {/$poss/i} @drivers ) { - my $choice = $poss; - $choice =~ s/^(.)/[$1]/; -- push(@driver_choices, $choice); +- push( @driver_choices, $choice ); - } - } - - my $driver; -- if (@driver_choices > 1) { +- if ( @driver_choices > 1 ) { - my ($default) = $driver_choices[0] =~ /\[(.)/; -- $driver = $build->prompt("Which database driver should be used? ".join(" ", @driver_choices), $default); -- } -- else { +- $driver = $build->prompt( +- "Which database driver should be used? " +- . join( " ", @driver_choices ), +- $default +- ); +- } else { - ($driver) = $driver_choices[0] =~ /\[(.)/; - } -- if ($driver =~ /^[mM]/) { +- if ( $driver =~ /^[mM]/ ) { - $driver = 'mysql'; -- } -- elsif ($driver =~ /^[pP]/) { +- } elsif ( $driver =~ /^[pP]/ ) { - $driver = 'Pg'; -- } -- elsif ($driver =~ /^[oO]/) { +- } elsif ( $driver =~ /^[oO]/ ) { - $driver = 'Oracle'; -- } -- elsif ($driver =~ /^[sS]/) { +- } elsif ( $driver =~ /^[sS]/ ) { - $driver = 'SQLite'; - } - -- my $test_db = $build->prompt("Which database should I use for testing the $driver driver?\n". -- "This database should already be present but doesn't have to ". -- "be preloaded for any schema", 'test'); -- my $test_host = $build->prompt("On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost'); -- my $test_user = $build->prompt("User name for connecting to database '$test_db'?", 'undef'); -- my $test_pass = $build->prompt("Password for connecting to database '$test_db'?", 'undef'); +- my $test_db = $build->prompt( +- "Which database should I use for testing the $driver driver?\n" +- . "This database should already be present but doesn't have to " +- . "be preloaded for any schema", +- 'test' +- ); +- my $test_host = $build->prompt( +- "On which host is database '$test_db' running (hostname, ip address or host:port)", +- 'localhost' +- ); +- my $test_user = $build->prompt( +- "User name for connecting to database '$test_db'?", 'undef' ); +- my $test_pass = $build->prompt( +- "Password for connecting to database '$test_db'?", 'undef' ); - - my $use_host = 1; -- if ($test_host eq 'undef' || $test_host eq 'localhost') { +- if ( $test_host eq 'undef' || $test_host eq 'localhost' ) { - $use_host = 0; - } - - my $test_dsn; -- if ($driver eq 'Pg' || $driver eq 'SQLite') { +- if ( $driver eq 'Pg' || $driver eq 'SQLite' ) { - $test_dsn = "dbi:$driver:dbname=$test_db"; - $mysql_ok = 0; -- } -- else { +- } else { - $test_dsn = "dbi:$driver:database=$test_db"; - $mysql_ok = 0; - } @@ -72,24 +81,30 @@ - $test_dsn .= ";host=$test_host"; - } - -- $build->notes(dbd_driver => $driver); -- $build->notes(test_db => $test_db); -- $build->notes(test_host => $test_host); -- $build->notes(test_user => $test_user eq 'undef' ? undef : $test_user); -- $build->notes(test_pass => $test_pass eq 'undef' ? undef : $test_pass); -- $build->notes(test_dsn => $test_dsn); -- -- $build->log_info(" - will run tests with database driver '$driver' and these settings:\n", -- " Database $test_db\n", -- " Host $test_host\n", -- " DSN $test_dsn\n", -- " User $test_user\n", -- " Password $test_pass\n"); -- $build->log_info(" - will not run the BioDBSeqFeature live ". -- "database tests (requires MySQL or Pg driver)\n") unless ($driver eq 'mysql' or $driver eq 'Pg'); -- } -- else { -- $build->log_info(" - will not run the BioDBGFF or BioDBSeqFeature live database tests\n"); +- $build->notes( dbd_driver => $driver ); +- $build->notes( test_db => $test_db ); +- $build->notes( test_host => $test_host ); +- $build->notes( +- test_user => $test_user eq 'undef' ? undef : $test_user ); +- $build->notes( +- test_pass => $test_pass eq 'undef' ? undef : $test_pass ); +- $build->notes( test_dsn => $test_dsn ); +- +- $build->log_info( +- " - will run tests with database driver '$driver' and these settings:\n", +- " Database $test_db\n", +- " Host $test_host\n", +- " DSN $test_dsn\n", +- " User $test_user\n", +- " Password $test_pass\n" +- ); +- $build->log_info( " - will not run the BioDBSeqFeature live " +- . "database tests (requires MySQL or Pg driver)\n" ) +- unless ( $driver eq 'mysql' or $driver eq 'Pg' ); +- } else { +- $build->log_info( +- " - will not run the BioDBGFF or BioDBSeqFeature live database tests\n" +- ); - } - + my $proceed = 0; Modified: head/biology/p5-BioPerl/pkg-descr ============================================================================== --- head/biology/p5-BioPerl/pkg-descr Mon Dec 19 15:54:24 2016 (r428939) +++ head/biology/p5-BioPerl/pkg-descr Mon Dec 19 15:54:29 2016 (r428940) @@ -1,8 +1,8 @@ -The Bioperl Project is an international association of developers of open +The BioPerl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research. -Bioperl is a collection of object-oriented Perl modules created by the -Bioperl Project. It forms the basis of a large number of bioinformatics and +BioPerl is a collection of object-oriented Perl modules created by the +BioPerl Project. It forms the basis of a large number of bioinformatics and genomics applications. (For an interesting aside on "How Perl saved the Human Genome Project", see Modified: head/biology/p5-BioPerl/pkg-plist ============================================================================== --- head/biology/p5-BioPerl/pkg-plist Mon Dec 19 15:54:24 2016 (r428939) +++ head/biology/p5-BioPerl/pkg-plist Mon Dec 19 15:54:29 2016 (r428940) @@ -15,6 +15,7 @@ bin/bp_fast_load_gff.pl bin/bp_fastam9_to_table.pl bin/bp_fetch.pl bin/bp_filter_search.pl +bin/bp_find-blast-matches.pl bin/bp_flanks.pl bin/bp_gccalc.pl bin/bp_genbank2gff.pl @@ -43,7 +44,6 @@ bin/bp_process_wormbase.pl bin/bp_query_entrez_taxa.pl bin/bp_remote_blast.pl bin/bp_revtrans-motif.pl -bin/bp_search2BSML.pl bin/bp_search2alnblocks.pl bin/bp_search2gff.pl bin/bp_search2table.pl @@ -139,18 +139,6 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/ClusterIO/unigene.pm %%SITE_PERL%%/Bio/CodonUsage/IO.pm %%SITE_PERL%%/Bio/CodonUsage/Table.pm -%%SITE_PERL%%/Bio/Coordinate/Chain.pm -%%SITE_PERL%%/Bio/Coordinate/Collection.pm -%%SITE_PERL%%/Bio/Coordinate/ExtrapolatingPair.pm -%%SITE_PERL%%/Bio/Coordinate/GeneMapper.pm -%%SITE_PERL%%/Bio/Coordinate/Graph.pm -%%SITE_PERL%%/Bio/Coordinate/MapperI.pm -%%SITE_PERL%%/Bio/Coordinate/Pair.pm -%%SITE_PERL%%/Bio/Coordinate/Result.pm -%%SITE_PERL%%/Bio/Coordinate/Result/Gap.pm -%%SITE_PERL%%/Bio/Coordinate/Result/Match.pm -%%SITE_PERL%%/Bio/Coordinate/ResultI.pm -%%SITE_PERL%%/Bio/Coordinate/Utils.pm %%SITE_PERL%%/Bio/DB/Ace.pm %%SITE_PERL%%/Bio/DB/BioFetch.pm %%SITE_PERL%%/Bio/DB/CUTG.pm @@ -257,7 +245,6 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/DB/SeqFeature/Store/berkeleydb.pm %%SITE_PERL%%/Bio/DB/SeqFeature/Store/berkeleydb3.pm %%SITE_PERL%%/Bio/DB/SeqFeature/Store/memory.pm -%%SITE_PERL%%/Bio/DB/SeqHound.pm %%SITE_PERL%%/Bio/DB/SeqI.pm %%SITE_PERL%%/Bio/DB/SeqVersion.pm %%SITE_PERL%%/Bio/DB/SeqVersion/gi.pm @@ -270,6 +257,7 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/DB/Taxonomy/greengenes.pm %%SITE_PERL%%/Bio/DB/Taxonomy/list.pm %%SITE_PERL%%/Bio/DB/Taxonomy/silva.pm +%%SITE_PERL%%/Bio/DB/Taxonomy/sqlite.pm %%SITE_PERL%%/Bio/DB/Universal.pm %%SITE_PERL%%/Bio/DB/UpdateableSeqI.pm %%SITE_PERL%%/Bio/DB/WebDBSeqI.pm @@ -502,6 +490,7 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Root/RootI.pm %%SITE_PERL%%/Bio/Root/Storable.pm %%SITE_PERL%%/Bio/Root/Test.pm +%%SITE_PERL%%/Bio/Root/TestObject.pm %%SITE_PERL%%/Bio/Root/Utilities.pm %%SITE_PERL%%/Bio/Root/Version.pm %%SITE_PERL%%/Bio/Search/BlastStatistics.pm @@ -543,6 +532,7 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Search/Result/GenericResult.pm %%SITE_PERL%%/Bio/Search/Result/HMMERResult.pm %%SITE_PERL%%/Bio/Search/Result/HmmpfamResult.pm +%%SITE_PERL%%/Bio/Search/Result/INFERNALResult.pm %%SITE_PERL%%/Bio/Search/Result/PullResultI.pm %%SITE_PERL%%/Bio/Search/Result/ResultFactory.pm %%SITE_PERL%%/Bio/Search/Result/ResultI.pm @@ -560,20 +550,16 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/SearchIO/IteratedSearchResultEventBuilder.pm %%SITE_PERL%%/Bio/SearchIO/SearchResultEventBuilder.pm %%SITE_PERL%%/Bio/SearchIO/SearchWriterI.pm -%%SITE_PERL%%/Bio/SearchIO/Writer/BSMLResultWriter.pm %%SITE_PERL%%/Bio/SearchIO/Writer/GbrowseGFF.pm %%SITE_PERL%%/Bio/SearchIO/Writer/HSPTableWriter.pm %%SITE_PERL%%/Bio/SearchIO/Writer/HTMLResultWriter.pm %%SITE_PERL%%/Bio/SearchIO/Writer/HitTableWriter.pm %%SITE_PERL%%/Bio/SearchIO/Writer/ResultTableWriter.pm %%SITE_PERL%%/Bio/SearchIO/Writer/TextResultWriter.pm -%%SITE_PERL%%/Bio/SearchIO/XML/BlastHandler.pm -%%SITE_PERL%%/Bio/SearchIO/XML/PsiBlastHandler.pm %%SITE_PERL%%/Bio/SearchIO/axt.pm %%SITE_PERL%%/Bio/SearchIO/blast.pm %%SITE_PERL%%/Bio/SearchIO/blast_pull.pm %%SITE_PERL%%/Bio/SearchIO/blasttable.pm -%%SITE_PERL%%/Bio/SearchIO/blastxml.pm %%SITE_PERL%%/Bio/SearchIO/cross_match.pm %%SITE_PERL%%/Bio/SearchIO/erpin.pm %%SITE_PERL%%/Bio/SearchIO/exonerate.pm @@ -744,7 +730,6 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Tools/Analysis/Protein/ELM.pm %%SITE_PERL%%/Bio/Tools/Analysis/Protein/GOR4.pm %%SITE_PERL%%/Bio/Tools/Analysis/Protein/HNN.pm -%%SITE_PERL%%/Bio/Tools/Analysis/Protein/Mitoprot.pm %%SITE_PERL%%/Bio/Tools/Analysis/Protein/NetPhos.pm %%SITE_PERL%%/Bio/Tools/Analysis/Protein/Scansite.pm %%SITE_PERL%%/Bio/Tools/Analysis/Protein/Sopma.pm @@ -756,7 +741,6 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Tools/ECnumber.pm %%SITE_PERL%%/Bio/Tools/EMBOSS/Palindrome.pm %%SITE_PERL%%/Bio/Tools/EPCR.pm -%%SITE_PERL%%/Bio/Tools/ERPIN.pm %%SITE_PERL%%/Bio/Tools/ESTScan.pm %%SITE_PERL%%/Bio/Tools/Eponine.pm %%SITE_PERL%%/Bio/Tools/Est2Genome.pm @@ -777,7 +761,6 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Tools/HMMER/Set.pm %%SITE_PERL%%/Bio/Tools/Hmmpfam.pm %%SITE_PERL%%/Bio/Tools/IUPAC.pm -%%SITE_PERL%%/Bio/Tools/Infernal.pm %%SITE_PERL%%/Bio/Tools/Lucy.pm %%SITE_PERL%%/Bio/Tools/MZEF.pm %%SITE_PERL%%/Bio/Tools/Match.pm @@ -805,18 +788,11 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Tools/Protparam.pm %%SITE_PERL%%/Bio/Tools/Pseudowise.pm %%SITE_PERL%%/Bio/Tools/QRNA.pm -%%SITE_PERL%%/Bio/Tools/RNAMotif.pm %%SITE_PERL%%/Bio/Tools/RandomDistFunctions.pm %%SITE_PERL%%/Bio/Tools/RepeatMasker.pm %%SITE_PERL%%/Bio/Tools/Run/GenericParameters.pm %%SITE_PERL%%/Bio/Tools/Run/ParametersI.pm %%SITE_PERL%%/Bio/Tools/Run/RemoteBlast.pm -%%SITE_PERL%%/Bio/Tools/Run/StandAloneBlast.pm -%%SITE_PERL%%/Bio/Tools/Run/StandAloneNCBIBlast.pm -%%SITE_PERL%%/Bio/Tools/Run/StandAloneWUBlast.pm -%%SITE_PERL%%/Bio/Tools/Run/WrapperBase.pm -%%SITE_PERL%%/Bio/Tools/Run/WrapperBase/CommandExts.pm -%%SITE_PERL%%/Bio/Tools/Run/hmmer3.pm %%SITE_PERL%%/Bio/Tools/Seg.pm %%SITE_PERL%%/Bio/Tools/SeqPattern.pm %%SITE_PERL%%/Bio/Tools/SeqPattern/Backtranslate.pm @@ -880,6 +856,69 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Variation/SeqDiff.pm %%SITE_PERL%%/Bio/Variation/VariantI.pm %%SITE_PERL%%/Bio/WebAgent.pm +%%PERL5_MAN1%%/bp_aacomp.pl.1.gz +%%PERL5_MAN1%%/bp_biofetch_genbank_proxy.pl.1.gz +%%PERL5_MAN1%%/bp_bioflat_index.pl.1.gz +%%PERL5_MAN1%%/bp_biogetseq.pl.1.gz +%%PERL5_MAN1%%/bp_blast2tree.pl.1.gz +%%PERL5_MAN1%%/bp_bulk_load_gff.pl.1.gz +%%PERL5_MAN1%%/bp_chaos_plot.pl.1.gz +%%PERL5_MAN1%%/bp_classify_hits_kingdom.pl.1.gz +%%PERL5_MAN1%%/bp_composite_LD.pl.1.gz +%%PERL5_MAN1%%/bp_dbsplit.pl.1.gz +%%PERL5_MAN1%%/bp_download_query_genbank.pl.1.gz +%%PERL5_MAN1%%/bp_extract_feature_seq.pl.1.gz +%%PERL5_MAN1%%/bp_fast_load_gff.pl.1.gz +%%PERL5_MAN1%%/bp_fastam9_to_table.pl.1.gz +%%PERL5_MAN1%%/bp_fetch.pl.1.gz +%%PERL5_MAN1%%/bp_filter_search.pl.1.gz +%%PERL5_MAN1%%/bp_find-blast-matches.pl.1.gz +%%PERL5_MAN1%%/bp_flanks.pl.1.gz +%%PERL5_MAN1%%/bp_gccalc.pl.1.gz +%%PERL5_MAN1%%/bp_genbank2gff.pl.1.gz +%%PERL5_MAN1%%/bp_genbank2gff3.pl.1.gz +%%PERL5_MAN1%%/bp_generate_histogram.pl.1.gz +%%PERL5_MAN1%%/bp_heterogeneity_test.pl.1.gz +%%PERL5_MAN1%%/bp_hivq.pl.1.gz +%%PERL5_MAN1%%/bp_hmmer_to_table.pl.1.gz +%%PERL5_MAN1%%/bp_index.pl.1.gz +%%PERL5_MAN1%%/bp_load_gff.pl.1.gz +%%PERL5_MAN1%%/bp_local_taxonomydb_query.pl.1.gz +%%PERL5_MAN1%%/bp_make_mrna_protein.pl.1.gz +%%PERL5_MAN1%%/bp_mask_by_search.pl.1.gz +%%PERL5_MAN1%%/bp_meta_gff.pl.1.gz +%%PERL5_MAN1%%/bp_mrtrans.pl.1.gz +%%PERL5_MAN1%%/bp_mutate.pl.1.gz +%%PERL5_MAN1%%/bp_netinstall.pl.1.gz +%%PERL5_MAN1%%/bp_nexus2nh.pl.1.gz +%%PERL5_MAN1%%/bp_nrdb.pl.1.gz +%%PERL5_MAN1%%/bp_oligo_count.pl.1.gz +%%PERL5_MAN1%%/bp_pairwise_kaks.pl.1.gz +%%PERL5_MAN1%%/bp_parse_hmmsearch.pl.1.gz +%%PERL5_MAN1%%/bp_process_gadfly.pl.1.gz +%%PERL5_MAN1%%/bp_process_sgd.pl.1.gz +%%PERL5_MAN1%%/bp_process_wormbase.pl.1.gz +%%PERL5_MAN1%%/bp_query_entrez_taxa.pl.1.gz +%%PERL5_MAN1%%/bp_remote_blast.pl.1.gz +%%PERL5_MAN1%%/bp_revtrans-motif.pl.1.gz +%%PERL5_MAN1%%/bp_search2alnblocks.pl.1.gz +%%PERL5_MAN1%%/bp_search2gff.pl.1.gz +%%PERL5_MAN1%%/bp_search2table.pl.1.gz +%%PERL5_MAN1%%/bp_search2tribe.pl.1.gz +%%PERL5_MAN1%%/bp_seq_length.pl.1.gz +%%PERL5_MAN1%%/bp_seqconvert.pl.1.gz +%%PERL5_MAN1%%/bp_seqcut.pl.1.gz +%%PERL5_MAN1%%/bp_seqfeature_load.pl.1.gz +%%PERL5_MAN1%%/bp_seqpart.pl.1.gz +%%PERL5_MAN1%%/bp_seqret.pl.1.gz +%%PERL5_MAN1%%/bp_seqretsplit.pl.1.gz +%%PERL5_MAN1%%/bp_split_seq.pl.1.gz +%%PERL5_MAN1%%/bp_sreformat.pl.1.gz +%%PERL5_MAN1%%/bp_taxid4species.pl.1.gz +%%PERL5_MAN1%%/bp_taxonomy2tree.pl.1.gz +%%PERL5_MAN1%%/bp_translate_seq.pl.1.gz +%%PERL5_MAN1%%/bp_tree2pag.pl.1.gz +%%PERL5_MAN1%%/bp_unflatten_seq.pl.1.gz %%PERL5_MAN3%%/Bio::Align::AlignI.3.gz %%PERL5_MAN3%%/Bio::Align::DNAStatistics.3.gz %%PERL5_MAN3%%/Bio::Align::Graphics.3.gz @@ -955,18 +994,6 @@ bin/bp_unflatten_seq.pl %%PERL5_MAN3%%/Bio::ClusterIO::unigene.3.gz %%PERL5_MAN3%%/Bio::CodonUsage::IO.3.gz %%PERL5_MAN3%%/Bio::CodonUsage::Table.3.gz -%%PERL5_MAN3%%/Bio::Coordinate::Chain.3.gz -%%PERL5_MAN3%%/Bio::Coordinate::Collection.3.gz -%%PERL5_MAN3%%/Bio::Coordinate::ExtrapolatingPair.3.gz -%%PERL5_MAN3%%/Bio::Coordinate::GeneMapper.3.gz -%%PERL5_MAN3%%/Bio::Coordinate::Graph.3.gz -%%PERL5_MAN3%%/Bio::Coordinate::MapperI.3.gz -%%PERL5_MAN3%%/Bio::Coordinate::Pair.3.gz -%%PERL5_MAN3%%/Bio::Coordinate::Result.3.gz -%%PERL5_MAN3%%/Bio::Coordinate::Result::Gap.3.gz -%%PERL5_MAN3%%/Bio::Coordinate::Result::Match.3.gz -%%PERL5_MAN3%%/Bio::Coordinate::ResultI.3.gz -%%PERL5_MAN3%%/Bio::Coordinate::Utils.3.gz %%PERL5_MAN3%%/Bio::DB::Ace.3.gz %%PERL5_MAN3%%/Bio::DB::BioFetch.3.gz %%PERL5_MAN3%%/Bio::DB::CUTG.3.gz @@ -1072,7 +1099,6 @@ bin/bp_unflatten_seq.pl %%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::berkeleydb.3.gz %%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::berkeleydb3.3.gz %%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::memory.3.gz -%%PERL5_MAN3%%/Bio::DB::SeqHound.3.gz %%PERL5_MAN3%%/Bio::DB::SeqI.3.gz %%PERL5_MAN3%%/Bio::DB::SeqVersion.3.gz %%PERL5_MAN3%%/Bio::DB::SeqVersion::gi.3.gz @@ -1085,6 +1111,7 @@ bin/bp_unflatten_seq.pl %%PERL5_MAN3%%/Bio::DB::Taxonomy::greengenes.3.gz %%PERL5_MAN3%%/Bio::DB::Taxonomy::list.3.gz %%PERL5_MAN3%%/Bio::DB::Taxonomy::silva.3.gz +%%PERL5_MAN3%%/Bio::DB::Taxonomy::sqlite.3.gz %%PERL5_MAN3%%/Bio::DB::Universal.3.gz %%PERL5_MAN3%%/Bio::DB::UpdateableSeqI.3.gz %%PERL5_MAN3%%/Bio::DB::WebDBSeqI.3.gz @@ -1317,6 +1344,7 @@ bin/bp_unflatten_seq.pl %%PERL5_MAN3%%/Bio::Root::RootI.3.gz %%PERL5_MAN3%%/Bio::Root::Storable.3.gz %%PERL5_MAN3%%/Bio::Root::Test.3.gz +%%PERL5_MAN3%%/Bio::Root::TestObject.3.gz %%PERL5_MAN3%%/Bio::Root::Utilities.3.gz %%PERL5_MAN3%%/Bio::Root::Version.3.gz %%PERL5_MAN3%%/Bio::Search::BlastStatistics.3.gz @@ -1358,6 +1386,7 @@ bin/bp_unflatten_seq.pl %%PERL5_MAN3%%/Bio::Search::Result::GenericResult.3.gz %%PERL5_MAN3%%/Bio::Search::Result::HMMERResult.3.gz %%PERL5_MAN3%%/Bio::Search::Result::HmmpfamResult.3.gz +%%PERL5_MAN3%%/Bio::Search::Result::INFERNALResult.3.gz %%PERL5_MAN3%%/Bio::Search::Result::PullResultI.3.gz %%PERL5_MAN3%%/Bio::Search::Result::ResultFactory.3.gz %%PERL5_MAN3%%/Bio::Search::Result::ResultI.3.gz @@ -1375,20 +1404,16 @@ bin/bp_unflatten_seq.pl %%PERL5_MAN3%%/Bio::SearchIO::IteratedSearchResultEventBuilder.3.gz %%PERL5_MAN3%%/Bio::SearchIO::SearchResultEventBuilder.3.gz %%PERL5_MAN3%%/Bio::SearchIO::SearchWriterI.3.gz -%%PERL5_MAN3%%/Bio::SearchIO::Writer::BSMLResultWriter.3.gz %%PERL5_MAN3%%/Bio::SearchIO::Writer::GbrowseGFF.3.gz %%PERL5_MAN3%%/Bio::SearchIO::Writer::HSPTableWriter.3.gz %%PERL5_MAN3%%/Bio::SearchIO::Writer::HTMLResultWriter.3.gz %%PERL5_MAN3%%/Bio::SearchIO::Writer::HitTableWriter.3.gz %%PERL5_MAN3%%/Bio::SearchIO::Writer::ResultTableWriter.3.gz %%PERL5_MAN3%%/Bio::SearchIO::Writer::TextResultWriter.3.gz -%%PERL5_MAN3%%/Bio::SearchIO::XML::BlastHandler.3.gz -%%PERL5_MAN3%%/Bio::SearchIO::XML::PsiBlastHandler.3.gz %%PERL5_MAN3%%/Bio::SearchIO::axt.3.gz %%PERL5_MAN3%%/Bio::SearchIO::blast.3.gz %%PERL5_MAN3%%/Bio::SearchIO::blast_pull.3.gz %%PERL5_MAN3%%/Bio::SearchIO::blasttable.3.gz -%%PERL5_MAN3%%/Bio::SearchIO::blastxml.3.gz %%PERL5_MAN3%%/Bio::SearchIO::cross_match.3.gz %%PERL5_MAN3%%/Bio::SearchIO::erpin.3.gz %%PERL5_MAN3%%/Bio::SearchIO::exonerate.3.gz @@ -1559,7 +1584,6 @@ bin/bp_unflatten_seq.pl %%PERL5_MAN3%%/Bio::Tools::Analysis::Protein::ELM.3.gz %%PERL5_MAN3%%/Bio::Tools::Analysis::Protein::GOR4.3.gz %%PERL5_MAN3%%/Bio::Tools::Analysis::Protein::HNN.3.gz -%%PERL5_MAN3%%/Bio::Tools::Analysis::Protein::Mitoprot.3.gz %%PERL5_MAN3%%/Bio::Tools::Analysis::Protein::NetPhos.3.gz %%PERL5_MAN3%%/Bio::Tools::Analysis::Protein::Scansite.3.gz %%PERL5_MAN3%%/Bio::Tools::Analysis::Protein::Sopma.3.gz @@ -1571,7 +1595,6 @@ bin/bp_unflatten_seq.pl %%PERL5_MAN3%%/Bio::Tools::ECnumber.3.gz %%PERL5_MAN3%%/Bio::Tools::EMBOSS::Palindrome.3.gz %%PERL5_MAN3%%/Bio::Tools::EPCR.3.gz -%%PERL5_MAN3%%/Bio::Tools::ERPIN.3.gz %%PERL5_MAN3%%/Bio::Tools::ESTScan.3.gz %%PERL5_MAN3%%/Bio::Tools::Eponine.3.gz %%PERL5_MAN3%%/Bio::Tools::Est2Genome.3.gz @@ -1592,7 +1615,6 @@ bin/bp_unflatten_seq.pl %%PERL5_MAN3%%/Bio::Tools::HMMER::Set.3.gz %%PERL5_MAN3%%/Bio::Tools::Hmmpfam.3.gz %%PERL5_MAN3%%/Bio::Tools::IUPAC.3.gz -%%PERL5_MAN3%%/Bio::Tools::Infernal.3.gz %%PERL5_MAN3%%/Bio::Tools::Lucy.3.gz %%PERL5_MAN3%%/Bio::Tools::MZEF.3.gz %%PERL5_MAN3%%/Bio::Tools::Match.3.gz @@ -1620,17 +1642,11 @@ bin/bp_unflatten_seq.pl %%PERL5_MAN3%%/Bio::Tools::Protparam.3.gz %%PERL5_MAN3%%/Bio::Tools::Pseudowise.3.gz %%PERL5_MAN3%%/Bio::Tools::QRNA.3.gz -%%PERL5_MAN3%%/Bio::Tools::RNAMotif.3.gz %%PERL5_MAN3%%/Bio::Tools::RandomDistFunctions.3.gz %%PERL5_MAN3%%/Bio::Tools::RepeatMasker.3.gz %%PERL5_MAN3%%/Bio::Tools::Run::GenericParameters.3.gz %%PERL5_MAN3%%/Bio::Tools::Run::ParametersI.3.gz %%PERL5_MAN3%%/Bio::Tools::Run::RemoteBlast.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::StandAloneBlast.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::StandAloneNCBIBlast.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::StandAloneWUBlast.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::WrapperBase.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::WrapperBase::CommandExts.3.gz %%PERL5_MAN3%%/Bio::Tools::Seg.3.gz %%PERL5_MAN3%%/Bio::Tools::SeqPattern.3.gz %%PERL5_MAN3%%/Bio::Tools::SeqPattern::Backtranslate.3.gz @@ -1694,246 +1710,3 @@ bin/bp_unflatten_seq.pl %%PERL5_MAN3%%/Bio::Variation::SeqDiff.3.gz %%PERL5_MAN3%%/Bio::Variation::VariantI.3.gz %%PERL5_MAN3%%/Bio::WebAgent.3.gz -%%PERL5_MAN1%%/bp_aacomp.pl.1.gz -%%PERL5_MAN1%%/bp_biofetch_genbank_proxy.pl.1.gz -%%PERL5_MAN1%%/bp_bioflat_index.pl.1.gz -%%PERL5_MAN1%%/bp_biogetseq.pl.1.gz -%%PERL5_MAN1%%/bp_blast2tree.pl.1.gz -%%PERL5_MAN1%%/bp_bulk_load_gff.pl.1.gz -%%PERL5_MAN1%%/bp_chaos_plot.pl.1.gz -%%PERL5_MAN1%%/bp_classify_hits_kingdom.pl.1.gz -%%PERL5_MAN1%%/bp_composite_LD.pl.1.gz -%%PERL5_MAN1%%/bp_dbsplit.pl.1.gz -%%PERL5_MAN1%%/bp_download_query_genbank.pl.1.gz -%%PERL5_MAN1%%/bp_extract_feature_seq.pl.1.gz -%%PERL5_MAN1%%/bp_fast_load_gff.pl.1.gz -%%PERL5_MAN1%%/bp_fastam9_to_table.pl.1.gz -%%PERL5_MAN1%%/bp_fetch.pl.1.gz -%%PERL5_MAN1%%/bp_filter_search.pl.1.gz -%%PERL5_MAN1%%/bp_flanks.pl.1.gz -%%PERL5_MAN1%%/bp_gccalc.pl.1.gz -%%PERL5_MAN1%%/bp_genbank2gff.pl.1.gz -%%PERL5_MAN1%%/bp_genbank2gff3.pl.1.gz -%%PERL5_MAN1%%/bp_generate_histogram.pl.1.gz -%%PERL5_MAN1%%/bp_heterogeneity_test.pl.1.gz -%%PERL5_MAN1%%/bp_hivq.pl.1.gz -%%PERL5_MAN1%%/bp_hmmer_to_table.pl.1.gz -%%PERL5_MAN1%%/bp_index.pl.1.gz -%%PERL5_MAN1%%/bp_load_gff.pl.1.gz -%%PERL5_MAN1%%/bp_local_taxonomydb_query.pl.1.gz -%%PERL5_MAN1%%/bp_make_mrna_protein.pl.1.gz -%%PERL5_MAN1%%/bp_mask_by_search.pl.1.gz -%%PERL5_MAN1%%/bp_meta_gff.pl.1.gz -%%PERL5_MAN1%%/bp_mrtrans.pl.1.gz -%%PERL5_MAN1%%/bp_mutate.pl.1.gz -%%PERL5_MAN1%%/bp_netinstall.pl.1.gz -%%PERL5_MAN1%%/bp_nexus2nh.pl.1.gz -%%PERL5_MAN1%%/bp_nrdb.pl.1.gz -%%PERL5_MAN1%%/bp_oligo_count.pl.1.gz -%%PERL5_MAN1%%/bp_pairwise_kaks.pl.1.gz -%%PERL5_MAN1%%/bp_parse_hmmsearch.pl.1.gz -%%PERL5_MAN1%%/bp_process_gadfly.pl.1.gz -%%PERL5_MAN1%%/bp_process_sgd.pl.1.gz -%%PERL5_MAN1%%/bp_process_wormbase.pl.1.gz -%%PERL5_MAN1%%/bp_query_entrez_taxa.pl.1.gz -%%PERL5_MAN1%%/bp_remote_blast.pl.1.gz -%%PERL5_MAN1%%/bp_revtrans-motif.pl.1.gz -%%PERL5_MAN1%%/bp_search2BSML.pl.1.gz -%%PERL5_MAN1%%/bp_search2alnblocks.pl.1.gz -%%PERL5_MAN1%%/bp_search2gff.pl.1.gz -%%PERL5_MAN1%%/bp_search2table.pl.1.gz -%%PERL5_MAN1%%/bp_search2tribe.pl.1.gz -%%PERL5_MAN1%%/bp_seq_length.pl.1.gz -%%PERL5_MAN1%%/bp_seqconvert.pl.1.gz -%%PERL5_MAN1%%/bp_seqcut.pl.1.gz -%%PERL5_MAN1%%/bp_seqfeature_load.pl.1.gz -%%PERL5_MAN1%%/bp_seqpart.pl.1.gz -%%PERL5_MAN1%%/bp_seqret.pl.1.gz -%%PERL5_MAN1%%/bp_seqretsplit.pl.1.gz -%%PERL5_MAN1%%/bp_split_seq.pl.1.gz -%%PERL5_MAN1%%/bp_sreformat.pl.1.gz -%%PERL5_MAN1%%/bp_taxid4species.pl.1.gz -%%PERL5_MAN1%%/bp_taxonomy2tree.pl.1.gz -%%PERL5_MAN1%%/bp_translate_seq.pl.1.gz -%%PERL5_MAN1%%/bp_tree2pag.pl.1.gz -%%PERL5_MAN1%%/bp_unflatten_seq.pl.1.gz -%%DATADIR%%/models/README -%%DATADIR%%/models/biblio.dia -%%DATADIR%%/models/bio_liveseq_variation.dia -%%DATADIR%%/models/bio_map.dia -%%DATADIR%%/models/bio_restriction.dia -%%DATADIR%%/models/bioperl.dia -%%DATADIR%%/models/coordinatemapper.dia -%%DATADIR%%/models/map_proposal.txt -%%DATADIR%%/models/maps_and_markers.dia -%%DATADIR%%/models/popgen.dia -%%DATADIR%%/models/population_proposal.txt -%%DATADIR%%/scripts/Bio-DB-GFF/README -%%DATADIR%%/scripts/Bio-DB-GFF/bp_bulk_load_gff.pl -%%DATADIR%%/scripts/Bio-DB-GFF/bp_fast_load_gff.pl -%%DATADIR%%/scripts/Bio-DB-GFF/bp_genbank2gff.pl -%%DATADIR%%/scripts/Bio-DB-GFF/bp_genbank2gff3.pl -%%DATADIR%%/scripts/Bio-DB-GFF/bp_generate_histogram.pl -%%DATADIR%%/scripts/Bio-DB-GFF/bp_load_gff.pl -%%DATADIR%%/scripts/Bio-DB-GFF/bp_meta_gff.pl -%%DATADIR%%/scripts/Bio-DB-GFF/bp_process_gadfly.pl -%%DATADIR%%/scripts/Bio-DB-GFF/bp_process_sgd.pl -%%DATADIR%%/scripts/Bio-DB-GFF/bp_process_wormbase.pl -%%DATADIR%%/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl -%%DATADIR%%/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl -%%DATADIR%%/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl -%%DATADIR%%/scripts/DB-HIV/bp_hivq.pl -%%DATADIR%%/scripts/DB/TAG -%%DATADIR%%/scripts/DB/bp_biofetch_genbank_proxy.pl -%%DATADIR%%/scripts/DB/bp_bioflat_index.pl -%%DATADIR%%/scripts/DB/bp_biogetseq.pl -%%DATADIR%%/scripts/DB/bp_flanks.pl -%%DATADIR%%/scripts/README -%%DATADIR%%/scripts/das/README -%%DATADIR%%/scripts/das/TAG -%%DATADIR%%/scripts/das/bp_das_server.pl -%%DATADIR%%/scripts/index/TAG -%%DATADIR%%/scripts/index/bp_fetch.pl -%%DATADIR%%/scripts/index/bp_index.pl -%%DATADIR%%/scripts/index/bp_seqret.pl -%%DATADIR%%/scripts/popgen/bp_composite_LD.pl -%%DATADIR%%/scripts/popgen/bp_heterogeneity_test.pl -%%DATADIR%%/scripts/searchio/README -%%DATADIR%%/scripts/searchio/TAG -%%DATADIR%%/scripts/searchio/bp_fastam9_to_table.pl -%%DATADIR%%/scripts/searchio/bp_filter_search.pl -%%DATADIR%%/scripts/searchio/bp_hmmer_to_table.pl -%%DATADIR%%/scripts/searchio/bp_parse_hmmsearch.pl -%%DATADIR%%/scripts/searchio/bp_search2table.pl -%%DATADIR%%/scripts/seq/TAG -%%DATADIR%%/scripts/seq/bp_extract_feature_seq.pl -%%DATADIR%%/scripts/seq/bp_make_mrna_protein.pl -%%DATADIR%%/scripts/seq/bp_seqconvert.pl -%%DATADIR%%/scripts/seq/bp_seqcut.pl -%%DATADIR%%/scripts/seq/bp_seqpart.pl -%%DATADIR%%/scripts/seq/bp_seqretsplit.pl -%%DATADIR%%/scripts/seq/bp_split_seq.pl -%%DATADIR%%/scripts/seq/bp_translate_seq.pl -%%DATADIR%%/scripts/seq/bp_unflatten_seq.pl -%%DATADIR%%/scripts/seqstats/TAG -%%DATADIR%%/scripts/seqstats/bp_aacomp.pl -%%DATADIR%%/scripts/seqstats/bp_chaos_plot.pl -%%DATADIR%%/scripts/seqstats/bp_gccalc.pl -%%DATADIR%%/scripts/seqstats/bp_oligo_count.pl -%%DATADIR%%/scripts/taxa/TAG -%%DATADIR%%/scripts/taxa/bp_classify_hits_kingdom.pl -%%DATADIR%%/scripts/taxa/bp_local_taxonomydb_query.pl -%%DATADIR%%/scripts/taxa/bp_query_entrez_taxa.pl -%%DATADIR%%/scripts/taxa/bp_taxid4species.pl -%%DATADIR%%/scripts/taxa/bp_taxonomy2tree.pl -%%DATADIR%%/scripts/tree/TAG -%%DATADIR%%/scripts/tree/bp_blast2tree.pl -%%DATADIR%%/scripts/tree/bp_nexus2nh.pl -%%DATADIR%%/scripts/tree/bp_tree2pag.pl 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