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- Update to 1.007001

Browse Source 
- 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
This commit is contained in:
Sunpoet Po-Chuan Hsieh 2016-12-19 15:54:29 +00:00
parent 2aeec3a360
commit 88681d6d69
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=428940
6 changed files with 180 additions and 383 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

58
biology/p5-BioPerl/Makefile
View File

@ -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:= ${BUILD_DEPENDS}
TEST_DEPENDS= p5-Test-Most>=0:devel/p5-Test-Most \
p5-URI>=0:net/p5-URI
USES= perl5
USE_PERL5= modbuild
NO_ARCH= yes
PORTDATA= *
PORTDOCS= *
PORTEXAMPLES= *
OPTIONS_DEFINE= DOCS EXAMPLES PGTEST SQLITETEST
PGTEST_DESC= Test PostGreSQL
SQLITETEST_DESC= Test SQLite
@ -70,7 +71,7 @@ SQLITETEST_RUN_DEPENDS= p5-DBD-SQLite>=1:databases/p5-DBD-SQLite
SQLITETEST_BUILD_DEPENDS= p5-DBD-SQLite>=1:databases/p5-DBD-SQLite
post-patch:
@${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>

5
biology/p5-BioPerl/distinfo
View File

@ -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

4
biology/p5-BioPerl/files/patch-Bio-Root-Build.pm
View File

@ -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 @@
}
}

123
biology/p5-BioPerl/files/patch-Build.PL
View File

@ -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->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");
- $build->log_info(
- " - will run tests with database driver '$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;

6
biology/p5-BioPerl/pkg-descr
View File

@ -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

367
biology/p5-BioPerl/pkg-plist
View File

@ -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
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%%PERL5_MAN1%%/bp_bioflat_index.pl.1.gz
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%%PERL5_MAN1%%/bp_blast2tree.pl.1.gz
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%%PERL5_MAN1%%/bp_composite_LD.pl.1.gz
%%PERL5_MAN1%%/bp_dbsplit.pl.1.gz
%%PERL5_MAN1%%/bp_download_query_genbank.pl.1.gz
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%%PERL5_MAN1%%/bp_gccalc.pl.1.gz
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%%PERL5_MAN1%%/bp_taxid4species.pl.1.gz
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%%DATADIR%%/scripts/DB/bp_biofetch_genbank_proxy.pl
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