diff options
author | Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org> | 2016-12-18 15:25:04 +0000 |
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committer | Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org> | 2016-12-18 15:25:04 +0000 |
commit | 99a028004e82c13204ee1c813f8ff0ff9624170c (patch) | |
tree | db15fde4441485f5e76bad10c5e853693e7e5778 /biology/p5-BioPerl | |
parent | 377f6fdc54d686dcecf480a4d2acd64895eb4673 (diff) | |
download | ports-99a028004e82c13204ee1c813f8ff0ff9624170c.tar.gz ports-99a028004e82c13204ee1c813f8ff0ff9624170c.zip |
- Move biology/p5-bioperl to biology/p5-BioPerl
- Sort *_DEPENDS
- Bump PORTREVISION for dependent ports
Notes
Notes:
svn path=/head/; revision=428868
Diffstat (limited to 'biology/p5-BioPerl')
-rw-r--r-- | biology/p5-BioPerl/Makefile | 92 | ||||
-rw-r--r-- | biology/p5-BioPerl/distinfo | 2 | ||||
-rw-r--r-- | biology/p5-BioPerl/files/patch-Bio-Root-Build.pm | 80 | ||||
-rw-r--r-- | biology/p5-BioPerl/files/patch-Build.PL | 99 | ||||
-rw-r--r-- | biology/p5-BioPerl/pkg-descr | 11 | ||||
-rw-r--r-- | biology/p5-BioPerl/pkg-plist | 1939 |
6 files changed, 2223 insertions, 0 deletions
diff --git a/biology/p5-BioPerl/Makefile b/biology/p5-BioPerl/Makefile new file mode 100644 index 000000000000..b4d1bc17a645 --- /dev/null +++ b/biology/p5-BioPerl/Makefile @@ -0,0 +1,92 @@ +# Created by: Johann Visagie <johann@egenetics.com> +# $FreeBSD$ + +PORTNAME= BioPerl +PORTVERSION= 1.6.924 +PORTREVISION= 5 +CATEGORIES= biology perl5 +MASTER_SITES= CPAN +MASTER_SITE_SUBDIR= CPAN:CJFIELDS +PKGNAMEPREFIX= p5- + +MAINTAINER= perl@FreeBSD.org +COMMENT= Collection of Perl modules for bioinformatics + +LICENSE= ART10 GPLv1 +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-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-GraphViz>=0:graphics/p5-GraphViz \ + p5-HTML-Parser>=0:www/p5-HTML-Parser \ + p5-HTML-TableExtract>=2:www/p5-HTML-TableExtract \ + 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-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-Set-Scalar>=0:devel/p5-Set-Scalar \ + p5-Sort-Naturally>=1: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-Writer>=0:textproc/p5-XML-SAX-Writer \ + p5-XML-Simple>=2:textproc/p5-XML-Simple \ + p5-XML-Twig>=0:textproc/p5-XML-Twig \ + p5-XML-Writer>=0:textproc/p5-XML-Writer \ + p5-YAML>=0:textproc/p5-YAML \ + p5-libwww>=0:www/p5-libwww \ + p5-libxml>=0:textproc/p5-libxml +RUN_DEPENDS:= ${BUILD_DEPENDS} + +USES= perl5 +USE_PERL5= modbuild +NO_ARCH= yes + +OPTIONS_DEFINE= DOCS EXAMPLES PGTEST SQLITETEST +PGTEST_DESC= Test PostGreSQL +SQLITETEST_DESC= Test SQLite +PGTEST_RUN_DEPENDS= p5-DBD-Pg>=3:databases/p5-DBD-Pg +PGTEST_BUILD_DEPENDS= p5-DBD-Pg>=3:databases/p5-DBD-Pg +SQLITETEST_RUN_DEPENDS= p5-DBD-SQLite>=1:databases/p5-DBD-SQLite +SQLITETEST_BUILD_DEPENDS= p5-DBD-SQLite>=1:databases/p5-DBD-SQLite + +post-patch: + @${FIND} ${WRKSRC}/examples ${WRKSRC}/doc -name "*.pl" -o -name "*.cgi" \ + -o -name "*.PL" | ${XARGS} ${REINPLACE_CMD} -i '' -Ee \ + '1s|(/usr)?/bin/perl|${PERL}|' + +post-install: + @${MKDIR} ${STAGEDIR}${DATADIR} + ${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${STAGEDIR}${DATADIR} + +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} +.endfor + ${CP} -R ${WRKSRC}/doc ${STAGEDIR}${DOCSDIR} + +post-install-EXAMPLES-on: + @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} + ${CP} -R ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR} + +.include <bsd.port.mk> diff --git a/biology/p5-BioPerl/distinfo b/biology/p5-BioPerl/distinfo new file mode 100644 index 000000000000..f8ce60817098 --- /dev/null +++ b/biology/p5-BioPerl/distinfo @@ -0,0 +1,2 @@ +SHA256 (BioPerl-1.6.924.tar.gz) = 616a7546bb3c58504de27304a0f6cb904e18b6bbcdb6a4ec8454f2bd37bb76d0 +SIZE (BioPerl-1.6.924.tar.gz) = 12623118 diff --git a/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm b/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm new file mode 100644 index 000000000000..b4433616c5fc --- /dev/null +++ b/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm @@ -0,0 +1,80 @@ +--- 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 +@@ -83,49 +83,9 @@ + } + } + closedir($scripts_dir); +- my $question = $int_ok ? "Install [a]ll BioPerl scripts, [n]one, ". +- "or choose groups [i]nteractively?" : "Install [a]ll BioPerl scripts ". +- "or [n]one?"; +- +- my $prompt = $accept ? 'a' : $self->prompt($question, 'a'); +- +- if ($prompt =~ /^[aA]/) { +- $self->log_info(" - will install all scripts\n"); +- $self->notes(chosen_scripts => 'all'); +- } +- elsif ($prompt =~ /^[iI]/) { +- $self->log_info(" - will install interactively:\n"); +- +- my @chosen_scripts; +- foreach my $group_dir (@group_dirs) { +- my $group = File::Basename::basename($group_dir); +- print " * group '$group' has:\n"; +- +- my @script_files = @{$self->rscan_dir($group_dir, qr/\.PLS$|\.pl$/)}; +- foreach my $script_file (@script_files) { +- my $script = File::Basename::basename($script_file); +- print " $script\n"; +- } +- +- my $result = $self->prompt(" Install scripts for group '$group'? [y]es [n]o [q]uit", 'n'); +- die if $result =~ /^[qQ]/; +- if ($result =~ /^[yY]/) { +- $self->log_info(" + will install group '$group'\n"); +- push(@chosen_scripts, @script_files); +- } +- else { +- $self->log_info(" - will not install group '$group'\n"); +- } +- } + +- my $chosen_scripts = @chosen_scripts ? join("|", @chosen_scripts) : 'none'; +- +- $self->notes(chosen_scripts => $chosen_scripts); +- } +- else { +- $self->log_info(" - won't install any scripts\n"); +- $self->notes(chosen_scripts => 'none'); +- } ++ $self->log_info(" - willt install all scripts\n"); ++ $self->notes(chosen_scripts => 'all'); + + print "\n"; + } +@@ -1153,22 +1113,9 @@ + sub prompt_for_network { + my ($self, $accept) = @_; + +- my $proceed = $accept ? 0 : $self->y_n( "Do you want to run tests that require connection to servers across the internet\n" +- . "(likely to cause some failures)? y/n", 'n'); +- +- if ($proceed) { +- $self->notes('network' => 1); +- $self->log_info(" - will run internet-requiring tests\n"); +- my $use_email = $self->y_n("Do you want to run tests requiring a valid email address? y/n",'n'); +- if ($use_email) { +- my $address = $self->prompt("Enter email address:"); +- $self->notes(email => $address); +- } +- } +- else { +- $self->notes(network => 0); +- $self->log_info(" - will not run internet-requiring tests\n"); +- } ++ my $proceed = 0; ++ $self->notes(network => 0); ++ $self->log_info(" - will not run internet-requiring tests\n"); + } + + =head2 print_build_script diff --git a/biology/p5-BioPerl/files/patch-Build.PL b/biology/p5-BioPerl/files/patch-Build.PL new file mode 100644 index 000000000000..4f890bf60809 --- /dev/null +++ b/biology/p5-BioPerl/files/patch-Build.PL @@ -0,0 +1,99 @@ +--- 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_requires => { +- 'CPAN' => 1.81, + 'Module::Build' => 0.2805, + 'Test::Harness' => 2.62, + 'Test::Most' => 0, +@@ -376,86 +375,8 @@ + + sub prompt_for_biodb { + my $accept = shift; +- my $proceed = $accept ? 0 : $build->y_n("Do you want to run the Bio::DB::GFF or ". +- "Bio::DB::SeqFeature::Store live database tests? ". +- "y/n", 'n'); +- +- if ($proceed) { +- my @driver_choices; +- foreach my $poss ('SQLite', 'mysql', 'Pg', 'Oracle') { +- if (grep {/$poss/i} @drivers) { +- my $choice = $poss; +- $choice =~ s/^(.)/[$1]/; +- push(@driver_choices, $choice); +- } +- } +- +- my $driver; +- if (@driver_choices > 1) { +- my ($default) = $driver_choices[0] =~ /\[(.)/; +- $driver = $build->prompt("Which database driver should be used? ".join(" ", @driver_choices), $default); +- } +- else { +- ($driver) = $driver_choices[0] =~ /\[(.)/; +- } +- if ($driver =~ /^[mM]/) { +- $driver = 'mysql'; +- } +- elsif ($driver =~ /^[pP]/) { +- $driver = 'Pg'; +- } +- elsif ($driver =~ /^[oO]/) { +- $driver = 'Oracle'; +- } +- elsif ($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 $use_host = 1; +- if ($test_host eq 'undef' || $test_host eq 'localhost') { +- $use_host = 0; +- } +- +- my $test_dsn; +- if ($driver eq 'Pg' || $driver eq 'SQLite') { +- $test_dsn = "dbi:$driver:dbname=$test_db"; +- $mysql_ok = 0; +- } +- else { +- $test_dsn = "dbi:$driver:database=$test_db"; +- $mysql_ok = 0; +- } +- if ($use_host) { +- $test_dsn .= ";host=$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"); +- } +- ++ my $proceed = 0; ++ $build->log_info(" - will not run the BioDBGFF or BioDBSeqFeature live database tests\n"); + $build->log_info("\n"); + return $proceed; + } diff --git a/biology/p5-BioPerl/pkg-descr b/biology/p5-BioPerl/pkg-descr new file mode 100644 index 000000000000..a993ffada2fe --- /dev/null +++ b/biology/p5-BioPerl/pkg-descr @@ -0,0 +1,11 @@ +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 +genomics applications. + +(For an interesting aside on "How Perl saved the Human Genome Project", see +http://www.bioperl.org/wiki/How_Perl_saved_human_genome) + +WWW: http://bioperl.org/ diff --git a/biology/p5-BioPerl/pkg-plist b/biology/p5-BioPerl/pkg-plist new file mode 100644 index 000000000000..4f532432a681 --- /dev/null +++ b/biology/p5-BioPerl/pkg-plist @@ -0,0 +1,1939 @@ +bin/bp_aacomp.pl +bin/bp_biofetch_genbank_proxy.pl +bin/bp_bioflat_index.pl +bin/bp_biogetseq.pl +bin/bp_blast2tree.pl +bin/bp_bulk_load_gff.pl +bin/bp_chaos_plot.pl +bin/bp_classify_hits_kingdom.pl +bin/bp_composite_LD.pl +bin/bp_das_server.pl +bin/bp_dbsplit.pl +bin/bp_download_query_genbank.pl +bin/bp_extract_feature_seq.pl +bin/bp_fast_load_gff.pl +bin/bp_fastam9_to_table.pl +bin/bp_fetch.pl +bin/bp_filter_search.pl +bin/bp_flanks.pl +bin/bp_gccalc.pl +bin/bp_genbank2gff.pl +bin/bp_genbank2gff3.pl +bin/bp_generate_histogram.pl +bin/bp_heterogeneity_test.pl +bin/bp_hivq.pl +bin/bp_hmmer_to_table.pl +bin/bp_index.pl +bin/bp_load_gff.pl +bin/bp_local_taxonomydb_query.pl +bin/bp_make_mrna_protein.pl +bin/bp_mask_by_search.pl +bin/bp_meta_gff.pl +bin/bp_mrtrans.pl +bin/bp_mutate.pl +bin/bp_netinstall.pl +bin/bp_nexus2nh.pl +bin/bp_nrdb.pl +bin/bp_oligo_count.pl +bin/bp_pairwise_kaks.pl +bin/bp_parse_hmmsearch.pl +bin/bp_process_gadfly.pl +bin/bp_process_sgd.pl +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 +bin/bp_search2tribe.pl +bin/bp_seq_length.pl +bin/bp_seqconvert.pl +bin/bp_seqcut.pl +bin/bp_seqfeature_delete.pl +bin/bp_seqfeature_gff3.pl +bin/bp_seqfeature_load.pl +bin/bp_seqpart.pl +bin/bp_seqret.pl +bin/bp_seqretsplit.pl +bin/bp_split_seq.pl +bin/bp_sreformat.pl +bin/bp_taxid4species.pl +bin/bp_taxonomy2tree.pl +bin/bp_translate_seq.pl +bin/bp_tree2pag.pl +bin/bp_unflatten_seq.pl +%%SITE_PERL%%/Bio/Align/AlignI.pm +%%SITE_PERL%%/Bio/Align/DNAStatistics.pm +%%SITE_PERL%%/Bio/Align/Graphics.pm +%%SITE_PERL%%/Bio/Align/PairwiseStatistics.pm +%%SITE_PERL%%/Bio/Align/ProteinStatistics.pm +%%SITE_PERL%%/Bio/Align/StatisticsI.pm +%%SITE_PERL%%/Bio/Align/Utilities.pm +%%SITE_PERL%%/Bio/AlignIO.pm +%%SITE_PERL%%/Bio/AlignIO/Handler/GenericAlignHandler.pm +%%SITE_PERL%%/Bio/AlignIO/arp.pm +%%SITE_PERL%%/Bio/AlignIO/bl2seq.pm +%%SITE_PERL%%/Bio/AlignIO/clustalw.pm +%%SITE_PERL%%/Bio/AlignIO/emboss.pm +%%SITE_PERL%%/Bio/AlignIO/fasta.pm +%%SITE_PERL%%/Bio/AlignIO/largemultifasta.pm +%%SITE_PERL%%/Bio/AlignIO/maf.pm +%%SITE_PERL%%/Bio/AlignIO/mase.pm +%%SITE_PERL%%/Bio/AlignIO/mega.pm +%%SITE_PERL%%/Bio/AlignIO/meme.pm +%%SITE_PERL%%/Bio/AlignIO/metafasta.pm +%%SITE_PERL%%/Bio/AlignIO/msf.pm +%%SITE_PERL%%/Bio/AlignIO/nexml.pm +%%SITE_PERL%%/Bio/AlignIO/nexus.pm +%%SITE_PERL%%/Bio/AlignIO/pfam.pm +%%SITE_PERL%%/Bio/AlignIO/phylip.pm +%%SITE_PERL%%/Bio/AlignIO/po.pm +%%SITE_PERL%%/Bio/AlignIO/proda.pm +%%SITE_PERL%%/Bio/AlignIO/prodom.pm +%%SITE_PERL%%/Bio/AlignIO/psi.pm +%%SITE_PERL%%/Bio/AlignIO/selex.pm +%%SITE_PERL%%/Bio/AlignIO/stockholm.pm +%%SITE_PERL%%/Bio/AlignIO/xmfa.pm +%%SITE_PERL%%/Bio/AnalysisI.pm +%%SITE_PERL%%/Bio/AnalysisParserI.pm +%%SITE_PERL%%/Bio/AnalysisResultI.pm +%%SITE_PERL%%/Bio/AnnotatableI.pm +%%SITE_PERL%%/Bio/Annotation/AnnotationFactory.pm +%%SITE_PERL%%/Bio/Annotation/Collection.pm +%%SITE_PERL%%/Bio/Annotation/Comment.pm +%%SITE_PERL%%/Bio/Annotation/DBLink.pm +%%SITE_PERL%%/Bio/Annotation/OntologyTerm.pm +%%SITE_PERL%%/Bio/Annotation/Reference.pm +%%SITE_PERL%%/Bio/Annotation/Relation.pm +%%SITE_PERL%%/Bio/Annotation/SimpleValue.pm +%%SITE_PERL%%/Bio/Annotation/StructuredValue.pm +%%SITE_PERL%%/Bio/Annotation/TagTree.pm +%%SITE_PERL%%/Bio/Annotation/Target.pm +%%SITE_PERL%%/Bio/Annotation/Tree.pm +%%SITE_PERL%%/Bio/Annotation/TypeManager.pm +%%SITE_PERL%%/Bio/AnnotationCollectionI.pm +%%SITE_PERL%%/Bio/AnnotationI.pm +%%SITE_PERL%%/Bio/Assembly/Contig.pm +%%SITE_PERL%%/Bio/Assembly/ContigAnalysis.pm +%%SITE_PERL%%/Bio/Assembly/IO.pm +%%SITE_PERL%%/Bio/Assembly/IO/ace.pm +%%SITE_PERL%%/Bio/Assembly/IO/bowtie.pm +%%SITE_PERL%%/Bio/Assembly/IO/maq.pm +%%SITE_PERL%%/Bio/Assembly/IO/phrap.pm +%%SITE_PERL%%/Bio/Assembly/IO/sam.pm +%%SITE_PERL%%/Bio/Assembly/IO/tigr.pm +%%SITE_PERL%%/Bio/Assembly/Scaffold.pm +%%SITE_PERL%%/Bio/Assembly/ScaffoldI.pm +%%SITE_PERL%%/Bio/Assembly/Singlet.pm +%%SITE_PERL%%/Bio/Assembly/Tools/ContigSpectrum.pm +%%SITE_PERL%%/Bio/Cluster/ClusterFactory.pm +%%SITE_PERL%%/Bio/Cluster/FamilyI.pm +%%SITE_PERL%%/Bio/Cluster/SequenceFamily.pm +%%SITE_PERL%%/Bio/Cluster/UniGene.pm +%%SITE_PERL%%/Bio/Cluster/UniGeneI.pm +%%SITE_PERL%%/Bio/ClusterI.pm +%%SITE_PERL%%/Bio/ClusterIO.pm +%%SITE_PERL%%/Bio/ClusterIO/dbsnp.pm +%%SITE_PERL%%/Bio/ClusterIO/unigene.pm +%%SITE_PERL%%/Bio/CodonUsage/IO.pm 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