diff options
| -rw-r--r-- | biology/bioperl/DESCR | 15 | ||||
| -rw-r--r-- | biology/bioperl/Makefile | 79 | ||||
| -rw-r--r-- | biology/bioperl/PLIST | 134 | ||||
| -rw-r--r-- | biology/bioperl/distinfo | 9 | ||||
| -rw-r--r-- | biology/bioperl/options.mk | 28 | ||||
| -rw-r--r-- | biology/bioperl/patches/patch-aa | 21 |
6 files changed, 153 insertions, 133 deletions
diff --git a/biology/bioperl/DESCR b/biology/bioperl/DESCR index 213f3419102..3bd07299f7f 100644 --- a/biology/bioperl/DESCR +++ b/biology/bioperl/DESCR @@ -1,11 +1,6 @@ - The Bioperl project is a coordinated effort to collect computational -methods routinely used in bioinformatics into a set of standard -CPAN-style, well-documented, and freely available Perl modules. Perl -provides unparalleled support for many tasks common in bioinformatics -yet there are no standard Perl modules for biology. Bioperl hopes to -help fill this void. +The Bioperl Project is an international association of developers of open +source Perl tools for bioinformatics, genomics and life science research. - Bioperl modules and source code will always be freely available -under the same terms as Perl itself. The Bioperl project is open to -all and we invite suggestions and participation from the larger -bioinformatics community. +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. diff --git a/biology/bioperl/Makefile b/biology/bioperl/Makefile index 04ea1a136aa..882e27bf254 100644 --- a/biology/bioperl/Makefile +++ b/biology/bioperl/Makefile @@ -1,33 +1,64 @@ -# $NetBSD: Makefile,v 1.24 2013/05/31 12:39:38 wiz Exp $ -# - -DISTNAME= bioperl-0.7.0 -PKGREVISION= 7 -CATEGORIES= biology -MASTER_SITES= http://bioperl.org/DIST/old_releases/ - -MAINTAINER= pkgsrc-users@NetBSD.org -HOMEPAGE= http://bioperl.org/ -COMMENT= Perl tools for computational molecular biology - -USE_TOOLS+= pax - -REPLACE_PERL+= Bio/LiveSeq/Chain.pm -REPLACE_PERL+= Bio/SeqIO/game/featureHandler.pm -REPLACE_PERL+= Bio/Tools/Blast/Run/postclient.pl -REPLACE_PERL+= examples/gsequence -REPLACE_PERL+= examples/*.pl -REPLACE_PERL+= examples/blast/*.pl -REPLACE_PERL+= examples/root_object/*.pl -REPLACE_PERL+= examples/root_object/vector/vector.pl -REPLACE_PERL+= examples/seq/*.pl +# $NetBSD: Makefile,v 1.25 2014/02/20 14:44:16 fhajny Exp $ +DISTNAME= BioPerl-1.6.923 +PKGNAME= ${DISTNAME:tl} +CATEGORIES= biology perl5 +MASTER_SITES= ${MASTER_SITE_PERL_CPAN:=Bio/} + +MAINTAINER= filip@joyent.com +HOMEPAGE= http://www.bioperl.org/ +COMMENT= Perl tools for computational molecular biology +LICENSE= ${PERL5_LICENSE} + +BUILD_DEPENDS+= p5-Module-Build>0.42:../../devel/p5-Module-Build +BUILD_DEPENDS+= p5-Test-Most-[0-9]*:../../devel/p5-Test-Most + +DEPENDS+= p5-Algorithm-Munkres-[0-9]*:../../math/p5-Algorithm-Munkres +DEPENDS+= p5-Array-Compare-[0-9]*:../../devel/p5-Array-Compare +DEPENDS+= p5-Bio-ASN1-EntrezGene-[0-9]*:../../biology/p5-Bio-ASN1-EntrezGene +DEPENDS+= p5-Clone-[0-9]*:../../devel/p5-Clone +DEPENDS+= p5-Convert-Binary-C-[0-9]*:../../devel/p5-Convert-Binary-C +DEPENDS+= p5-DB_File-[0-9]*:../../databases/p5-DB_File +DEPENDS+= p5-Data-Stag>=0.11:../../devel/p5-Data-Stag +DEPENDS+= p5-Error-[0-9]*:../../devel/p5-Error +DEPENDS+= p5-ExtUtils-Manifest>=1.52:../../devel/p5-ExtUtils-Manifest +DEPENDS+= p5-GD-[0-9]*:../../graphics/p5-GD +DEPENDS+= p5-Graph>=0.50:../../devel/p5-Graph +DEPENDS+= p5-GraphViz-[0-9]*:../../graphics/p5-GraphViz +DEPENDS+= p5-HTML-Parser>=3:../../www/p5-HTML-Parser +DEPENDS+= p5-HTML-TableExtract-[0-9]*:../../www/p5-HTML-TableExtract +DEPENDS+= p5-IO-String-[0-9]*:../../devel/p5-IO-String +DEPENDS+= p5-List-MoreUtils-[0-9]*:../../devel/p5-List-MoreUtils +DEPENDS+= p5-PostScript-[0-9]*:../../print/p5-PostScript +DEPENDS+= p5-SOAP-Lite-[0-9]*:../../net/p5-SOAP-Lite +DEPENDS+= p5-SVG-Graph>=0.01:../../graphics/p5-SVG-Graph +DEPENDS+= p5-SVG>=2.26:../../graphics/p5-SVG +DEPENDS+= p5-Set-Scalar-[0-9]*:../../devel/p5-Set-Scalar +DEPENDS+= p5-Sort-Naturally-[0-9]*:../../devel/p5-Sort-Naturally +DEPENDS+= p5-Spreadsheet-ParseExcel-[0-9]*:../../math/p5-Spreadsheet-ParseExcel +DEPENDS+= p5-Storable>=2.05:../../devel/p5-Storable +DEPENDS+= p5-XML-Parser-[0-9]*:../../textproc/p5-XML-Parser +DEPENDS+= p5-XML-SAX-Writer-[0-9]*:../../textproc/p5-XML-SAX-Writer +DEPENDS+= p5-XML-SAX>=0.15:../../textproc/p5-XML-SAX +DEPENDS+= p5-XML-Simple-[0-9]*:../../textproc/p5-XML-Simple +DEPENDS+= p5-XML-Twig-[0-9]*:../../textproc/p5-XML-Twig +DEPENDS+= p5-XML-Writer>=0.4:../../textproc/p5-XML-Writer +DEPENDS+= p5-YAML-[0-9]*:../../textproc/p5-YAML +DEPENDS+= p5-libwww-[0-9]*:../../www/p5-libwww +DEPENDS+= p5-libxml-[0-9]*:../../textproc/p5-libxml + +USE_TOOLS+= pax + +REPLACE_PERL+= scripts/*/*.pl + +PERL5_MODULE_TYPE= Module::Build PERL5_PACKLIST= auto/Bio/.packlist INSTALLATION_DIRS= share/examples/bioperl post-install: - cd ${WRKSRC}/examples && pax -rw . ${DESTDIR}${PREFIX}/share/examples/bioperl + cd ${WRKSRC}/examples && ${PAX} -rw . ${DESTDIR}${PREFIX}/share/examples/bioperl +.include "options.mk" .include "../../lang/perl5/module.mk" .include "../../mk/bsd.pkg.mk" diff --git a/biology/bioperl/PLIST b/biology/bioperl/PLIST index 22976d99fe5..4e2abdf7029 100644 --- a/biology/bioperl/PLIST +++ b/biology/bioperl/PLIST @@ -1,74 +1,62 @@ -@comment $NetBSD: PLIST,v 1.2 2009/06/14 17:34:33 joerg Exp $ -share/examples/bioperl/blast/out/blastn.2.gz -share/examples/bioperl/blast/out/blastn.2.wu.gz -share/examples/bioperl/blast/out/blastp.1.gcg.gz -share/examples/bioperl/blast/out/blastp.1.gz -share/examples/bioperl/blast/out/blastp.2.gz -share/examples/bioperl/blast/out/blastp.2.nogap.gz -share/examples/bioperl/blast/out/blastp.2.wu -share/examples/bioperl/blast/out/blastp.205.gz -share/examples/bioperl/blast/out/blastp.2a.gz -share/examples/bioperl/blast/out/blastp.2b.gz -share/examples/bioperl/blast/out/blastp.email.html.gz -share/examples/bioperl/blast/out/blastx.2 -share/examples/bioperl/blast/out/blastx.2.email.gz -share/examples/bioperl/blast/out/blastx.208.gz -share/examples/bioperl/blast/out/tblastn.206.out.gz -share/examples/bioperl/blast/seq/acc1.dna.fasta -share/examples/bioperl/blast/seq/seqs.fasta -share/examples/bioperl/blast/seq/yal011w.dna.fasta -share/examples/bioperl/blast/seq/yel009c.fasta -share/examples/bioperl/blast/seq/ymr284w.fasta -share/examples/bioperl/blast/blast_config.pl -share/examples/bioperl/blast/blast_seq.pl -share/examples/bioperl/blast/example.table1 -share/examples/bioperl/blast/example.table2 -share/examples/bioperl/blast/html.pl -share/examples/bioperl/blast/parse_blast.pl -share/examples/bioperl/blast/parse_blast2.pl -share/examples/bioperl/blast/parse_multi.pl -share/examples/bioperl/blast/parse_positions.pl -share/examples/bioperl/blast/print_blasts.pl -share/examples/bioperl/blast/retrieve_blast.pl -share/examples/bioperl/blast/run_blast_remote.pl -share/examples/bioperl/blosum62.bla -share/examples/bioperl/change_gene.pl -share/examples/bioperl/clustalw.pl -share/examples/bioperl/getGenBank.pl -share/examples/bioperl/gon250.bla -share/examples/bioperl/gsequence -share/examples/bioperl/hitdisplay.pl -share/examples/bioperl/psw.pl -share/examples/bioperl/restriction.pl +@comment $NetBSD: PLIST,v 1.3 2014/02/20 14:44:16 fhajny Exp $ +share/examples/bioperl/Bio-DB-GFF/load_ucsc.pl +share/examples/bioperl/align/FastAlign.pl +share/examples/bioperl/align/align_on_codons.pl +share/examples/bioperl/align/aligntutorial.pl +share/examples/bioperl/align/clustalw.pl +share/examples/bioperl/align/simplealign.pl +share/examples/bioperl/bioperl.pl +share/examples/bioperl/cluster/dbsnp.pl +share/examples/bioperl/contributed/nmrpdb_parse.pl +share/examples/bioperl/contributed/prosite2perl.pl +share/examples/bioperl/contributed/rebase2list.pl +share/examples/bioperl/db/dbfetch +share/examples/bioperl/db/est_tissue_query.pl +share/examples/bioperl/db/gb2features.pl +share/examples/bioperl/db/getGenBank.pl +share/examples/bioperl/db/get_seqs.pl +share/examples/bioperl/db/rfetch.pl +share/examples/bioperl/db/use_registry.pl +share/examples/bioperl/generate_random_seq.pl +share/examples/bioperl/liveseq/change_gene.pl +share/examples/bioperl/longorf.pl +share/examples/bioperl/make_primers.pl +share/examples/bioperl/popgen/parse_calc_stats.pl +share/examples/bioperl/quality/svgtrace.pl share/examples/bioperl/rev_and_trans.pl -share/examples/bioperl/seq_pattern.pl -share/examples/bioperl/simplealign.pl -share/examples/bioperl/standaloneblast.pl -share/examples/bioperl/test-genscan.pl -share/examples/bioperl/root_object/Outer.pm -share/examples/bioperl/root_object/Bar.pm -share/examples/bioperl/root_object/Foo.pm -share/examples/bioperl/root_object/vector/Person.pm -share/examples/bioperl/root_object/vector/PersonManager.pm -share/examples/bioperl/root_object/vector/vector.out -share/examples/bioperl/root_object/vector/vector.pl -share/examples/bioperl/root_object/destroy.pl -share/examples/bioperl/root_object/error.out -share/examples/bioperl/root_object/error.pl -share/examples/bioperl/root_object/filehandle.out -share/examples/bioperl/root_object/filehandle.pl -share/examples/bioperl/root_object/io.out -share/examples/bioperl/root_object/io.pl -share/examples/bioperl/root_object/read.pl -share/examples/bioperl/root_object/read.test -share/examples/bioperl/root_object/read.test2 -share/examples/bioperl/root_object/read.test3 -share/examples/bioperl/root_object/utilities.pl -share/examples/bioperl/seq/seq.fasta.gz -share/examples/bioperl/seq/id.list -share/examples/bioperl/seq/seq1.fasta -share/examples/bioperl/seq/seq2.fasta -share/examples/bioperl/seq/seqs1.pl -share/examples/bioperl/seq/seqs2.pl -share/examples/bioperl/seq/seqs3.pl -share/examples/bioperl/seq/seqtools.pl +share/examples/bioperl/revcom_dir.pl +share/examples/bioperl/root/README +share/examples/bioperl/root/exceptions1.pl +share/examples/bioperl/root/exceptions2.pl +share/examples/bioperl/root/exceptions3.pl +share/examples/bioperl/root/exceptions4.pl +share/examples/bioperl/root/lib/TestInterface.pm +share/examples/bioperl/root/lib/TestObject.pm +share/examples/bioperl/searchio/blast_example.pl +share/examples/bioperl/searchio/custom_writer.pl +share/examples/bioperl/searchio/hitwriter.pl +share/examples/bioperl/searchio/hspwriter.pl +share/examples/bioperl/searchio/htmlwriter.pl +share/examples/bioperl/searchio/psiblast_features.pl +share/examples/bioperl/searchio/psiblast_iterations.pl +share/examples/bioperl/searchio/rawwriter.pl +share/examples/bioperl/searchio/resultwriter.pl +share/examples/bioperl/searchio/waba2gff.pl +share/examples/bioperl/searchio/waba2gff3.pl +share/examples/bioperl/sirna/TAG +share/examples/bioperl/sirna/rnai_finder.cgi +share/examples/bioperl/structure/structure-io.pl +share/examples/bioperl/subsequence.cgi +share/examples/bioperl/tk/gsequence.pl +share/examples/bioperl/tk/hitdisplay.pl +share/examples/bioperl/tools/extract_genes.pl +share/examples/bioperl/tools/gb_to_gff.pl +share/examples/bioperl/tools/gff2ps.pl +share/examples/bioperl/tools/parse_codeml.pl +share/examples/bioperl/tools/psw.pl +share/examples/bioperl/tools/reverse-translate.pl +share/examples/bioperl/tools/run_genscan.pl +share/examples/bioperl/tools/run_primer3.pl +share/examples/bioperl/tools/seq_pattern.pl +share/examples/bioperl/tools/standaloneblast.pl +share/examples/bioperl/tree/paup2phylip.pl diff --git a/biology/bioperl/distinfo b/biology/bioperl/distinfo index bfc2f7d9e35..d23a048951e 100644 --- a/biology/bioperl/distinfo +++ b/biology/bioperl/distinfo @@ -1,6 +1,5 @@ -$NetBSD: distinfo,v 1.4 2006/10/02 21:34:28 rillig Exp $ +$NetBSD: distinfo,v 1.5 2014/02/20 14:44:16 fhajny Exp $ -SHA1 (bioperl-0.7.0.tar.gz) = c86abeeb5f2e2b98d1577d9cefd51ce15bbcb6b6 -RMD160 (bioperl-0.7.0.tar.gz) = 41c4162d8d8ec5b406ba34d0d48702700d62108d -Size (bioperl-0.7.0.tar.gz) = 1329985 bytes -SHA1 (patch-aa) = 2e1064f4d7c343cf62f53f2a179a3a1841220dc7 +SHA1 (BioPerl-1.6.923.tar.gz) = eacdb736820efad9205a9ed2150190d7ee89a5ed +RMD160 (BioPerl-1.6.923.tar.gz) = d111ceb0dd60ccef1473e378f4ed8d67dad6013e +Size (BioPerl-1.6.923.tar.gz) = 12562520 bytes diff --git a/biology/bioperl/options.mk b/biology/bioperl/options.mk new file mode 100644 index 00000000000..b4544c146ca --- /dev/null +++ b/biology/bioperl/options.mk @@ -0,0 +1,28 @@ +# $NetBSD: options.mk,v 1.1 2014/02/20 14:44:16 fhajny Exp $ + +PKG_OPTIONS_VAR= PKG_OPTIONS.bioperl +PKG_SUPPORTED_OPTIONS+= mysql pgsql sqlite + +.include "../../mk/bsd.options.mk" + +### +### MySQL support +### +.if !empty(PKG_OPTIONS:Mmysql) +.include "../../mk/mysql.buildlink3.mk" +DEPENDS+= p5-DBD-${MYSQL_PKG_PREFIX}-[0-9]*:../../databases/p5-DBD-mysql +.endif + +### +### PostgreSQL support +### +.if !empty(PKG_OPTIONS:Mpgsql) +DEPENDS+= p5-DBD-postgresql-[0-9]*:../../databases/p5-DBD-postgresql +.endif + +### +### SQLite support +### +.if !empty(PKG_OPTIONS:Msqlite) +DEPENDS+= p5-DBD-SQLite-[0-9]*:../../databases/p5-DBD-SQLite +.endif diff --git a/biology/bioperl/patches/patch-aa b/biology/bioperl/patches/patch-aa deleted file mode 100644 index caf202de248..00000000000 --- a/biology/bioperl/patches/patch-aa +++ /dev/null @@ -1,21 +0,0 @@ -$NetBSD: patch-aa,v 1.3 2006/10/02 21:34:28 rillig Exp $ - -If LWP::UserAgent is not available, exit before the module is required -implicitly by Bio::DB::GDB. - ---- t/GDB.t.orig 2001-03-01 10:11:15.000000000 +0100 -+++ t/GDB.t 2006-10-02 23:30:15.000000000 +0200 -@@ -33,10 +33,9 @@ BEGIN { - foreach ( 1..$NUMTESTS) { skip(1,1); } - $error = 1; - } --} -- --if( $error == 1 ) { -- exit(0); -+ if( $error == 1 ) { -+ exit(0); -+ } - } - - use Bio::DB::GDB; |