Index: head/biology/p5-bioperl-run/pkg-descr =================================================================== --- head/biology/p5-bioperl-run/pkg-descr (revision 428871) +++ head/biology/p5-bioperl-run/pkg-descr (nonexistent) @@ -1,5 +0,0 @@ -Bioperl-run contain modules that provides a PERL interface to various -bioinformatics applications. This allows various applications to be used -with common Bioperl objects. - -WWW: https://github.com/bioperl/bioperl-run Property changes on: head/biology/p5-bioperl-run/pkg-descr ___________________________________________________________________ Deleted: fbsd:nokeywords ## -1 +0,0 ## -yes \ No newline at end of property Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property Index: head/biology/p5-bioperl-run/distinfo =================================================================== --- head/biology/p5-bioperl-run/distinfo (revision 428871) +++ head/biology/p5-bioperl-run/distinfo (nonexistent) @@ -1,2 +0,0 @@ -SHA256 (bioperl-bioperl-run-1.6.901-96ccd93_GH0.tar.gz) = 13f6c0b47b70a2bc5e9f633bc011378a85f78a7f0c0d334246acbc1a8f3b343c -SIZE (bioperl-bioperl-run-1.6.901-96ccd93_GH0.tar.gz) = 13941085 Property changes on: head/biology/p5-bioperl-run/distinfo ___________________________________________________________________ Deleted: fbsd:nokeywords ## -1 +0,0 ## -yes \ No newline at end of property Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property Index: head/biology/p5-bioperl-run/pkg-plist =================================================================== --- head/biology/p5-bioperl-run/pkg-plist (revision 428871) +++ head/biology/p5-bioperl-run/pkg-plist (nonexistent) @@ -1,263 +0,0 @@ -bin/bp_bioperl_application_installer -bin/bp_multi_hmmsearch -bin/bp_panalysis -bin/bp_papplmaker -bin/bp_run_neighbor -bin/bp_run_protdist -%%SITE_PERL%%/Bio/DB/ESoap.pm -%%SITE_PERL%%/Bio/DB/ESoap/WSDL.pm -%%SITE_PERL%%/Bio/DB/SoapEUtilities.pm -%%SITE_PERL%%/Bio/DB/SoapEUtilities/DocSumAdaptor.pm -%%SITE_PERL%%/Bio/DB/SoapEUtilities/FetchAdaptor.pm -%%SITE_PERL%%/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm 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-%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::QuickTree.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Raxml.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::SLR.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Semphy.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::Primate.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::Primer3.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::Prints.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::Profile.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::Promoterwise.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::Pseudowise.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::RNAMotif.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::RepeatMasker.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::Samtools.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::Samtools::Config.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::Seg.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::Signalp.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::Simprot.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::StandAloneBlastPlus.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::StandAloneBlastPlus::BlastMethods.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::TigrAssembler.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::Tmhmm.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::TribeMCL.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::Vista.3.gz -%%PERL5_MAN3%%/Bio::Tools::Run::tRNAscanSE.3.gz -%%PORTDOCS%%%%DOCSDIR%%/AUTHORS -%%PORTDOCS%%%%DOCSDIR%%/Changes -%%PORTDOCS%%%%DOCSDIR%%/INSTALL.PROGRAMS -%%PORTDOCS%%%%DOCSDIR%%/README Property changes on: head/biology/p5-bioperl-run/pkg-plist ___________________________________________________________________ Deleted: fbsd:nokeywords ## -1 +0,0 ## -yes \ No newline at end of property Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property Index: head/biology/p5-bioperl-run/Makefile =================================================================== --- head/biology/p5-bioperl-run/Makefile (revision 428871) +++ head/biology/p5-bioperl-run/Makefile (nonexistent) @@ -1,48 +0,0 @@ -# Created by: Mauricio Herrera Cuadra -# $FreeBSD$ - -PORTNAME= bioperl-run -PORTVERSION= 1.6.901 -PORTREVISION= 1 -CATEGORIES= biology perl5 -PKGNAMEPREFIX= p5- - -MAINTAINER= perl@FreeBSD.org -COMMENT= Wrapper modules for common bioinformatics tools - -LICENSE= ART10 GPLv3 -LICENSE_COMB= dual - -BUILD_DEPENDS= p5-bioperl>=1.6.0:biology/p5-bioperl \ - p5-IPC-Run>=0:devel/p5-IPC-Run \ - p5-Algorithm-Diff>=0:devel/p5-Algorithm-Diff \ - p5-XML-Twig>=0:textproc/p5-XML-Twig \ - p5-File-Sort>=0:misc/p5-File-Sort \ - p5-Config-Any>=0:devel/p5-Config-Any -RUN_DEPENDS:= ${BUILD_DEPENDS} - -CONFLICTS= p5-bioperl-run-1.[13579]* - -USE_GITHUB= yes -GH_ACCOUNT= bioperl -GH_TAGNAME= 96ccd93 - -USES= perl5 shebangfix -USE_PERL5= modbuild -SHEBANG_FILES= scripts/* - -OPTIONS_DEFINE= DOCS - -post-build: - (cd ${WRKSRC} && ${PERL} ./Build manifest) - -post-install: -.for i in bioperl_application_installer multi_hmmsearch panalysis papplmaker run_neighbor run_protdist - ${CP} ${WRKSRC}/scripts/${i}.PLS ${STAGEDIR}${PREFIX}/bin/bp_${i} -.endfor - @${MKDIR} ${STAGEDIR}${DOCSDIR} -.for doc in AUTHORS Changes INSTALL.PROGRAMS README - ${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR} -.endfor - -.include Property changes on: head/biology/p5-bioperl-run/Makefile ___________________________________________________________________ Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:keywords ## -1 +0,0 ## -FreeBSD=%H \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property Index: head/biology/p5-bioperl-run/files/patch-Build.PL =================================================================== --- head/biology/p5-bioperl-run/files/patch-Build.PL (revision 428871) +++ head/biology/p5-bioperl-run/files/patch-Build.PL (nonexistent) @@ -1,12 +0,0 @@ ---- ./Build.PL.orig 2014-07-26 04:49:03.000000000 +0200 -+++ ./Build.PL 2014-08-04 09:33:15.000000000 +0200 -@@ -42,7 +42,8 @@ - #create_makefile_pl => 'passthrough' - ); - --my $accept = $build->args->{accept}; -+# my $accept = $build->args->{accept}; -+my $accept = 1; - - # Optionally have script files installed. - if ($build->args('install_scripts') or $accept ? 0 : $build->y_n("Install scripts? y/n", 'n')) { Property changes on: head/biology/p5-bioperl-run/files/patch-Build.PL ___________________________________________________________________ Deleted: fbsd:nokeywords ## -1 +0,0 ## -yes \ No newline at end of property Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 428871) +++ head/biology/Makefile (revision 428872) @@ -1,112 +1,112 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += ariadne SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += biojava SUBDIR += blat SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += chemeq SUBDIR += clustalw SUBDIR += consed SUBDIR += crux SUBDIR += diamond SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa SUBDIR += hmmer SUBDIR += htslib SUBDIR += iolib SUBDIR += jalview SUBDIR += jellyfish SUBDIR += lagan SUBDIR += lamarc SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += molden SUBDIR += mopac SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-toolkit SUBDIR += njplot SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-GFF3 SUBDIR += p5-Bio-Glite SUBDIR += p5-Bio-Graphics SUBDIR += p5-Bio-MAGETAB SUBDIR += p5-Bio-NEXUS SUBDIR += p5-Bio-Phylo SUBDIR += p5-Bio-SCF SUBDIR += p5-BioPerl - SUBDIR += p5-bioperl-run + SUBDIR += p5-BioPerl-Run SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plink SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += ssaha SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += treeviewx SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/p5-BioPerl-Run/Makefile =================================================================== --- head/biology/p5-BioPerl-Run/Makefile (nonexistent) +++ head/biology/p5-BioPerl-Run/Makefile (revision 428872) @@ -0,0 +1,50 @@ +# Created by: Mauricio Herrera Cuadra +# $FreeBSD$ + +PORTNAME= BioPerl-Run +PORTVERSION= 1.6.901 +PORTREVISION= 2 +CATEGORIES= biology perl5 +PKGNAMEPREFIX= p5- + +MAINTAINER= perl@FreeBSD.org +COMMENT= Wrapper modules for common bioinformatics tools + +LICENSE= ART10 GPLv3 +LICENSE_COMB= dual + +BUILD_DEPENDS= p5-Algorithm-Diff>=0:devel/p5-Algorithm-Diff \ + p5-BioPerl>=1.6.0:biology/p5-BioPerl \ + p5-Config-Any>=0:devel/p5-Config-Any \ + p5-File-Sort>=0:misc/p5-File-Sort \ + p5-IPC-Run>=0:devel/p5-IPC-Run \ + p5-XML-Twig>=0:textproc/p5-XML-Twig +RUN_DEPENDS:= ${BUILD_DEPENDS} + +CONFLICTS= p5-bioperl-run-1.[13579]* + +USE_GITHUB= yes +GH_ACCOUNT= bioperl +GH_PROJECT= bioperl-run +GH_TAGNAME= 96ccd93 + +NO_ARCH= yes +USES= perl5 shebangfix +USE_PERL5= modbuild +SHEBANG_FILES= scripts/* + +OPTIONS_DEFINE= DOCS + +post-build: + (cd ${WRKSRC} && ${PERL} ./Build manifest) + +post-install: +.for i in bioperl_application_installer multi_hmmsearch panalysis papplmaker run_neighbor run_protdist + ${CP} ${WRKSRC}/scripts/${i}.PLS ${STAGEDIR}${PREFIX}/bin/bp_${i} +.endfor + @${MKDIR} ${STAGEDIR}${DOCSDIR} +.for doc in AUTHORS Changes INSTALL.PROGRAMS README + ${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR} +.endfor + +.include Property changes on: head/biology/p5-BioPerl-Run/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/p5-BioPerl-Run/distinfo =================================================================== --- head/biology/p5-BioPerl-Run/distinfo (nonexistent) +++ head/biology/p5-BioPerl-Run/distinfo (revision 428872) @@ -0,0 +1,2 @@ +SHA256 (bioperl-bioperl-run-1.6.901-96ccd93_GH0.tar.gz) = 13f6c0b47b70a2bc5e9f633bc011378a85f78a7f0c0d334246acbc1a8f3b343c +SIZE (bioperl-bioperl-run-1.6.901-96ccd93_GH0.tar.gz) = 13941085 Property changes on: head/biology/p5-BioPerl-Run/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/p5-BioPerl-Run/pkg-plist =================================================================== --- head/biology/p5-BioPerl-Run/pkg-plist (nonexistent) +++ head/biology/p5-BioPerl-Run/pkg-plist (revision 428872) @@ -0,0 +1,263 @@ +bin/bp_bioperl_application_installer +bin/bp_multi_hmmsearch +bin/bp_panalysis +bin/bp_papplmaker +bin/bp_run_neighbor 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+%%PERL5_MAN3%%/Bio::Tools::Run::RepeatMasker.3.gz +%%PERL5_MAN3%%/Bio::Tools::Run::Samtools.3.gz +%%PERL5_MAN3%%/Bio::Tools::Run::Samtools::Config.3.gz +%%PERL5_MAN3%%/Bio::Tools::Run::Seg.3.gz +%%PERL5_MAN3%%/Bio::Tools::Run::Signalp.3.gz +%%PERL5_MAN3%%/Bio::Tools::Run::Simprot.3.gz +%%PERL5_MAN3%%/Bio::Tools::Run::StandAloneBlastPlus.3.gz +%%PERL5_MAN3%%/Bio::Tools::Run::StandAloneBlastPlus::BlastMethods.3.gz +%%PERL5_MAN3%%/Bio::Tools::Run::TigrAssembler.3.gz +%%PERL5_MAN3%%/Bio::Tools::Run::Tmhmm.3.gz +%%PERL5_MAN3%%/Bio::Tools::Run::TribeMCL.3.gz +%%PERL5_MAN3%%/Bio::Tools::Run::Vista.3.gz +%%PERL5_MAN3%%/Bio::Tools::Run::tRNAscanSE.3.gz +%%PORTDOCS%%%%DOCSDIR%%/AUTHORS +%%PORTDOCS%%%%DOCSDIR%%/Changes +%%PORTDOCS%%%%DOCSDIR%%/INSTALL.PROGRAMS +%%PORTDOCS%%%%DOCSDIR%%/README Property changes on: head/biology/p5-BioPerl-Run/pkg-plist ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/p5-BioPerl-Run/files/patch-Build.PL =================================================================== --- head/biology/p5-BioPerl-Run/files/patch-Build.PL (nonexistent) +++ head/biology/p5-BioPerl-Run/files/patch-Build.PL (revision 428872) @@ -0,0 +1,12 @@ +--- ./Build.PL.orig 2014-07-26 04:49:03.000000000 +0200 ++++ ./Build.PL 2014-08-04 09:33:15.000000000 +0200 +@@ -42,7 +42,8 @@ + #create_makefile_pl => 'passthrough' + ); + +-my $accept = $build->args->{accept}; ++# my $accept = $build->args->{accept}; ++my $accept = 1; + + # Optionally have script files installed. + if ($build->args('install_scripts') or $accept ? 0 : $build->y_n("Install scripts? y/n", 'n')) { Property changes on: head/biology/p5-BioPerl-Run/files/patch-Build.PL ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/p5-BioPerl-Run/pkg-descr =================================================================== --- head/biology/p5-BioPerl-Run/pkg-descr (nonexistent) +++ head/biology/p5-BioPerl-Run/pkg-descr (revision 428872) @@ -0,0 +1,5 @@ +Bioperl-run contain modules that provides a PERL interface to various +bioinformatics applications. This allows various applications to be used +with common Bioperl objects. + +WWW: https://github.com/bioperl/bioperl-run Property changes on: head/biology/p5-BioPerl-Run/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property