BSD Portsbiology/p5-BioPerl 1.007008 FreeBSD
Collection of Perl modules for bioinformatics
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- License
- ART10, GPLv1+
- Categories
- biology, perl5
- Package size
- 2691.5 KiB, 8490.9 KiB installed
Description
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)
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/p5-BioPerl | 1.007008 |
| DragonFly | biology/p5-BioPerl | 1.007008 |
| HardenedBSD | biology/p5-BioPerl | 1.007008 |
| GhostBSD | biology/p5-BioPerl | 1.007008 |
Install
Binary package:
pkg install p5-BioPerlFrom the ports tree:
cd /usr/ports/biology/p5-BioPerl/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= p5-BioPerl>0:biology/p5-BioPerlPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 1.007008 | 1.007008 | 1.007007_1 | 1.007008 | 1.007008 |
| FreeBSD:14:quarterly | 1.007008 | 1.007008 | n/a | 1.007008 | 1.007008 |
| FreeBSD:15:latest | 1.007008 | 1.007008 | n/a | 1.007008 | 1.007008 |
| FreeBSD:15:quarterly | 1.007008 | 1.007008 | n/a | n/a | n/a |
| FreeBSD:16:latest | 1.007008 | 1.007008 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Build 23
p5-Data-Stag>=0: devel/p5-Data-Stagp5-Error>=0: lang/p5-Errorp5-Graph>=0: math/p5-Graphp5-HTTP-Message>=0: www/p5-HTTP-Messagep5-IO-String>=0: devel/p5-IO-Stringp5-IO-Stringy>=0: devel/p5-IO-Stringyp5-IPC-Run>=0: devel/p5-IPC-Runp5-List-MoreUtils>=0: lang/p5-List-MoreUtilsp5-Module-Build>=0: devel/p5-Module-Buildp5-Set-Scalar>=0: devel/p5-Set-Scalarp5-Test-Most>=0: devel/p5-Test-Mostp5-Test-RequiresInternet>=0: devel/p5-Test-RequiresInternetp5-URI>=0: net/p5-URIp5-XML-DOM>=0: textproc/p5-XML-DOMp5-XML-LibXML>=0: textproc/p5-XML-LibXMLp5-XML-SAX>=0: textproc/p5-XML-SAXp5-XML-SAX-Base>=0: textproc/p5-XML-SAX-Basep5-XML-SAX-Writer>=0: textproc/p5-XML-SAX-Writerp5-XML-Twig>=0: textproc/p5-XML-Twigp5-XML-Writer>=0: textproc/p5-XML-Writerp5-YAML>=0: textproc/p5-YAMLp5-libwww>=0: www/p5-libwwwp5-libxml>=0: textproc/p5-libxml
Runtime 23
p5-Data-Stag>=0: devel/p5-Data-Stagp5-Error>=0: lang/p5-Errorp5-Graph>=0: math/p5-Graphp5-HTTP-Message>=0: www/p5-HTTP-Messagep5-IO-String>=0: devel/p5-IO-Stringp5-IO-Stringy>=0: devel/p5-IO-Stringyp5-IPC-Run>=0: devel/p5-IPC-Runp5-List-MoreUtils>=0: lang/p5-List-MoreUtilsp5-Module-Build>=0: devel/p5-Module-Buildp5-Set-Scalar>=0: devel/p5-Set-Scalarp5-Test-Most>=0: devel/p5-Test-Mostp5-Test-RequiresInternet>=0: devel/p5-Test-RequiresInternetp5-URI>=0: net/p5-URIp5-XML-DOM>=0: textproc/p5-XML-DOMp5-XML-LibXML>=0: textproc/p5-XML-LibXMLp5-XML-SAX>=0: textproc/p5-XML-SAXp5-XML-SAX-Base>=0: textproc/p5-XML-SAX-Basep5-XML-SAX-Writer>=0: textproc/p5-XML-SAX-Writerp5-XML-Twig>=0: textproc/p5-XML-Twigp5-XML-Writer>=0: textproc/p5-XML-Writerp5-YAML>=0: textproc/p5-YAMLp5-libwww>=0: www/p5-libwwwp5-libxml>=0: textproc/p5-libxml
Test 2
p5-Test-Memory-Cycle>=0: devel/p5-Test-Memory-Cyclep5-Test-Weaken>=0: devel/p5-Test-Weaken
The full lists below include those, and their dependencies in turn.
Build dependencies 75
- converters/libiconv
- converters/p5-Encode-Locale
- converters/p5-MIME-Base32
- converters/p5-MIME-Base64
- converters/p5-Text-Iconv
- devel/p5-Algorithm-Diff
- devel/p5-Class-Data-Inheritable
- devel/p5-Clone
- devel/p5-Data-Stag
- devel/p5-Devel-StackTrace
- devel/p5-Exception-Class
- devel/p5-Exporter-Tiny
- devel/p5-Heap
- devel/p5-IO-HTML
- devel/p5-IO-String
- devel/p5-IO-Stringy
- devel/p5-IO-Tty
- devel/p5-IPC-Run
- devel/p5-Module-Build
- devel/p5-Set-Object
- devel/p5-Set-Scalar
- devel/p5-Sub-Uplevel
- devel/p5-Test-Deep
- devel/p5-Test-Differences
- devel/p5-Test-Exception
- devel/p5-Test-Most
- devel/p5-Test-RequiresInternet
- devel/p5-Test-Warn
- devel/p5-Tie-IxHash
- devel/p5-TimeDate
- devel/readline
- lang/p5-Error
- lang/p5-List-MoreUtils
- lang/p5-List-MoreUtils-XS
- lang/p5-Try-Tiny
- lang/perl5.42
- math/p5-Graph
- net/p5-Net-HTTP
- net/p5-URI
- print/indexinfo
- security/p5-Authen-NTLM
- security/p5-Digest-HMAC
- security/p5-IO-Socket-SSL
- security/p5-Net-SSLeay
- sysutils/p5-File-Listing
- textproc/expat2
- textproc/libxml2
- textproc/p5-HTML-Entities-Numbered
- textproc/p5-Text-Diff
- textproc/p5-XML-DOM
- textproc/p5-XML-Filter-BufferText
- textproc/p5-XML-LibXML
- textproc/p5-XML-NamespaceSupport
- textproc/p5-XML-Parser
- textproc/p5-XML-RegExp
- textproc/p5-XML-SAX
- textproc/p5-XML-SAX-Base
- textproc/p5-XML-SAX-Writer
- textproc/p5-XML-Twig
- textproc/p5-XML-Writer
- textproc/p5-XML-XPath
- textproc/p5-XML-XPathEngine
- textproc/p5-YAML
- textproc/p5-libxml
- www/p5-HTML-Parser
- www/p5-HTML-Tagset
- www/p5-HTML-Tree
- www/p5-HTTP-Cookies
- www/p5-HTTP-Date
- www/p5-HTTP-Message
- www/p5-HTTP-Negotiate
- www/p5-LWP-MediaTypes
- www/p5-Mozilla-CA
- www/p5-WWW-RobotRules
- www/p5-libwww
Run dependencies 75
- converters/libiconv
- converters/p5-Encode-Locale
- converters/p5-MIME-Base32
- converters/p5-MIME-Base64
- converters/p5-Text-Iconv
- devel/p5-Algorithm-Diff
- devel/p5-Class-Data-Inheritable
- devel/p5-Clone
- devel/p5-Data-Stag
- devel/p5-Devel-StackTrace
- devel/p5-Exception-Class
- devel/p5-Exporter-Tiny
- devel/p5-Heap
- devel/p5-IO-HTML
- devel/p5-IO-String
- devel/p5-IO-Stringy
- devel/p5-IO-Tty
- devel/p5-IPC-Run
- devel/p5-Module-Build
- devel/p5-Set-Object
- devel/p5-Set-Scalar
- devel/p5-Sub-Uplevel
- devel/p5-Test-Deep
- devel/p5-Test-Differences
- devel/p5-Test-Exception
- devel/p5-Test-Most
- devel/p5-Test-RequiresInternet
- devel/p5-Test-Warn
- devel/p5-Tie-IxHash
- devel/p5-TimeDate
- devel/readline
- lang/p5-Error
- lang/p5-List-MoreUtils
- lang/p5-List-MoreUtils-XS
- lang/p5-Try-Tiny
- lang/perl5.42
- math/p5-Graph
- net/p5-Net-HTTP
- net/p5-URI
- print/indexinfo
- security/p5-Authen-NTLM
- security/p5-Digest-HMAC
- security/p5-IO-Socket-SSL
- security/p5-Net-SSLeay
- sysutils/p5-File-Listing
- textproc/expat2
- textproc/libxml2
- textproc/p5-HTML-Entities-Numbered
- textproc/p5-Text-Diff
- textproc/p5-XML-DOM
- textproc/p5-XML-Filter-BufferText
- textproc/p5-XML-LibXML
- textproc/p5-XML-NamespaceSupport
- textproc/p5-XML-Parser
- textproc/p5-XML-RegExp
- textproc/p5-XML-SAX
- textproc/p5-XML-SAX-Base
- textproc/p5-XML-SAX-Writer
- textproc/p5-XML-Twig
- textproc/p5-XML-Writer
- textproc/p5-XML-XPath
- textproc/p5-XML-XPathEngine
- textproc/p5-YAML
- textproc/p5-libxml
- www/p5-HTML-Parser
- www/p5-HTML-Tagset
- www/p5-HTML-Tree
- www/p5-HTTP-Cookies
- www/p5-HTTP-Date
- www/p5-HTTP-Message
- www/p5-HTTP-Negotiate
- www/p5-LWP-MediaTypes
- www/p5-Mozilla-CA
- www/p5-WWW-RobotRules
- www/p5-libwww
Configuration
Options name: biology_BioPerl
| Option | Default | Description |
|---|---|---|
| DOCS | off | Build and/or install documentation |
| EXAMPLES | off | Build and/or install examples |
- USES
- perl5 shebangfix
- Service scripts
- none
Files
pkg-plist 1073
- bin/bp_aacomp
- bin/bp_bioflat_index
- bin/bp_biogetseq
- bin/bp_dbsplit
- bin/bp_extract_feature_seq
- bin/bp_fastam9_to_table
- bin/bp_fetch
- bin/bp_filter_search
- bin/bp_find-blast-matches
- bin/bp_gccalc
- bin/bp_genbank2gff3
- bin/bp_index
- bin/bp_local_taxonomydb_query
- bin/bp_make_mrna_protein
- bin/bp_mask_by_search
- bin/bp_mrtrans
- bin/bp_mutate
- bin/bp_nexus2nh
- bin/bp_nrdb
- bin/bp_oligo_count
- bin/bp_process_gadfly
- bin/bp_process_sgd
- bin/bp_revtrans-motif
- bin/bp_search2alnblocks
- bin/bp_search2gff
- bin/bp_search2table
- bin/bp_search2tribe
- bin/bp_seq_length
- bin/bp_seqconvert
- bin/bp_seqcut
- bin/bp_seqpart
- bin/bp_seqret
- bin/bp_seqretsplit
- bin/bp_split_seq
- bin/bp_sreformat
- bin/bp_taxid4species
- bin/bp_taxonomy2tree
- bin/bp_translate_seq
- bin/bp_tree2pag
- bin/bp_unflatten_seq
- %%SITE_PERL%%/Bio/Align/AlignI.pm
- %%SITE_PERL%%/Bio/Align/DNAStatistics.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/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/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/CodonUsage/IO.pm
- %%SITE_PERL%%/Bio/CodonUsage/Table.pm
- %%SITE_PERL%%/Bio/DB/DBFetch.pm
- %%SITE_PERL%%/Bio/DB/Failover.pm
- %%SITE_PERL%%/Bio/DB/Fasta.pm
- %%SITE_PERL%%/Bio/DB/FileCache.pm
- %%SITE_PERL%%/Bio/DB/Flat.pm
- %%SITE_PERL%%/Bio/DB/Flat/BDB.pm
- %%SITE_PERL%%/Bio/DB/Flat/BDB/embl.pm
- %%SITE_PERL%%/Bio/DB/Flat/BDB/fasta.pm
- %%SITE_PERL%%/Bio/DB/Flat/BDB/genbank.pm
- %%SITE_PERL%%/Bio/DB/Flat/BDB/swiss.pm
The first 100 are listed.
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| BioPerl-1.7.8.tar.gz | 7.527658e+06 | c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738 |
Master sites 1
- CPAN
Commit history 0
No commits in the history this site was built from.