BSD Portsbiology/p5-BioPerl-Run 1.007003 FreeBSD
Wrapper modules for common bioinformatics tools
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- License
- ART10, GPLv1+
- Categories
- biology, perl5
- Package size
- 549.9 KiB, 1702.0 KiB installed
Description
Bioperl-run contain modules that provides a PERL interface to various bioinformatics applications. This allows various applications to be used with common Bioperl objects.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/p5-BioPerl-Run | 1.007003 |
| DragonFly | biology/p5-BioPerl-Run | 1.007003 |
| HardenedBSD | biology/p5-BioPerl-Run | 1.007003 |
| GhostBSD | biology/p5-BioPerl-Run | 1.007003 |
Install
Binary package:
pkg install p5-BioPerl-RunFrom the ports tree:
cd /usr/ports/biology/p5-BioPerl-Run/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= p5-BioPerl-Run>0:biology/p5-BioPerl-RunPackages
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 | 1.007003 | 1.007003 | 1.007003 | 1.007003 | 1.007003 |
| FreeBSD:14:quarterly | 1.007003 | 1.007003 | n/a | 1.007003 | 1.007003 |
| FreeBSD:15:latest | 1.007003 | 1.007003 | n/a | 1.007003 | 1.007003 |
| FreeBSD:15:quarterly | 1.007003 | 1.007003 | n/a | n/a | n/a |
| FreeBSD:16:latest | 1.007003 | 1.007003 | 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 9
p5-Algorithm-Diff>=0: devel/p5-Algorithm-Diffp5-Bio-Cluster>=0: biology/p5-Bio-Clusterp5-Bio-FeatureIO>=0: biology/p5-Bio-FeatureIOp5-BioPerl>=1.007000: biology/p5-BioPerlp5-Config-Any>=0: devel/p5-Config-Anyp5-File-Sort>=0: misc/p5-File-Sortp5-IO-String>=0: devel/p5-IO-Stringp5-IPC-Run>=0: devel/p5-IPC-Runp5-XML-Twig>=0: textproc/p5-XML-Twig
Runtime 9
p5-Algorithm-Diff>=0: devel/p5-Algorithm-Diffp5-Bio-Cluster>=0: biology/p5-Bio-Clusterp5-Bio-FeatureIO>=0: biology/p5-Bio-FeatureIOp5-BioPerl>=1.007000: biology/p5-BioPerlp5-Config-Any>=0: devel/p5-Config-Anyp5-File-Sort>=0: misc/p5-File-Sortp5-IO-String>=0: devel/p5-IO-Stringp5-IPC-Run>=0: devel/p5-IPC-Runp5-XML-Twig>=0: textproc/p5-XML-Twig
The full lists below include those, and their dependencies in turn.
Build dependencies 91
- biology/p5-Bio-Cluster
- biology/p5-Bio-FeatureIO
- biology/p5-Bio-Variation
- biology/p5-BioPerl
- converters/libiconv
- converters/p5-Cpanel-JSON-XS
- 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-Config-Any
- devel/p5-Config-General
- devel/p5-Config-Tiny
- devel/p5-Data-Stag
- devel/p5-Devel-StackTrace
- devel/p5-Exception-Class
- devel/p5-Exporter-Tiny
- devel/p5-File-Slurp-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-Module-Pluggable
- 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/p5-Tree-DAG_Node
- devel/readline
- lang/p5-Error
- lang/p5-List-MoreUtils
- lang/p5-List-MoreUtils-XS
- lang/p5-Try-Tiny
- lang/perl5.42
- math/p5-Graph
- misc/p5-File-Sort
- 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-DOM-XPath
- 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-Expat
- textproc/p5-XML-SAX-Writer
- textproc/p5-XML-Simple
- textproc/p5-XML-Twig
- textproc/p5-XML-Writer
- textproc/p5-XML-XPath
- textproc/p5-XML-XPathEngine
- textproc/p5-YAML
- textproc/p5-YAML-LibYAML
- 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 91
- biology/p5-Bio-Cluster
- biology/p5-Bio-FeatureIO
- biology/p5-Bio-Variation
- biology/p5-BioPerl
- converters/libiconv
- converters/p5-Cpanel-JSON-XS
- 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-Config-Any
- devel/p5-Config-General
- devel/p5-Config-Tiny
- devel/p5-Data-Stag
- devel/p5-Devel-StackTrace
- devel/p5-Exception-Class
- devel/p5-Exporter-Tiny
- devel/p5-File-Slurp-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-Module-Pluggable
- 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/p5-Tree-DAG_Node
- devel/readline
- lang/p5-Error
- lang/p5-List-MoreUtils
- lang/p5-List-MoreUtils-XS
- lang/p5-Try-Tiny
- lang/perl5.42
- math/p5-Graph
- misc/p5-File-Sort
- 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-DOM-XPath
- 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-Expat
- textproc/p5-XML-SAX-Writer
- textproc/p5-XML-Simple
- textproc/p5-XML-Twig
- textproc/p5-XML-Writer
- textproc/p5-XML-XPath
- textproc/p5-XML-XPathEngine
- textproc/p5-YAML
- textproc/p5-YAML-LibYAML
- 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
No port depends on this one.
Configuration
Options name: biology_BioPerl-Run
| Option | Default | Description |
|---|---|---|
| DOCS | off | Build and/or install documentation |
- USES
- perl5 shebangfix
- Service scripts
- none
Files
pkg-plist 204
- 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
- %%SITE_PERL%%/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm
- %%SITE_PERL%%/Bio/DB/SoapEUtilities/GQueryAdaptor.pm
- %%SITE_PERL%%/Bio/DB/SoapEUtilities/LinkAdaptor.pm
- %%SITE_PERL%%/Bio/DB/SoapEUtilities/Result.pm
- %%SITE_PERL%%/Bio/Factory/EMBOSS.pm
- %%SITE_PERL%%/Bio/Tools/Run/Alignment/Amap.pm
- %%SITE_PERL%%/Bio/Tools/Run/Alignment/Blat.pm
- %%SITE_PERL%%/Bio/Tools/Run/Alignment/DBA.pm
- %%SITE_PERL%%/Bio/Tools/Run/Alignment/Exonerate.pm
- %%SITE_PERL%%/Bio/Tools/Run/Alignment/Gmap.pm
- %%SITE_PERL%%/Bio/Tools/Run/Alignment/Kalign.pm
- %%SITE_PERL%%/Bio/Tools/Run/Alignment/Lagan.pm
- %%SITE_PERL%%/Bio/Tools/Run/Alignment/MAFFT.pm
- %%SITE_PERL%%/Bio/Tools/Run/Alignment/MSAProbs.pm
- %%SITE_PERL%%/Bio/Tools/Run/Alignment/Muscle.pm
- %%SITE_PERL%%/Bio/Tools/Run/Alignment/Pal2Nal.pm
- %%SITE_PERL%%/Bio/Tools/Run/Alignment/Probalign.pm
- %%SITE_PERL%%/Bio/Tools/Run/Alignment/Probcons.pm
- %%SITE_PERL%%/Bio/Tools/Run/Alignment/Proda.pm
- %%SITE_PERL%%/Bio/Tools/Run/Alignment/Sim4.pm
- %%SITE_PERL%%/Bio/Tools/Run/Alignment/StandAloneFasta.pm
- %%SITE_PERL%%/Bio/Tools/Run/Analysis/soap.pm
- %%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory/soap.pm
- %%SITE_PERL%%/Bio/Tools/Run/BEDTools.pm
- %%SITE_PERL%%/Bio/Tools/Run/BEDTools/Config.pm
- %%SITE_PERL%%/Bio/Tools/Run/BlastPlus.pm
- %%SITE_PERL%%/Bio/Tools/Run/BlastPlus/Config.pm
- %%SITE_PERL%%/Bio/Tools/Run/Coil.pm
- %%SITE_PERL%%/Bio/Tools/Run/EMBOSSApplication.pm
- %%SITE_PERL%%/Bio/Tools/Run/EMBOSSacd.pm
- %%SITE_PERL%%/Bio/Tools/Run/ERPIN.pm
- %%SITE_PERL%%/Bio/Tools/Run/Ensembl.pm
- %%SITE_PERL%%/Bio/Tools/Run/Eponine.pm
- %%SITE_PERL%%/Bio/Tools/Run/FootPrinter.pm
- %%SITE_PERL%%/Bio/Tools/Run/Genemark.pm
- %%SITE_PERL%%/Bio/Tools/Run/Genewise.pm
- %%SITE_PERL%%/Bio/Tools/Run/Genscan.pm
- %%SITE_PERL%%/Bio/Tools/Run/Glimmer.pm
- %%SITE_PERL%%/Bio/Tools/Run/Hmmer.pm
- %%SITE_PERL%%/Bio/Tools/Run/Infernal.pm
- %%SITE_PERL%%/Bio/Tools/Run/MCS.pm
- %%SITE_PERL%%/Bio/Tools/Run/Match.pm
- %%SITE_PERL%%/Bio/Tools/Run/Mdust.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/FastTree.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Gerp.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/Base.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/FEL.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/REL.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/LVB.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Njtree/Best.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Base.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Consense.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phyml.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/QuickTree.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Raxml.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/SLR.pm
- %%SITE_PERL%%/Bio/Tools/Run/Phylo/Semphy.pm
- %%SITE_PERL%%/Bio/Tools/Run/Primate.pm
- %%SITE_PERL%%/Bio/Tools/Run/Primer3.pm
- %%SITE_PERL%%/Bio/Tools/Run/Prints.pm
- %%SITE_PERL%%/Bio/Tools/Run/Profile.pm
- %%SITE_PERL%%/Bio/Tools/Run/Promoterwise.pm
- %%SITE_PERL%%/Bio/Tools/Run/Pseudowise.pm
- %%SITE_PERL%%/Bio/Tools/Run/RNAMotif.pm
- %%SITE_PERL%%/Bio/Tools/Run/RepeatMasker.pm
- %%SITE_PERL%%/Bio/Tools/Run/Samtools.pm
- %%SITE_PERL%%/Bio/Tools/Run/Samtools/Config.pm
- %%SITE_PERL%%/Bio/Tools/Run/Seg.pm
- %%SITE_PERL%%/Bio/Tools/Run/Signalp.pm
- %%SITE_PERL%%/Bio/Tools/Run/Simprot.pm
- %%SITE_PERL%%/Bio/Tools/Run/StandAloneBlast.pm
- %%SITE_PERL%%/Bio/Tools/Run/StandAloneBlastPlus.pm
- %%SITE_PERL%%/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm
- %%SITE_PERL%%/Bio/Tools/Run/StandAloneNCBIBlast.pm
- %%SITE_PERL%%/Bio/Tools/Run/StandAloneWUBlast.pm
- %%SITE_PERL%%/Bio/Tools/Run/Tmhmm.pm
The first 100 are listed.
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| BioPerl-Run-1.007003.tar.gz | 5.138162e+06 | e62e529352f0644bc26509065595d0a47fb6217e5f1301acad76182c2f062071 |
Master sites 1
- CPAN
Commit history 0
No commits in the history this site was built from.