bioperl_1.6.924-1_all.deb


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Description

bioperl - Perl tools for computational molecular biology

Property Value
Distribution Debian 8 (Jessie)
Repository Debian Main amd64
Package name bioperl
Package version 1.6.924
Package release 1
Package architecture all
Package type deb
Installed size 895 B
Download size 409.50 KB
Official Mirror ftp.br.debian.org
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. It is well-accepted
throughout the community and used in many high-profile projects, e.g.,
Ensembl.
The recommended packages are needed to run some of the included
binaries, for a detailed explanation including the specific Perl
modules please see README.Debian.
The suggested package enhances the manual pages.

Alternatives

Package Version Architecture Repository
bioperl_1.6.924-1_all.deb 1.6.924 all Debian Main
bioperl - - -

Requires

Name Value
libbio-perl-perl = 1.6.924-1
perl -

Download

Type URL
Binary Package bioperl_1.6.924-1_all.deb
Source Package bioperl

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install bioperl deb package:
    # sudo apt-get install bioperl

Files

Path
/usr/bin/bp_aacomp
/usr/bin/bp_biofetch_genbank_proxy
/usr/bin/bp_bioflat_index
/usr/bin/bp_biogetseq
/usr/bin/bp_blast2tree
/usr/bin/bp_bulk_load_gff
/usr/bin/bp_chaos_plot
/usr/bin/bp_classify_hits_kingdom
/usr/bin/bp_composite_LD
/usr/bin/bp_das_server
/usr/bin/bp_dbsplit
/usr/bin/bp_download_query_genbank
/usr/bin/bp_extract_feature_seq
/usr/bin/bp_fast_load_gff
/usr/bin/bp_fastam9_to_table
/usr/bin/bp_fetch
/usr/bin/bp_filter_search
/usr/bin/bp_flanks
/usr/bin/bp_gccalc
/usr/bin/bp_genbank2gff
/usr/bin/bp_genbank2gff3
/usr/bin/bp_generate_histogram
/usr/bin/bp_heterogeneity_test
/usr/bin/bp_hivq
/usr/bin/bp_hmmer_to_table
/usr/bin/bp_index
/usr/bin/bp_load_gff
/usr/bin/bp_local_taxonomydb_query
/usr/bin/bp_make_mrna_protein
/usr/bin/bp_mask_by_search
/usr/bin/bp_meta_gff
/usr/bin/bp_mrtrans
/usr/bin/bp_mutate
/usr/bin/bp_netinstall
/usr/bin/bp_nexus2nh
/usr/bin/bp_nrdb
/usr/bin/bp_oligo_count
/usr/bin/bp_pairwise_kaks
/usr/bin/bp_parse_hmmsearch
/usr/bin/bp_process_gadfly
/usr/bin/bp_process_sgd
/usr/bin/bp_process_wormbase
/usr/bin/bp_query_entrez_taxa
/usr/bin/bp_remote_blast
/usr/bin/bp_revtrans-motif
/usr/bin/bp_search2BSML
/usr/bin/bp_search2alnblocks
/usr/bin/bp_search2gff
/usr/bin/bp_search2table
/usr/bin/bp_search2tribe
/usr/bin/bp_seq_length
/usr/bin/bp_seqconvert
/usr/bin/bp_seqcut
/usr/bin/bp_seqfeature_delete
/usr/bin/bp_seqfeature_gff3
/usr/bin/bp_seqfeature_load
/usr/bin/bp_seqpart
/usr/bin/bp_seqret
/usr/bin/bp_seqretsplit
/usr/bin/bp_split_seq
/usr/bin/bp_sreformat
/usr/bin/bp_taxid4species
/usr/bin/bp_taxonomy2tree
/usr/bin/bp_translate_seq
/usr/bin/bp_tree2pag
/usr/bin/bp_unflatten_seq
/usr/share/doc/bioperl/AUTHORS.gz
/usr/share/doc/bioperl/BUGS.gz
/usr/share/doc/bioperl/DEPRECATED
/usr/share/doc/bioperl/README.gz
/usr/share/doc/bioperl/changelog.Debian.gz
/usr/share/doc/bioperl/changelog.gz
/usr/share/doc/bioperl/copyright
/usr/share/doc/bioperl/examples/bioperl.pl.gz
/usr/share/doc/bioperl/examples/generate_random_seq.pl
/usr/share/doc/bioperl/examples/longorf.pl.gz
/usr/share/doc/bioperl/examples/make_primers.pl.gz
/usr/share/doc/bioperl/examples/rev_and_trans.pl
/usr/share/doc/bioperl/examples/revcom_dir.pl
/usr/share/doc/bioperl/examples/subsequence.cgi.gz
/usr/share/doc/bioperl/examples/Bio-DB-GFF/load_ucsc.pl.gz
/usr/share/doc/bioperl/examples/align/FastAlign.pl.gz
/usr/share/doc/bioperl/examples/align/align_on_codons.pl.gz
/usr/share/doc/bioperl/examples/align/aligntutorial.pl
/usr/share/doc/bioperl/examples/align/clustalw.pl.gz
/usr/share/doc/bioperl/examples/align/simplealign.pl.gz
/usr/share/doc/bioperl/examples/cluster/dbsnp.pl
/usr/share/doc/bioperl/examples/contributed/nmrpdb_parse.pl.gz
/usr/share/doc/bioperl/examples/contributed/prosite2perl.pl
/usr/share/doc/bioperl/examples/contributed/rebase2list.pl
/usr/share/doc/bioperl/examples/db/dbfetch.gz
/usr/share/doc/bioperl/examples/db/est_tissue_query.pl.gz
/usr/share/doc/bioperl/examples/db/gb2features.pl.gz
/usr/share/doc/bioperl/examples/db/getGenBank.pl
/usr/share/doc/bioperl/examples/db/get_seqs.pl
/usr/share/doc/bioperl/examples/db/rfetch.pl
/usr/share/doc/bioperl/examples/db/use_registry.pl
/usr/share/doc/bioperl/examples/liveseq/change_gene.pl
/usr/share/doc/bioperl/examples/popgen/parse_calc_stats.pl
/usr/share/doc/bioperl/examples/quality/svgtrace.pl
/usr/share/doc/bioperl/examples/root/README.gz
/usr/share/doc/bioperl/examples/root/exceptions1.pl.gz
/usr/share/doc/bioperl/examples/root/exceptions2.pl.gz
/usr/share/doc/bioperl/examples/root/exceptions3.pl
/usr/share/doc/bioperl/examples/root/exceptions4.pl
/usr/share/doc/bioperl/examples/root/lib/TestInterface.pm
/usr/share/doc/bioperl/examples/root/lib/TestObject.pm
/usr/share/doc/bioperl/examples/searchio/blast_example.pl.gz
/usr/share/doc/bioperl/examples/searchio/custom_writer.pl
/usr/share/doc/bioperl/examples/searchio/hitwriter.pl
/usr/share/doc/bioperl/examples/searchio/hspwriter.pl
/usr/share/doc/bioperl/examples/searchio/htmlwriter.pl
/usr/share/doc/bioperl/examples/searchio/psiblast_features.pl
/usr/share/doc/bioperl/examples/searchio/psiblast_iterations.pl
/usr/share/doc/bioperl/examples/searchio/rawwriter.pl
/usr/share/doc/bioperl/examples/searchio/resultwriter.pl
/usr/share/doc/bioperl/examples/searchio/waba2gff.pl
/usr/share/doc/bioperl/examples/searchio/waba2gff3.pl.gz
/usr/share/doc/bioperl/examples/sirna/TAG
/usr/share/doc/bioperl/examples/sirna/rnai_finder.cgi.gz
/usr/share/doc/bioperl/examples/structure/structure-io.pl
/usr/share/doc/bioperl/examples/tk/gsequence.pl.gz
/usr/share/doc/bioperl/examples/tk/hitdisplay.pl
/usr/share/doc/bioperl/examples/tools/extract_genes.pl
/usr/share/doc/bioperl/examples/tools/gb_to_gff.pl
/usr/share/doc/bioperl/examples/tools/gff2ps.pl.gz
/usr/share/doc/bioperl/examples/tools/parse_codeml.pl
/usr/share/doc/bioperl/examples/tools/psw.pl
/usr/share/doc/bioperl/examples/tools/reverse-translate.pl
/usr/share/doc/bioperl/examples/tools/run_genscan.pl
/usr/share/doc/bioperl/examples/tools/run_primer3.pl
/usr/share/doc/bioperl/examples/tools/seq_pattern.pl
/usr/share/doc/bioperl/examples/tools/standaloneblast.pl.gz
/usr/share/doc/bioperl/examples/tree/paup2phylip.pl
/usr/share/man/man1/bp_aacomp.1p.gz
/usr/share/man/man1/bp_biofetch_genbank_proxy.1p.gz
/usr/share/man/man1/bp_bioflat_index.1p.gz
/usr/share/man/man1/bp_biogetseq.1p.gz
/usr/share/man/man1/bp_blast2tree.1p.gz
/usr/share/man/man1/bp_bulk_load_gff.1p.gz
/usr/share/man/man1/bp_chaos_plot.1p.gz
/usr/share/man/man1/bp_classify_hits_kingdom.1p.gz
/usr/share/man/man1/bp_composite_LD.1p.gz
/usr/share/man/man1/bp_dbsplit.1p.gz
/usr/share/man/man1/bp_download_query_genbank.1p.gz
/usr/share/man/man1/bp_extract_feature_seq.1p.gz
/usr/share/man/man1/bp_fast_load_gff.1p.gz
/usr/share/man/man1/bp_fastam9_to_table.1p.gz
/usr/share/man/man1/bp_fetch.1p.gz
/usr/share/man/man1/bp_filter_search.1p.gz
/usr/share/man/man1/bp_flanks.1p.gz
/usr/share/man/man1/bp_gccalc.1p.gz
/usr/share/man/man1/bp_genbank2gff.1p.gz
/usr/share/man/man1/bp_genbank2gff3.1p.gz
/usr/share/man/man1/bp_generate_histogram.1p.gz
/usr/share/man/man1/bp_heterogeneity_test.1p.gz
/usr/share/man/man1/bp_hivq.1p.gz
/usr/share/man/man1/bp_hmmer_to_table.1p.gz
/usr/share/man/man1/bp_index.1p.gz
/usr/share/man/man1/bp_load_gff.1p.gz
/usr/share/man/man1/bp_local_taxonomydb_query.1p.gz
/usr/share/man/man1/bp_make_mrna_protein.1p.gz
/usr/share/man/man1/bp_mask_by_search.1p.gz
/usr/share/man/man1/bp_meta_gff.1p.gz
/usr/share/man/man1/bp_mrtrans.1p.gz
/usr/share/man/man1/bp_mutate.1p.gz
/usr/share/man/man1/bp_netinstall.1p.gz
/usr/share/man/man1/bp_nexus2nh.1p.gz
/usr/share/man/man1/bp_nrdb.1p.gz
/usr/share/man/man1/bp_oligo_count.1p.gz
/usr/share/man/man1/bp_pairwise_kaks.1p.gz
/usr/share/man/man1/bp_parse_hmmsearch.1p.gz
/usr/share/man/man1/bp_process_gadfly.1p.gz
/usr/share/man/man1/bp_process_sgd.1p.gz
/usr/share/man/man1/bp_process_wormbase.1p.gz
/usr/share/man/man1/bp_query_entrez_taxa.1p.gz
/usr/share/man/man1/bp_remote_blast.1p.gz
/usr/share/man/man1/bp_revtrans-motif.1p.gz
/usr/share/man/man1/bp_search2BSML.1p.gz
/usr/share/man/man1/bp_search2alnblocks.1p.gz
/usr/share/man/man1/bp_search2gff.1p.gz
/usr/share/man/man1/bp_search2table.1p.gz
/usr/share/man/man1/bp_search2tribe.1p.gz
/usr/share/man/man1/bp_seq_length.1p.gz
/usr/share/man/man1/bp_seqconvert.1p.gz
/usr/share/man/man1/bp_seqcut.1p.gz
/usr/share/man/man1/bp_seqfeature_load.1p.gz
/usr/share/man/man1/bp_seqpart.1p.gz
/usr/share/man/man1/bp_seqret.1p.gz
/usr/share/man/man1/bp_seqretsplit.1p.gz
/usr/share/man/man1/bp_split_seq.1p.gz
/usr/share/man/man1/bp_sreformat.1p.gz
/usr/share/man/man1/bp_taxid4species.1p.gz
/usr/share/man/man1/bp_taxonomy2tree.1p.gz
/usr/share/man/man1/bp_translate_seq.1p.gz
/usr/share/man/man1/bp_tree2pag.1p.gz
/usr/share/man/man1/bp_unflatten_seq.1p.gz

Changelog

2014-07-13 - Charles Plessy <plessy@debian.org>
bioperl (1.6.924-1) unstable; urgency=medium
* New upstream release.
2014-01-18 - Charles Plessy <plessy@debian.org>
bioperl (1.6.923-1) unstable; urgency=medium
* New upstream release.
* Does not need non-free libmath-random-perl anymore.
* Build-depend on libmodule-build-perl (>= 0.420000).  Despite Lintian's
warning that it is useless, the package does not build without.
* Conforms to Policy version 3.9.5.
2013-09-22 - Charles Plessy <plessy@debian.org>
bioperl (1.6.922-1) unstable; urgency=low
* New upstream release.
* Replaces and Breaks grinder (<< 0.5.3-3~) because of overlaping contents.
Closes: #722910
* Stop Replacing and Breaking bioperl ( << 1.6.9 ): not needed anymore. 
2013-09-08 - Charles Plessy <plessy@debian.org>
bioperl (1.6.920-1) unstable; urgency=low
* New upstream release (Closes: #720776)
* Adjusted Depends and Recommends (4 additions).
* Removed patch ‘fix_berkeleydb3_temp_file_creation’ applied upstream.
* Use canonical VCS URLs. 
2012-05-08 - Andreas Tille <tille@debian.org>
bioperl (1.6.901-4) unstable; urgency=low
* debian/upstream: Add additional citation data
[ Olivier Sallou ]
* add missing dependency
* Switch to standards 3.9.4
2012-03-02 - Olivier Sallou <osallou@debian.org>
bioperl (1.6.901-3) unstable; urgency=low
* Team upload.
[ Olivier Sallou ]
+ add patch fix_berkeleydb3_temp_file_creation (Closes: #661793).
Fixed upstream for next release. 
* debian/control: update Standards version
* debian/copyright: update Format to latest officiel URL v1.0
* debian/patches/fix_examples_perl_location: fix wrong perl location
* debian/rules: fix file access rights in dh_install
2011-12-14 - Andreas Tille <tille@debian.org>
bioperl (1.6.901-2) unstable; urgency=low
[ Luca Capello ]
* debian/control:
+ add Recommends: to some libraries already in libbio-perl-perl's
for binaries showing help output (Closes: #650412).
* debian/README.Debian:
+ new file with a more detailed explanation about the above.
[ Andreas Tille ]
* debian/source/format: 3.0 (quilt)
* Added myself to Uploaders
2011-06-17 - Charles Plessy <plessy@debian.org>
bioperl (1.6.901-1) unstable; urgency=low
* New upstream release.
* Point debian/watch to search.cpan.org.
* Build using dh and overrides:
- Use Debhelper 8 (debian/rules, debian/control).
- Simplified debian/rules.
* Split into libbio-perl-perl, as discussed with the Debian Perl team.
(debian/control, debian/bioperl.install, debian libbio-perl-perl.install)
* debian/control:
- Incremented Standards-Version to reflect conformance with Policy 3.9.2.
No other changes needed.
- Vcs-Browser URL made redirectable to viewvc.
- Removed useless ‘svn’ in the Vcs-Svn URL.
2010-02-26 - Charles Plessy <plessy@debian.org>
bioperl (1.6.1-2) unstable; urgency=low
* Removed bibliographic information from the long description
(debian/control).
* Incremented Standards-Version to reflect conformance with Policy 3.8.4
(debian/control, no changes needed).
* Build-depends on libxml-sax-expatxs-perl to avoid downloading DTDs during
the tests and therefore fail when network is not available
(debian/control, Closes: #562442).
* Depend on the ${misc:Depends} substvar (debian/control).
2009-09-30 - Charles Plessy <plessy@debian.org>
bioperl (1.6.1-1) unstable; urgency=low
* New upstream release with new features and many corrections in the
test suite (Closes: #533976).
* debian/rules: trigger network tests with DEB_MAINTAINER_MODE.
* debian/control:
- Build-depend on perl-modules >= 5.10.1 to have ExtUtils::Manifest 1.52 or
higher, and on libtest-pod-perl.
- Added liblist-moreutils-perl, libspreadsheet-writeexcel-perl,
libsvg-perl, and libxml-simple-perl, libdbd-pg-perl, libdbd-mysql-perl,
libdbd-sqlite3-perl to build and package dependencies (needed by some
components of Bioperl, and therefore for the tests).

See Also

Package Description
biosig-tools_1.3.0-2+b2_amd64.deb format conversion tools for biomedical data formats
biosquid-dev_1.9g+cvs20050121-4_amd64.deb headers and static library for biological sequence analysis
biosquid_1.9g+cvs20050121-4_amd64.deb utilities for biological sequence analysis
bip_0.8.9-1+b1_amd64.deb multiuser irc proxy with conversation replay and more
bird-bgp_1.4.5-1+deb8u1_amd64.deb Internet Routing Daemon [BGP-only version]
bird-doc_1.4.5-1+deb8u1_all.deb Internet Routing Daemon - documentatio
bird6_1.4.5-1+deb8u1_all.deb Internet Routing Daemon [transitional packages]
bird_1.4.5-1+deb8u1_amd64.deb Internet Routing Daemon
birthday_1.6.2-4_amd64.deb Display information about pending events on login
bisho_0.27.2+git20111122.9e68ef3d-2_amd64.deb Meego web services settings
bison++_1.21.11-3.1_amd64.deb Generate a parser in c or c++ from BNF notation
bison_3.0.2.dfsg-2_amd64.deb YACC-compatible parser generator
bisonc++-doc_4.09.02-1_all.deb Bison-style parser generator for C++
bisonc++_4.09.02-1_amd64.deb Bison-style parser generator for C++
bist_0.5.2-1_amd64.deb chemical drawing tool
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