libbiojava-java_1.7.1-5_all.deb


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Description

libbiojava-java - Java API to biological data and applications (default version)

Property Value
Distribution Debian 8 (Jessie)
Repository Debian Main amd64
Package name libbiojava-java
Package version 1.7.1
Package release 5
Package architecture all
Package type deb
Installed size 184 B
Download size 47.24 KB
Official Mirror ftp.br.debian.org
BioJava is an open-source project dedicated to providing a Java framework
for processing biological data. It includes objects for manipulating
sequences, file parsers, DAS client and server support, access to BioSQL
and Ensembl databases, and powerful analysis and statistical routines
including a dynamic programming toolkit.
BioJava is provided by a vibrant community which meets annually at
the Bioinformatics Open Source Conference (BOSC) that traditionally
accompanies the Intelligent Systems in Molecular Biology (ISMB)
meeting. Much like BioPerl, the employment of this library is valuable
for everybody active in the field because of the many tricks of the
trade one learns just by communicating on the mailing list.
This is a wrapper package which should enable smooth upgrades to new
versions.

Alternatives

Package Version Architecture Repository
libbiojava-java_1.7.1-5_all.deb 1.7.1 all Debian Main
libbiojava-java - - -

Requires

Name Value
libbiojava1.7-java -

Conflicts

Name Value
libbiojava1.6-java -

Replaces

Name Value
libbiojava1.6-java -

Download

Type URL
Binary Package libbiojava-java_1.7.1-5_all.deb
Source Package biojava-live

Install Howto

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

Files

Path
/usr/share/doc/libbiojava-java/README
/usr/share/doc/libbiojava-java/README.biosql
/usr/share/doc/libbiojava-java/changelog.Debian.gz
/usr/share/doc/libbiojava-java/copyright
/usr/share/doc/libbiojava-java/dtd/BlastLikeDataSetCollection.dtd.gz
/usr/share/doc/libbiojava-java/resources/META-INF/services/org.biojava.bio.program.formats.Format
/usr/share/doc/libbiojava-java/resources/META-INF/services/org.biojava.directory.SequenceDBProvider
/usr/share/doc/libbiojava-java/resources/obda/naming/core.xml.gz
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/gui/sequence/NoDesc.html
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/gui/sequence/NoSample.txt
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/gui/sequence/aprDesc.html
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/gui/sequence/aprExamp.apr
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/gui/sequence/fastaDesc.html
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/gui/sequence/fastaExamp.fasta
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/gui/sequence/msfDesc.html
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/gui/sequence/msfExamp.msf
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/molbio/RestrictionEnzymeManager.properties
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/molbio/rebase_common.dat.gz
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/program/sax/blastxml/NCBI_BlastOutput.dtd
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/program/sax/blastxml/NCBI_BlastOutput.mod.gz
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/program/sax/blastxml/NCBI_Entity.mod
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/program/unigene/createUnigene.sql
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/proteomics/ProteaseManager.xml
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/seq/TranslationTables.xml.gz
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/seq/io/FeatureQualifier.xml.gz
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/structure/blosum62.mat
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/structure/standardaminos.pdb.gz
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/symbol/AlphabetManager.xml.gz
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/symbol/CodonPrefTables.xml.gz
/usr/share/doc/libbiojava-java/resources/org/biojava/bio/symbol/ResidueProperties.xml.gz
/usr/share/doc/libbiojava-java/resources/org/biojava/ontology/colonel-west.pred
/usr/share/doc/libbiojava-java/resources/org/biojava/ontology/core.agregate.pred
/usr/share/doc/libbiojava-java/resources/org/biojava/ontology/core.list.pred
/usr/share/doc/libbiojava-java/resources/org/biojava/ontology/core.onto
/usr/share/doc/libbiojava-java/resources/org/biojava/ontology/core.pred.gz
/usr/share/doc/libbiojava-java/resources/org/biojava/ontology/core.set.pred
/usr/share/doc/libbiojava-java/resources/org/biojava/ontology/ontology.pred
/usr/share/java/biojava.jar

Changelog

2014-05-20 - Olivier Sallou <osallou@debian.org>
biojava-live (1:1.7.1-5) unstable; urgency=medium
* d/control: use libcommons-collections3 instead of 
libcommons-collection in runtime deps (Closes: #748473).
2014-01-31 - Olivier Sallou <osallou@debian.org>
biojava-live (1:1.7.1-4) unstable; urgency=low
[ Andreas Tille ]
* debian/upstream:
- Author conform to BibTeX syntax
- Add eprint
[ Olivier Sallou ]
* Fix watch file to follow biojava v1, not v3
2013-09-10 - Olivier Sallou <osallou@debian.org>
biojava-live (1:1.7.1-3) unstable; urgency=low
* Use libcommons-collections3-java instead of libcommons-collections-java 
2012-04-18 - Andreas Tille <tille@debian.org>
biojava-live (1:1.7.1-2) unstable; urgency=low
[ Jari Aalto ]
* Remove quilt and upgrade to packaging format "3.0 quilt" which
includes patch management built-in.
* Update buildxml.patch to DEP-3 and run "quilt refresh" to make it
apply cleanly.
* Update to Standards-Version to 3.9.3 (no changes needed) and debhelper 9.
* Update obsolete depends default-jdk-builddep to default-jdk.
Closes: #669122
* Fix wrong-section-according-to-package-name (Lintian) by changing
section from science to java.
* Fix needless-dependency-on-jre (Lintian) by removing jre dependencies.
* Fix duplicate-short-description (Lintian).
* Fix extended-description-is-probably-too-short (Lintian).
[ Andreas Tille ]
* debian/control:
- Short-Desc: Java 1.7 API is missleading regarding JDK version - rather
add the version at the end and declare the version-less metapackage as
default version
- Dropped default-jre-headless from Depends according to Java policy
- Fixed Vcs fields
* debian/watch: enable detecting new versions
* debian/{control,upstream}: Moved citations from long description to
upstream file
* libbiojava*.lintian: removed because now useless
* debian/compat: 9
* debian/copyright: Rewritten to be compliant with DEP5 and verified
using `cme fix dpkg-copyright`
* debian/rules: s/dh_clean -k/dh_prep/
2010-01-20 - Steffen Moeller <moeller@debian.org>
biojava-live (1:1.7.1-1) unstable; urgency=low
* New upstream version.
* New epoch
- because of an unfortunate versioning of previous upload
- to indicate the now happening BioJava Hackathon in Cambridge, UK
2009-06-26 - Andreas Tille <tille@debian.org>
biojava-live (1.7.svn.20090419-3) unstable; urgency=low
* debian/control:
- Conflicts: libbiojava1.6-java
- Replaces: libbiojava1.6-java
- Enhanced long description of libbiojava-java-doc
Closes: #522269
* debian/rules: set JAVA_HOME to enable proper clean target
2009-06-22 - Andreas Tille <tille@debian.org>
biojava-live (1.7.svn.20090419-2) unstable; urgency=low
* Add Build Depends: ant-optional
Closes: #533896
* Standards-Version: 3.8.2 (no changes needed)
2009-04-19 - Steffen Moeller <moeller@debian.org>
biojava-live (1.7.svn.20090419-1) unstable; urgency=low
* New upstream version, addressing structures.
* Removed dependency on libjgrapht, so biojava can go to main.
* Conformance to 3.8.1 (no changes required).
2009-03-09 - Andreas Tille <tille@debian.org>
biojava-live (1.6.1.svn.20090306-1) experimental; urgency=low
[ Andreas Tille ]
* Initial release (Closes:#491025).
[ Steffen Moeller ]
* Added dependency to quilt.
* Moved -doc to section doc.
* Added symlinks to jar file with pseudo-soname
* Need to be placed in contrib section as a start because of dependency
to libjgrapht that is still in contrib.
2008-07-13 - Steffen Moeller <moeller@debian.org>
biojava-live (1.6.0.svn.20080716-1) UNRELEASED; urgency=low
* Renamed to biojava-live in analogy to upstream's name
and to keep the opportunity to add a biojava meta package
later on.
* License issue fixed that led to previous rejection of biojava.

See Also

Package Description
libbiojava1.7-java_1.7.1-5_all.deb Java API to biological data and applications (version 1.7)
libbiojava3-java-doc_3.1.0+dfsg-2_all.deb [Biology] Documentation for BioJava
libbiojava3-java_3.1.0+dfsg-2_all.deb Java API to biological data and applications (default version)
libbiojava3.0-java_3.1.0+dfsg-2_all.deb Java API to biological data and applications (version 3)
libbiosig-dev_1.3.0-2+b2_amd64.deb I/O library for biomedical data - development files
libbiosig1_1.3.0-2+b2_amd64.deb I/O library for biomedical data - dynamic library
libbisho-common-dev_0.27.2+git20111122.9e68ef3d-2_amd64.deb Meego web services settings library (development files)
libbisho-common0_0.27.2+git20111122.9e68ef3d-2_amd64.deb Meego web services settings library
libbison-dev_3.0.2.dfsg-2_amd64.deb YACC-compatible parser generator - development library
libbit-vector-minimal-perl_1.3-4_all.deb object-oriented wrapper around vec()
libbit-vector-perl_7.3-1+b2_amd64.deb Perl module for bit vectors and more
libbitcoin-dev_2.0-2.2_amd64.deb Bitcoin toolkit library for asynchronous apps - development headers
libbitcoin0_2.0-2.2_amd64.deb Bitcoin toolkit library for asynchronous apps
libbitmask-dev_2.0-2_amd64.deb header files and docs for libbitmask
libbitmask1_2.0-2_amd64.deb supports multi-word bitmask operations
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