libbiojava-java_1.7.1-8_all.deb


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Description

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

Property Value
Distribution Debian 10 (Buster)
Repository Debian Main amd64
Package name libbiojava-java
Package version 1.7.1
Package release 8
Package architecture all
Package type deb
Installed size 118 B
Download size 47.31 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_1.7.1-8_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_1.7.1-8_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

2018-11-01 - Andreas Tille <tille@debian.org>
biojava-live (1:1.7.1-8) unstable; urgency=medium
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
* Remove trailing whitespace in debian/changelog
* Remove trailing whitespace in debian/rules
* Set release to 8 since CORBA classes are removed in Java 11, and no
replacement available in Debian (Closes: #912643)
2018-01-23 - Andreas Tille <tille@debian.org>
biojava-live (1:1.7.1-7) unstable; urgency=medium
* Remove leftover of debhelper migration from d/rules
Closes: #870060
* debhelper 11
* Standards-Version: 4.1.3
2017-09-26 - Andreas Tille <tille@debian.org>
biojava-live (1:1.7.1-6) unstable; urgency=medium
* Moved packaging to Git
* cme fix dpkg-control
* Replace cdbs variables by those provided by /usr/share/dpkg/default.mk
* d/rules: use dh
* Move debian/upstream to debian/upstream/metadata
* DEP5 issues
* debhelper 10
* make build reproducible
Closes: #859958
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)

See Also

Package Description
libbiojava1.7-java_1.7.1-8_all.deb Java API to biological data and applications (version 1.7)
libbiojava4-java-doc_4.2.12+dfsg-2_all.deb [Biology] Documentation for BioJava
libbiojava4-java_4.2.12+dfsg-2_all.deb Java API to biological data and applications (default version)
libbiojava4.0-java_4.2.12+dfsg-2_all.deb Java API to biological data and applications (version 4)
libbiometric-dev_0.9.61-2_amd64.deb Biometric Identification DRIVER API - development files
libbiometric0_0.9.61-2_amd64.deb Biometric Identification library
libbioparser-dev_1.2.1-1_all.deb library for parsing several formats in bioinformatics
libbiosig-dev_1.9.3-2_amd64.deb I/O library for biomedical data - development files
libbiosig2_1.9.3-2_amd64.deb I/O library for biomedical data - dynamic library
libbison-dev_3.3.2.dfsg-1_amd64.deb YACC-compatible parser generator - development library
libbit-vector-minimal-perl_1.3-5_all.deb object-oriented wrapper around vec()
libbit-vector-perl_7.4-1+b5_amd64.deb Perl module for bit vectors and more
libbitmask-dev_2.0-3_amd64.deb header files and docs for libbitmask
libbitmask1_2.0-3_amd64.deb supports multi-word bitmask operations
libbitstream-dev_1.5-1_all.deb C headers giving access to binary streams like MPEG or DVB
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