biomaj_1.2.3-4_all.deb


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Description

biomaj - biological data-bank updater

Property Value
Distribution Debian 8 (Jessie)
Repository Debian Main amd64
Package name biomaj
Package version 1.2.3
Package release 4
Package architecture all
Package type deb
Installed size 4.64 KB
Download size 4.08 MB
Official Mirror ftp.br.debian.org
BioMAJ downloads remote data banks, checks their status and applies
transformation workflows, with consistent state, to provide ready-to-use
data for biologists and bioinformaticians. For example, it can transform
original FASTA files into BLAST indexes. It is very flexible and its
post-processing facilities can be extended very easily.

Alternatives

Package Version Architecture Repository
biomaj_1.2.3-4_all.deb 1.2.3 all Debian Main
biomaj - - -

Requires

Name Value
ant >= 1.9.1
ant-contrib -
debconf >= 0.5
debconf -
debconf-2.0 -
default-jre -
java6-runtime -
junit4 -
libcommons-cli-java -
libcommons-codec-java -
libcommons-dbcp-java >= 1.2
libcommons-httpclient-java -
libcommons-logging-java -
libcommons-net2-java >= 2.2
libcommons-pool-java >= 1.5
libhsqldb-java -
libjcommon-java >= 1.0
libjdom1-java >= 1.1
libjets3t-java -
libjgoodies-forms-java >= 1.3
libjsch-java >= 0.1.42
liblog4j1.2-java -
libmail-java -
libmysql-java -
liboro-java >= 2.0
libregexp-java >= 1.4
libsaxonb-java >= 0.9
mysql-client -
perl -

Download

Type URL
Binary Package biomaj_1.2.3-4_all.deb
Source Package biomaj

Install Howto

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

Files

Path
/etc/biomaj/general.conf
/etc/biomaj/unix_command_system.cfg
/etc/biomaj/db_properties/admin/alu.properties
/etc/biomaj/db_properties/admin/sts.properties
/usr/bin/biomaj
/usr/share/biomaj/console_help.txt
/usr/share/biomaj/general.conf
/usr/share/biomaj/global.properties.tpl
/usr/share/biomaj/bin/Configurator.class
/usr/share/biomaj/bin/Configurator.java
/usr/share/biomaj/bin/antRunAsync.sh
/usr/share/biomaj/bin/biomaj.sh
/usr/share/biomaj/bin/create_database.sh
/usr/share/biomaj/bin/env.sh
/usr/share/biomaj/bin/import_statefiles.old.sh
/usr/share/biomaj/bin/import_statefiles.sh
/usr/share/biomaj/bin/init_test.sh
/usr/share/biomaj/bin/migration.sh
/usr/share/biomaj/bin/shutdown_dbserver.sh
/usr/share/biomaj/bin/start_dbserver.sh
/usr/share/biomaj/conf/process/ProcessBiomajLib.pm
/usr/share/biomaj/conf/process/biomaj_drmaa.pl
/usr/share/biomaj/conf/process/dbiblast.sh
/usr/share/biomaj/conf/process/dbifasta.sh
/usr/share/biomaj/conf/process/dbiflat.sh
/usr/share/biomaj/conf/process/dbigcg.sh
/usr/share/biomaj/conf/process/fastacmdTLSE.pl
/usr/share/biomaj/conf/process/formatdbTLSE.pl
/usr/share/biomaj/conf/process/indexSrsTLSE.pl
/usr/share/biomaj/conf/process/linkfile.sh
/usr/share/biomaj/conf/process/sendMailTLSE.pl
/usr/share/biomaj/conf/process/unix_command_system.cfg
/usr/share/biomaj/lib/biomaj.jar
/usr/share/biomaj/sql/hsql-to_1.2.sql
/usr/share/biomaj/sql/hsql.sql
/usr/share/biomaj/sql/hsql_addconstraints.sql
/usr/share/biomaj/sql/hsql_removeconstraints.sql
/usr/share/biomaj/sql/mysql-to_1.2.sql
/usr/share/biomaj/sql/mysql.sql
/usr/share/biomaj/workflows/bank.xsd
/usr/share/biomaj/workflows/bank_statefile.xsd
/usr/share/biomaj/workflows/biomaj_common.xml
/usr/share/biomaj/workflows/handle_process.xml
/usr/share/biomaj/workflows/messages.properties
/usr/share/biomaj/workflows/mirror.xml
/usr/share/biomaj/workflows/process.xsd
/usr/share/biomaj/workflows/session.xsd
/usr/share/doc-base/biomaj
/usr/share/doc/biomaj/UsersGuide_BioMAJ_EN.odt
/usr/share/doc/biomaj/UsersGuide_BioMAJ_EN.pdf.gz
/usr/share/doc/biomaj/biomaj.1
/usr/share/doc/biomaj/changelog.Debian.gz
/usr/share/doc/biomaj/copyright
/usr/share/lintian/overrides/biomaj
/usr/share/man/man1/biomaj.1.gz
/var/lib/biomaj/migration/update.pl

Changelog

2014-10-17 - Emmanuel Bourg <ebourg@apache.org>
biomaj (1.2.3-4) unstable; urgency=medium
* Team upload.
* Replaced the dependency on libgnumail-java with libmail-java
* Standards-Version updated to 3.9.6 (no changes)
* Switch to debhelper level 9
* debian/copyright:
- Fixed the short name for the BSD license
- Reordered the paragraphs to avoid a Lintian warning about unsued files
2013-11-10 - Olivier Sallou <osallou@debian.org>
biomaj (1.2.3-3) unstable; urgency=low
* d/control: remove dependency on mysql-server but rather set it
to mysql-client as server can be remote.
2013-11-06 - Olivier Sallou <osallou@debian.org>
biomaj (1.2.3-2) unstable; urgency=low
* d/control: Fix browse url for svn 
d/config: Fix test for non-interactive mode
2013-10-30 - Olivier Sallou <osallou@debian.org>
biomaj (1.2.3-1) unstable; urgency=low
* New upstream release (fixes on local storage and stage option).
2013-08-30 - Olivier Sallou <osallou@debian.org>
biomaj (1.2.2-2) unstable; urgency=low
* d/postinst: Fix install in noninteractive mode (Closes: #721773).
2013-06-18 - Olivier Sallou <osallou@debian.org>
biomaj (1.2.2-1) unstable; urgency=low
* New upstream release with minor fixes
d/patches/series: upstream bug 15914 fixed.
2013-06-18 - Olivier Sallou <osallou@debian.org>
biomaj (1.2.1-3) unstable; urgency=low
* Add patch to manage ant properties api change (Closes: #712328).
2013-05-19 - Olivier Sallou <osallou@debian.org>
biomaj (1.2.1-2) unstable; urgency=low
* Add patch to match libjgoodies-form-java  >1.3,
FormFactory replaced by FormSpecs (Closes: #708454)
d/control: Depends on libjgoodies-form-java > 1.3
2012-10-19 - Olivier Sallou <osallou@debian.org>
biomaj (1.2.1-1) unstable; urgency=low
* New usptream release
* Add Japanase debconf translation (Closes: #690698)
Thanks to victory <victory.deb@gmail.com>
2012-10-04 - Olivier Sallou <osallou@debian.org>
biomaj (1.2.0-10) unstable; urgency=low
* debian/rules, debian/postinst: fix permissions on
properties file.

See Also

Package Description
bioperl-run_1.6.9-2_all.deb BioPerl wrappers: scripts
bioperl_1.6.924-1_all.deb Perl tools for computational molecular biology
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++
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