Enable bank post-processing using external scripts

• more generic command line scripts
• enable to override KL_WORKING_DIR, KL_CONF_DIR and KL_JRE_ARGS variables before calling command-line scripts
• enable to override conf/dbms.conf properties using JRE -D arguments
• ensure to have default values setup for install.sh tool
• refactor Log system; enables none, console or file; added KL_LOG_TYPE JRE command-line argument
• enable the use of external scripts for bank post-processing tasks
• enable FTP download resume
• upgrade to new XStream, Bioinformatics-Core and Bioinformatics-UI libraries
• annotator.sh tool uses the new native binary ZML data format (more suitable for large data files)

new release in preparation

v4.5.0

enable to override DBMSConfigurator props using JRE -D arguments; pre…

Support of Aspera

• add support of Aspera; enabled for EBI and NCBI only
• fix some bugs in the handling of Taxonomy Data (short path)

Add new cmdline tools

New features:

• Cmd-line tool to check descriptor files (solved issue #8)
• Cmd-line tool to delete banks (solved isseu #6)

Fixes:

• bank history handling

Enhancements:

• Cmd-line tool Install sends template-based emails (solved issue #2)
• Cmd-line tool Install now uses a resume mode by default
• Cmd-line tool Install now accepts arguments in addition of global descriptor (solved issue #4)
• Configuration directory can be configured from the command line
• Enhance logs for large banks installation (solved issue #3)
• Add Galaxy wrapper to expose banks to BLAST tool
• Update descriptors (solved issue #7)
• Smart copy of local files (solved issue #5)

Refer to the user manual to install and use BeeDeeM:

• BeeDeeM manual on GitBook
• BeeDeeM manual on GitHub: Introduction and Table of Content.

Add handling of bank release date

These are the new features :

• handle data provider release date
• smartly update bank by controlling release date
• dump list of databanks using Galaxy format
• get sequences count from BLAST index (blastdbcmd support)
• fix Lucene indexing for Lustre FS
• fix some bank installation descriptors
• end of JDK 1.7 support; please use Java 1.8+
• run BeeDeeM functional tests on a regular basis using Travis-CI

To install and use BeeDeeM, please refer to the user manual:

• BeeDeeM manual on GitBook
• BeeDeeM manual on GitHub: Introduction and Table of Content.

Add the "info" tool.

To install and use BeeDeeM, please refer to the user manual:

• BeeDeeM manual on GitBook
• BeeDeeM manual on GitHub: Introduction and Table of Content.