Fix installation for special banks under Nextflow

Update done to enable ORSON workflow to install particular data sets such as CLEAN and BUSCO.

Patch release

Updated release of BeeDeeM with minor fixes and updated documentation.

Introducing new BeeDeeM unique command-line tools

New version of BeeDeeM introducing new command line tools.

• Major change, not backward compatible are:

  • All old scripts (install.sh, query.sh, etc.) have been replaced by a unique command: bdm. That command accepts sub-commands, namely: install, query, etc. Use bdm -h to get general help, and bdm <command> -h to get help on a particular .
  • Drop native support of Windows system; users or invited to rely on Windows Subsystem Linux

• Minor fixes:

  • Improvement of the cluster job submission system
  • Enable arguments passing to external scripts (pre- and post-processing)
  • Improvement of Uniprot description handling; only retain RecName or SubName from entries, better parsing of EC numbers.
  • Several bug fixes.

Maintenance release

• redesign job scheduler API
• add support of SLURM scheduler
• add CONDA packaging

Update Biojava 1.9.6 Uniprot Parser

Update Legacy Biojava 1.9.6 Uniprot Parser code to handle new FT lines text format introduced on 2019_12 release. The update Biojava code is available at https://github.com/pgdurand/biojava-legacy.

Switch to BLAST v5 bank format

Novelties in this release of BeeDeeM are :

• get bank installation date from data provider
• command-line Install tool: enable to pass a full path to a descriptor (.dsc) file
• switch to makblastdb 2.9.0; so, now BeeDeeM prepare BLAST bank v5
• update test suite to better identify changes in data format made by bank providers
• enhance bank query system for ontologies (IPR, GO, Taxonomy, etc)
• simplify use of Singularity container
• enhance log messages to better understand what happens on bank installation failure
• enhance bank installation resume steps
• fix minor bugs

Enhance Bank Query Framework

• Enhance Bank Query Framework:
  • better use of stdout, stderr on the command-line
  • add -o argument to redirect results of query to a file
  • enable the use of file of entry IDs
  • enable to query NCBI Taxonomy using names (organism, phylum, etc) in addition to TaxID
• Handle NCBI Taxonomy merged.dmp data file to keep track of classification updates
• New descriptors to install Uniprot Proteomes, Silva and MEROPS

Add support for Cluster Scheduler

BeeDeeM is now capable of submitting jobs to cluster using native schedulers.

First support has been added to use PBS Pro job manager.

add bank pre/post processing

New features :

• all ones from 4.6.x pre-releases
• enable to switch on/off GO, Taxonomy and Enzyme data path during Annotator processing
• auto-creation of databank JSON property files

enhance software configuration

• enable use of HTTP/HTTPS protocol as an alternative way of loading files when FTP does not work
• enable to override KL_WORKING_DIR, KL_CONF_DIR, KL_LOG_XXX and KL_DEBUG variables before calling command-line scripts using environment variables
• enable to override conf/dbms.conf properties using environment variables, too. For this feature to work on the command line, replace '.' separator of variable names by '__' (double underscore); e.g. to override 'mirror.path' variable definition (as usually defined in conf/dbms.conf file), do this on bash shell: export KL_mirror__path="/path/to/banks".
• new Singularity recipe with a fully autonomous software; no need anymore of setting up an external conf directory