/usr/share/biomaj/console_help.txt is in biomaj 1.2.3-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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biomaj --update <dbname1> [<dbname2> ...] --stage <task>|--console|--verbose|--debug|--new|--fromscratch --status <dbname> --dbtype
<dbtype>|--online|--updating --rebuild <dbname> --process <name1> [<name2> ...]|--meta <arg1> [<arg2> ...]|--block <arg1> [<arg2>
...]|--console|--verbose|--debug --remove <dbname> --paths <path1> [<path2> ...]|--all|--keep-dir-prod|--console|--verbose|--debug --import <bank>
--move-production-directories <dbname> --index <file> --change-dbname <dbname1> <dbname2> --clean-database --view-log --version --help
MAIN OPTIONS: DESCRIPTION
--conf-location (-C) Absolute path to general.conf. Default value is BIOMAJ_ROOT
--update (-d) <dbname> [<dbname> ...] Update specified bank (dbname)
update options:
--stage (-s) <task> Stop update at given stage :
preprocess|sync|postprocess|deployment
--console (-c) Show update progress in a window
--verbose (-v) Verbose mode
--debug (-V) Extra verbose mode
--new (-N) Start a new update cycle even if a unclosed update cycle is open (ps:previous sessions are
ignored)
--fromscratch (-z) Force update from scratch of the bank by skipping the repository verification
--status (-S) <dbname> Display bank status. If dbname is specified, detailed information for given bank is displayed
status options:
--dbtype (-t) <dbtype> Filter bank list according given dbtype
--online (-o) Display only online banks
--updating (-u) Display only currently updating banks
--rebuild (-b) <dbname> Rebuild given bank (downgrade the current version checks data and rerun post-processing)
--process|--meta|--block|--console|--verbose|--debug
--process (-P) <name> [<name> ...] Force the execution of process
--meta (-M) <arg> [<arg> ...] Force the execution of metaprocess
--block (-B) <arg> [<arg> ...] Force the execution of block
--console (-c) Show update progress in a window
--verbose (-v) Verbose mode
--debug (-V) Extra verbose mode
--remove (-r) <dbname> Delete production directories. If no option is specified, interactive mode is used
remove options:
--paths (-p) <path> [<path> ...] Directly specify the directories paths to be deleted
--all (-a) Delete all directories
--keep-dir-prod (-k) Delete/keep production directory
--all-no-history (-A) Same as all but keeps no info about the bank in the database
--console (-c) Show update progress in a window
--verbose (-v) Verbose mode
--debug (-V) Extra verbose mode
--import (-I) <bank> Populate database for a bank according to its properties file and production directory.
Data tree directory must be in compliance with the bank properties files and biomaj tree
directory organisation
--move-production-directories (-e) <dbname> Export all production directories to the new version directory determined by the properties
data.dir and version.dir
--index (-i) <file> Generate an index of all banks in repository
Default location is : ${statefiles.dir}/index.xml
--change-dbname (-n) <dbname> <dbname> Change the name of the bank on the repository
--clean-database (-l) Delete files that no longer exist from database.
--view-log (-L) Show graphical log browser
--version (-w) Version information
--help (-h) Display current help message
Biomaj is a workflow engine dedicated to biological bank managenemt. This software is governed by the CeCILL license under French
law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the
CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info".
Copyright or Copr. INRIA/INRA
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