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Last update on 25. Nov 2018 .
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ARB: Basic ARB-Shell Commands

OCCURRENCE

shell

 

COMMANDS

'arb [filename]'

Starts the main program ARB_NT which also includes the database server.
The database server is memory based. That means:
  • All changes are only temporary until the database is saved.
  • The database is a single file which can be copied, deleted, renamed ...

The database file should have the suffix '.arb'.

'arb_clean'

Stops all your ARB processes and removes all temporary files in the /tmp directory. It does not kill non-arb processes. That means if you start programs via the GDE interface you have to stop them yourself: (phylip, desoete, ...)
enter 'ps -ux'   or 'ps -f'
search the process-id PID and kill it with
'kill -9 PID'

'arb_panic'

Sends a signal (HANGUP) to ARB_NT to force saving the database in ASCII mode. Because arb_panic bypasses any running operation of ARB_NT,
THE SAVED DATABASE MAY CONTAIN INCONSISTENT DATA.
It interactively asked for file name and whether it should kill arb after saving.

'arb_2_ascii filename [dest_filename]'

Converts any ARB database to ASCII format.
Also tries to recover corrupt files (if dest_filename is skipped). Backup first!!!

´arb_2_bin [-m] [-r] [-c][tree_xxx] database [newdatabase]´

Purpose: Converts a database to binary format
Options:
         -m            create map file too
         -r            try to repair destroyed database
         -c[tree_xxx]  optimize database compression using tree_xxx or largest tree
 

NOTES

It is very useful to start a performance meter to see whether there are running background jobs (fastdnaml, phylip...)

All arb_... commands show some basic usage info if you call them with parameter '--help'

i.e. arb_ntree --help
 

WARNINGS

Don't destroy an existing arb file with arb_panic.

 

BUGS

No bugs known