
User scripts
------------

Scripts stored SH are delivered to users with ARB releases.


User scripts:

        arb                                     Used to start arb
        arb_clean                               Kill running arb processes (does not kill pt servers)
        arb_installubuntu4arb.sh                Install Ubuntu environment for ARB
        arb_remote                              Run ARB on a remote machine using ssh
        arb_panic                               Try to save database of running ARB (e.g. if ARB does not react)
        arb_repair                              Try to repair a broken database
        arb_who                                 Show arb processes

        dszmconnect.pl                          adapter between the ARB program package and the DSZM website
        example_batch_probe_match.sh            probe match from command line


Scripts used by ARB or from other scripts:

        arb_dnapars                             wrapper for dnapars
        arb_echo                                spread parameters to multiple lines
        arb_fastdnaml                           wrapper for fastdnaml
        arb_ign                                 used to ignore some arguments from command line
        arb_ludwig                              (alias for arb_remote)
        arb_phyml                               wrapper for phyml
        arb_proml                               wrapper for proml
        arb_protml                              wrapper for protml
        arb_protpars                            wrapper for protpars
        arb_raxml                               wrapper for raxml
        arb_sleep                               Keeps terminal windows open for 60 seconds (unused)
        arb_textedit                            Used to edit textfiles
        arb_textprint                           Used to print textfiles
        arb_wait                                Keep terminal windows open until user presses ENTER
        
Undocumented / maybe obsolete:
                                         @@@ FIXME: examine and remove or document these scripts 
        arb_ale                                 
        arb_bootstrap
        arb_hindex
        arb_history
        arb_index

