source: trunk/HELP_SOURCE/source/arb_commands.hlp

Last change on this file was 19532, checked in by westram, 5 weeks ago
  • reintegrates 'help' into 'trunk'
    • tweak arb documentation:
      • automatically link
        • ticket references to arb bug tracker (only affects html version).
        • found URLs.
      • page titles
        • warn about long titles.
        • introduce SUBTITLEs (automatically triggered by multi-line titles in source files).
        • increase allowed length (limited by subwindow width).
      • cleanup header sections in all helpfiles.
      • fix and/or update several help files.
      • document syntax of help sources.
      • build issues:
        • when xml validation fails, next build no longer uses invalid xml ⇒ keeps failing.
        • remove output files on error (including files below ARBHOME/lib).
        • pipe output through logs to ensure proper wrapping in Entering/Leaving lines.
    • moves Tree admin + NDS menu entries to top of menu
  • adds: log:branches/help@18783:19531
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 2.2 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4
5#       sub topics:
6SUB     arb_gde.hlp
7SUB     arb_db.hlp
8SUB     arb_envar.hlp
9
10# format described in ../help.readme
11
12
13TITLE           ARB: Basic ARB-Shell Commands
14
15OCCURRENCE      shell
16
17SECTION         COMMANDS
18
19        'arb [filename]'
20
21                Starts the main program ARB_NT which also includes the database
22                server.
23
24                The database server is memory based. That means:
25
26                        - All changes are only temporary until the
27                          database is saved.
28                        - The database is a single file which can be copied,
29                          deleted, renamed ...
30
31                The database file should have the suffix '.arb'.
32
33
34        'arb_clean'
35
36                Stops all your ARB processes and removes all temporary files in
37                the /tmp directory.
38                It does not kill non-arb processes. That means if you start
39                programs via the GDE interface you have to stop them yourself:
40                (phylip, desoete, ...)
41
42                        enter 'ps -ux'   or 'ps -f'
43                        search the process-id PID and kill it with
44                        'kill -9 PID'
45
46        'arb_panic'
47
48                Sends a signal (HANGUP) to ARB_NT to force saving the
49                database in ASCII mode.
50                Because arb_panic bypasses any running operation of ARB_NT,
51
52                THE SAVED DATABASE MAY CONTAIN INCONSISTENT DATA.
53
54                It interactively asked for file name and whether it should
55                kill arb after saving.
56
57        'arb_2_ascii filename [dest_filename]'
58
59                Converts any ARB database to ASCII format.
60
61                Also tries to recover corrupt files (if dest_filename is skipped).
62                Backup first!!!
63
64        'arb_2_bin [-m] [-r] [-c][tree_xxx] database [newdatabase]'
65
66                Purpose: Converts a database to binary format
67
68                Options:
69                         -m            create map file too
70                         -r            try to repair destroyed database
71                         -c[tree_xxx]  optimize database compression using tree_xxx or largest tree
72
73NOTES           It is very useful to start a performance meter to see
74                whether there are running background jobs (fastdnaml, phylip...)
75
76                All arb_... commands show some basic usage info if you call
77                them with parameter '--help'
78
79                        i.e.    arb_ntree --help
80
81WARNINGS        Don't destroy an existing arb file with arb_panic.
82
83BUGS            No bugs known
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