| 1 | # main topics: |
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| 2 | UP arb.hlp |
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| 3 | UP glossary.hlp |
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| 4 | |
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| 5 | # sub topics: |
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| 6 | SUB arb_gde.hlp |
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| 7 | SUB arb_db.hlp |
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| 8 | SUB arb_envar.hlp |
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| 9 | |
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| 10 | # format described in ../help.readme |
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| 11 | |
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| 12 | |
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| 13 | TITLE ARB: Basic ARB-Shell Commands |
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| 14 | |
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| 15 | OCCURRENCE shell |
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| 16 | |
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| 17 | SECTION COMMANDS |
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| 18 | |
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| 19 | 'arb [filename]' |
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| 20 | |
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| 21 | Starts the ARB main program (arb_ntree) which also |
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| 22 | acts as the database server for other ARB modules. |
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| 23 | |
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| 24 | The database server is memory based. That means: |
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| 25 | |
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| 26 | - All changes are only temporary until the |
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| 27 | database is saved. |
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| 28 | - The database is a single file which can be copied, |
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| 29 | deleted, renamed ... |
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| 30 | |
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| 31 | The database file should have the suffix '.arb'. |
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| 32 | |
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| 33 | |
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| 34 | 'arb_clean' |
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| 35 | |
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| 36 | Stops all your ARB processes and removes all temporary files in |
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| 37 | the /tmp directory. |
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| 38 | It does not kill non-arb processes. That means if you start |
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| 39 | programs via the GDE interface you have to stop them yourself: |
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| 40 | (phylip, desoete, ...) |
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| 41 | |
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| 42 | enter 'ps -ux' or 'ps -f' |
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| 43 | search the process-id PID and kill it with |
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| 44 | 'kill -9 PID' |
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| 45 | |
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| 46 | 'arb_panic' |
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| 47 | |
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| 48 | Sends a signal (HANGUP) to ARB to force saving the database in ASCII mode. |
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| 49 | Because arb_panic bypasses any running operation of ARB, |
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| 50 | |
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| 51 | THE SAVED DATABASE MAY CONTAIN INCONSISTENT DATA. |
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| 52 | |
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| 53 | It interactively asked for file name and whether it should |
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| 54 | kill arb after saving. |
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| 55 | |
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| 56 | 'arb_2_ascii filename [dest_filename]' |
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| 57 | |
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| 58 | Converts any ARB database to ASCII format. |
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| 59 | |
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| 60 | Also tries to recover corrupt files (if dest_filename is skipped). |
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| 61 | Backup first!!! |
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| 62 | |
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| 63 | 'arb_2_bin [-m] [-r] [-c][tree_xxx] database [newdatabase]' |
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| 64 | |
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| 65 | Purpose: Converts a database to binary format |
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| 66 | |
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| 67 | Options: |
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| 68 | -m create map file too |
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| 69 | -r try to repair destroyed database |
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| 70 | -c[tree_xxx] optimize database compression using tree_xxx or largest tree |
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| 71 | |
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| 72 | NOTES It is very useful to start a performance meter to see |
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| 73 | whether there are running background jobs (fastdnaml, phylip...) |
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| 74 | |
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| 75 | All arb_... commands show some basic usage info if you call |
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| 76 | them with parameter '--help' |
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| 77 | |
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| 78 | i.e. arb_ntree --help |
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| 79 | |
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| 80 | WARNINGS Don't destroy an existing arb file with arb_panic. |
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| 81 | |
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| 82 | BUGS No bugs known |
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