| 1 | |
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| 2 | User scripts |
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| 3 | ------------ |
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| 4 | |
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| 5 | Scripts stored SH are delivered to users with ARB releases. |
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| 6 | |
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| 7 | |
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| 8 | User scripts: |
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| 9 | |
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| 10 | arb Used to start arb |
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| 11 | arb_clean Kill running arb processes (does not kill pt servers) |
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| 12 | arb_installubuntu4arb.sh Install Ubuntu environment for ARB |
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| 13 | arb_remote Run ARB on a remote machine using ssh |
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| 14 | arb_panic Try to save database of running ARB (e.g. if ARB does not react) |
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| 15 | arb_repair Try to repair a broken database |
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| 16 | arb_who Show arb processes |
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| 17 | |
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| 18 | dszmconnect.pl adapter between the ARB program package and the DSZM website |
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| 19 | example_batch_probe_match.sh probe match from command line |
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| 20 | |
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| 21 | |
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| 22 | Scripts used by ARB or from other scripts: |
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| 23 | |
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| 24 | arb_dnapars wrapper for dnapars |
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| 25 | arb_echo spread parameters to multiple lines |
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| 26 | arb_fastdnaml wrapper for fastdnaml |
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| 27 | arb_ign used to ignore some arguments from command line |
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| 28 | arb_ludwig (alias for arb_remote) |
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| 29 | arb_phyml wrapper for phyml |
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| 30 | arb_proml wrapper for proml |
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| 31 | arb_protml wrapper for protml |
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| 32 | arb_protpars wrapper for protpars |
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| 33 | arb_raxml wrapper for raxml |
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| 34 | arb_sleep Keeps terminal windows open for 60 seconds (unused) |
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| 35 | arb_textedit Used to edit textfiles |
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| 36 | arb_textprint Used to print textfiles |
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| 37 | arb_wait Keep terminal windows open until user presses ENTER |
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| 38 | |
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| 39 | Undocumented / maybe obsolete: |
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| 40 | @@@ FIXME: examine and remove or document these scripts |
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| 41 | arb_ale |
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| 42 | arb_bootstrap |
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| 43 | arb_hindex |
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| 44 | arb_history |
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| 45 | arb_index |
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| 46 | |
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