|
Last change
on this file was
19532,
checked in by westram, 4 months ago
|
- reintegrates 'help' into 'trunk'
- tweak arb documentation:
- automatically link
- ticket references to arb
 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
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File size:
1.2 KB
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| 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 subtopic.hlp |
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| 7 | |
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| 8 | # format described in ../help.readme |
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| 9 | |
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| 10 | |
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| 11 | TITLE Start a console |
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| 12 | |
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| 13 | OCCURRENCE ARB_NT/Tools/Start XTERM |
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| 14 | |
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| 15 | DESCRIPTION Starts a console window from ARB. |
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| 16 | |
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| 17 | The shell in the console uses the same environment as the running arb session. |
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| 18 | From this environment you may call perl-scripts |
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| 19 | - delivered with ARB (e.g. in $ARBHOME/PERL_SCRIPTS) or |
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| 20 | - your own scripts. |
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| 21 | |
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| 22 | The main reason for the execution environment is the ability to easily access the |
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| 23 | database currently loaded into ARB. |
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| 24 | |
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| 25 | NOTES The console window is started in the same way |
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| 26 | as done to call external tools (like RAxML). |
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| 27 | |
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| 28 | See ARB_XTERM in LINK{arb_envar.hlp} to customize the |
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| 29 | way arb starts consoles. |
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| 30 | |
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| 31 | EXAMPLES of existing scripts: |
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| 32 | |
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| 33 | * listMarkedSpecies.pl (save names of currently marked species to a textfile) |
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| 34 | * markSpecies.pl (mark species according to content of a textfile) |
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| 35 | * arb_read_tree (import tree from newick treefile) |
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| 36 | |
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| 37 | WARNINGS None |
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| 38 | |
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| 39 | BUGS No bugs known |
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