source: branches/profile/GDEHELP/ARB_GDEmenus.source

Last change on this file was 11874, checked in by westram, 5 years ago
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  • Property svn:keywords set to Author Date Id Revision
File size: 2.9 KB
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1// special conventions:
2//
3// * each external command ('itemmethod') runs in its separate directory under ~/.arb_tmp
4// * if sequences are exported ARB writes them in GenBank format into a tmpfile (e.g. sth like '/tmp/gde3170_0')
5//   In 'itemmethod' every occurrance of 'TmpInputFile' (as specified at entry 'in:') is replaced by the name of that tempfile.
6//   Some macros defined below expect that placeholder, i.e. always use 'TmpInputFile' for 'in:'!
7// * if sequences are (re-)imported, ARB prepares a temporary output-file. itemmethod shall use the placeholder 'TmpOutputFile'
8//   to generate its content. Always use 'TmpOutputFile' for 'out:'.
9//   Do not remove TmpOutputFile using RM_LOCAL_FILES. It is expected and will be removed by ARB_GDE (after command termination).
10// * 'arg:DISPLAY_FUNC' shall be a single command (to be chainable with && in itemmethod)
11
12// GOTO_LOCAL_DIR and RM_LOCAL_FILES need to be used on top-script level
13// (opening sub-shells might change value of $$)
14
15#define GOTO_LOCAL_DIR          mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$
16#define RM_LOCAL_FILES(FILES)   GOTO_LOCAL_DIR ; cd .. ; rm -rf $$
17
18#define GENERATE(OUTFILE,FORMAT) arb_convert_aln --arb-notify -GenBank TmpInputFile -FORMAT OUTFILE
19
20#define GEN_PHYLIP(OUTFILE)     GENERATE(OUTFILE,phylip)
21#define GEN_FASTDNAML(OUTFILE)  GENERATE(OUTFILE,fastdnaml)
22#define GEN_NEXUS(OUTFILE)      GENERATE(OUTFILE,NEXUS)
23
24#define RUN_IN_WINDOW(cmd)      ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; cmd ;arb_wait@@
25// Note: @@ will result in a single quote. see ../ARB_GDE/GDE_ParseMenu.cxx@WHY_USE_DOUBLE_AT
26
27#define STOP_ON_FAILURE(WHAT_FAILED) (arb_message "Error running WHAT_FAILED (inspect console for details)";false)
28// intended use '( command || STOP_ON_FAILURE(command-description)) && ( dependent-command || STOP_ON_FAILURE(dependent-command-description) && ...)'
29
30#include <warning.genmenu>
31
32menu:Export
33menumeta: E
34#include <export.genmenu>
35
36menu:Print
37menumeta: r
38#include <pretty_print.genmenu>
39
40menu:Import
41menumeta:I
42#include <import.genmenu>
43
44menu:Align
45menumeta:A
46#include <align.genmenu>
47
48menu:User
49menumeta:U
50#include <start_arb.genmenu>
51
52menu:SAI
53menumeta:S
54#include <dnamlrates.genmenu>
55
56menu:Incremental phylogeny
57menumeta:c
58#include <inc_fastdnaml.genmenu>
59
60menu:Phylogeny Distance Matrix
61menumeta:D
62#include <phylip_dist_org.genmenu>
63#include <phylip_dist.genmenu>
64
65menu:Phylogeny max. parsimony
66menumeta:p
67#include <phylip_pars.genmenu>
68
69menu:Phylogeny max. Likelyhood EXP
70menumeta:X
71#include <fastdnaml.genmenu>
72
73menu:Phylogeny max. Likelyhood
74menumeta:L
75#define RAXML_DNA
76#include <raxml.genmenu>
77#undef RAXML_DNA
78#include <raxml.genmenu>
79
80#define PHYML_DNA
81#include <phyml_20130708.genmenu>
82#undef PHYML_DNA
83#include <phyml_20130708.genmenu>
84
85#include <phyml.genmenu>
86
87#include <phylip_ml.genmenu>
88
89menu:Phylogeny (Other)
90menumeta:O
91#include <puzzle.genmenu>
92#include <desoete.genmenu>
93
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