1 | // special conventions: |
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2 | // |
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3 | // * each external command ('itemmethod') runs in its separate directory under ~/.arb_tmp |
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4 | // * if sequences are exported ARB writes them in GenBank format into a tmpfile (e.g. sth like '/tmp/gde3170_0') |
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5 | // In 'itemmethod' every occurrence of 'TmpInputFile' (as specified at entry 'in:') is replaced by the name of that tempfile. |
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6 | // Some macros defined below expect that placeholder, i.e. always use 'TmpInputFile' for 'in:'! |
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7 | // * if sequences are (re-)imported, ARB prepares a temporary output-file. itemmethod shall use the placeholder 'TmpOutputFile' |
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8 | // to generate its content. Always use 'TmpOutputFile' for 'out:'. |
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9 | // Do not remove TmpOutputFile using RM_LOCAL_FILES. It is expected and will be removed by ARB_GDE (after command termination). |
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10 | // * 'arg:DISPLAY_FUNC' shall be a single command (to be chainable with && in itemmethod) |
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11 | |
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12 | // GOTO_LOCAL_DIR and RM_LOCAL_FILES need to be used on top-script level |
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13 | // (opening sub-shells might change value of $$) |
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14 | |
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15 | #define GOTO_LOCAL_DIR mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ |
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16 | #define RM_LOCAL_FILES(FILES) GOTO_LOCAL_DIR ; cd .. ; rm -rf $$ |
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17 | |
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18 | #define GENERATE(OUTFILE,FORMAT) arb_convert_aln --arb-notify -GenBank TmpInputFile -FORMAT OUTFILE |
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19 | |
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20 | #define GEN_PHYLIP(OUTFILE) GENERATE(OUTFILE,phylip) |
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21 | #define GEN_FASTDNAML(OUTFILE) GENERATE(OUTFILE,fastdnaml) |
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22 | #define GEN_NEXUS(OUTFILE) GENERATE(OUTFILE,NEXUS) |
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23 | |
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24 | #define TEE_TO(cmd,log) ( cmd 2>&1 ) | tee log |
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25 | |
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26 | #define RUN_IN_WINDOW_TO_LOG(cmd,log) ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; TEE_TO(cmd,log); arb_wait@@ |
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27 | #define RUN_IN_WINDOW(cmd) RUN_IN_WINDOW_TO_LOG(cmd,win_$AGDE_JOBID.log); arb_catlog win_$AGDE_JOBID.log |
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28 | // Note: @@ will result in a single quote. see ../ARB_GDE/GDE_ParseMenu.cxx@WHY_USE_DOUBLE_AT |
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29 | // $AGDE_JOBID differs between calls and gets derived from item-entry |
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30 | |
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31 | #define STOP_ON_FAILURE(WHAT_FAILED) (arb_message "Error running WHAT_FAILED (inspect console for details)";false) |
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32 | // intended use '( command || STOP_ON_FAILURE(command-description)) && ( dependent-command || STOP_ON_FAILURE(dependent-command-description) && ...)' |
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33 | |
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34 | #include <warning.genmenu> |
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35 | |
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36 | // ---------------------------------------- |
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37 | menu:Export |
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38 | menumeta: E |
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39 | #include <export.genmenu> |
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40 | |
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41 | // ---------------------------------------- |
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42 | menu:Print |
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43 | menumeta: r |
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44 | #include <pretty_print.genmenu> |
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45 | |
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46 | #include <sativa.genmenu> |
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47 | |
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48 | // ---------------------------------------- |
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49 | menu:Import |
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50 | menumeta:I |
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51 | #include <import.genmenu> |
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52 | |
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53 | // ---------------------------------------- |
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54 | menu:Align |
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55 | menumeta:A |
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56 | #include <align.genmenu> |
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57 | |
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58 | // ---------------------------------------- |
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59 | menu:SAI |
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60 | menumeta:S |
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61 | #include <dnamlrates.genmenu> |
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62 | |
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63 | // ---------------------------------------- |
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64 | menu:Incremental phylogeny |
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65 | menumeta:c |
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66 | #include <inc_fastdnaml.genmenu> |
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67 | |
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68 | // ---------------------------------------- |
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69 | menu:Phylogeny Distance Matrix |
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70 | menumeta:D |
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71 | #include <phylip_dist_org.genmenu> |
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72 | #include <phylip_dist.genmenu> |
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73 | |
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74 | // ---------------------------------------- |
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75 | menu:Phylogeny max. parsimony |
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76 | menumeta:p |
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77 | #include <phylip_pars.genmenu> |
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78 | |
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79 | // ---------------------------------------- |
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80 | menu:Phylogeny max. Likelihood EXP |
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81 | menumeta:X |
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82 | #include <fastdnaml.genmenu> |
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83 | |
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84 | // ---------------------------------------- |
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85 | menu:Phylogeny max. Likelihood |
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86 | menumeta:L |
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87 | |
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88 | #define RAXML_NUC |
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89 | #include <raxml7.genmenu> |
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90 | #undef RAXML_NUC |
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91 | #include <raxml7.genmenu> |
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92 | |
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93 | #define PHYML_NUC |
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94 | #include <phyml_20130708.genmenu> |
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95 | #undef PHYML_NUC |
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96 | #include <phyml_20130708.genmenu> |
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97 | |
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98 | #include <phyml.genmenu> |
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99 | #include <phylip_ml.genmenu> |
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100 | |
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101 | #include <raxml8.genmenu> |
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102 | |
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103 | // ---------------------------------------- |
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104 | menu:Phylogeny (Other) |
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105 | menumeta:O |
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106 | |
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107 | #define FASTTREE_NUC |
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108 | #include <fasttree.genmenu> |
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109 | #undef FASTTREE_NUC |
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110 | #include <fasttree.genmenu> |
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111 | |
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112 | #include <mrbayes.genmenu> |
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113 | #include <puzzle.genmenu> |
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114 | #include <desoete.genmenu> |
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115 | |
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116 | // ---------------------------------------- |
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117 | // custom menu 'User' is loaded into 'Tools'-menu |
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118 | // (has no members by default; meant to be used from custom .menu definitions) |
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119 | menu:User |
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120 | menumeta:U |
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121 | |
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