| 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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