| 1 | #!/bin/bash |
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| 2 | set -e |
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| 3 | |
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| 4 | BASES_PER_THREAD=300 |
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| 5 | SELF=`basename "$0"` |
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| 6 | |
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| 7 | # set up environment |
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| 8 | if [ -z "$ARB_LIBRARY_PATH" ]; then |
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| 9 | # special handling for standalone use |
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| 10 | if [ -z "$LD_LIBRARY_PATH" ]; then |
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| 11 | LD_LIBRARY_PATH="$ARBHOME/lib" |
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| 12 | else |
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| 13 | LD_LIBRARY_PATH="$ARBHOME/lib:$LD_LIBRARY_PATH" |
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| 14 | fi |
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| 15 | else |
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| 16 | # normal arb integration; compare to ../../GDEHELP/ARB_GDEmenus.source@RUN_IN_WINDOW |
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| 17 | LD_LIBRARY_PATH="${ARB_LIBRARY_PATH}" |
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| 18 | fi |
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| 19 | export LD_LIBRARY_PATH |
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| 20 | |
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| 21 | # always wait on exit |
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| 22 | # called at exit of script (by trap) and on error |
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| 23 | # e.g. if ctrl-c is pressed |
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| 24 | wait_and_exit() { |
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| 25 | # do not recurse |
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| 26 | trap EXIT |
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| 27 | |
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| 28 | # kill any backgrounded processes |
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| 29 | local JOBS=`jobs -r` |
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| 30 | if [ -n "${JOBS}" ]; then |
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| 31 | read -p "Press ENTER to terminate child processes and close window" |
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| 32 | local JOBPIDS=`jobs -p` |
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| 33 | kill ${JOBPIDS} |
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| 34 | else |
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| 35 | read -p "Press ENTER to close window" |
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| 36 | fi |
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| 37 | exit |
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| 38 | } |
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| 39 | |
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| 40 | on_exit() { |
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| 41 | wait_and_exit |
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| 42 | } |
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| 43 | trap on_exit EXIT |
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| 44 | |
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| 45 | # return true if argument is file in path executable by user |
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| 46 | can_run() { |
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| 47 | which "$1" &>/dev/null && test -x `which "$1" &>/dev/null` |
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| 48 | } |
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| 49 | |
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| 50 | # show error in ARB and exit |
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| 51 | report_error() { |
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| 52 | echo "ARB ERROR: $*" |
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| 53 | arb_message "$SELF failed with: $*" |
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| 54 | wait_and_exit |
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| 55 | } |
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| 56 | |
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| 57 | # create named temporary directory |
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| 58 | prepare_tmp_dir() { |
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| 59 | ARB_TMP="$HOME/.arb_tmp" |
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| 60 | NAME="$1" |
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| 61 | DATE=`date +%Y-%m-%d--%H-%M-%S` |
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| 62 | for N in "" ".2" ".3" ".4"; do |
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| 63 | DIR="$ARB_TMP/$NAME--$DATE$N" |
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| 64 | if [ -e "$DIR" ]; then |
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| 65 | continue; |
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| 66 | else |
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| 67 | mkdir -p "$DIR" |
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| 68 | echo "$DIR" |
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| 69 | return |
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| 70 | fi |
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| 71 | done |
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| 72 | report_error "Unable to create temporary directory" |
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| 73 | } |
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| 74 | |
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| 75 | dump_features() { |
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| 76 | case `uname` in |
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| 77 | Darwin) |
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| 78 | sysctl machdep.cpu.features |
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| 79 | ;; |
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| 80 | Linux) |
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| 81 | grep -m1 flags /proc/cpuinfo 2>/dev/null |
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| 82 | ;; |
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| 83 | esac |
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| 84 | } |
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| 85 | cpu_has_feature() { |
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| 86 | dump_features | grep -qi "$1" &>/dev/null |
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| 87 | } |
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| 88 | |
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| 89 | cpu_get_cores() { |
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| 90 | # honor Torque/PBS num processes (or make sure we follow, if enforced) |
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| 91 | if [ ! -z "$PBS_NP" ]; then |
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| 92 | echo "$PBS_NP" |
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| 93 | return |
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| 94 | fi |
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| 95 | # extract physical CPUs from host |
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| 96 | case `uname` in |
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| 97 | Darwin) |
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| 98 | sysctl -n hw.ncpu |
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| 99 | ;; |
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| 100 | Linux) |
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| 101 | grep -c "^processor" /proc/cpuinfo |
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| 102 | ;; |
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| 103 | esac |
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| 104 | } |
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| 105 | |
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| 106 | extract_line_suffix() { |
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| 107 | local LOG="$1" |
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| 108 | local PREFIX="$2" |
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| 109 | perl -e "while (<>) { if (/^${PREFIX}\s*/) { print $'; } }" <"$LOG" |
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| 110 | } |
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| 111 | |
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| 112 | extract_likelihood() { |
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| 113 | local LOG="$1" |
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| 114 | local PREFIX="$2" |
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| 115 | local SUFFIX="`extract_line_suffix $LOG $PREFIX`" |
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| 116 | if [ -z "$SUFFIX" ]; then |
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| 117 | local FAILED_DETECTION="failed to detect likelyhood" |
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| 118 | echo $FAILED_DETECTION |
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| 119 | arb_message "$SELF warning: $FAILED_DETECTION" |
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| 120 | else |
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| 121 | echo "$SUFFIX" |
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| 122 | fi |
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| 123 | } |
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| 124 | |
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| 125 | TREEFILE=arb_export.tree |
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| 126 | |
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| 127 | export_input_tree() { |
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| 128 | # expect user selected an 'Input tree' in arb and export it to $TREEFILE |
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| 129 | if [ -z "$INPUTTREE" ]; then |
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| 130 | report_error "you have to select an 'Input tree'" |
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| 131 | fi |
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| 132 | |
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| 133 | arb_export_tree "$INPUTTREE" > "$TREEFILE" |
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| 134 | } |
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| 135 | |
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| 136 | # -------------------------- |
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| 137 | # protocols helpers |
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| 138 | |
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| 139 | bootstrap_and_consenseIfReq() { |
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| 140 | # run $BOOTSTRAP BS searches |
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| 141 | $RAXML -b "$SEED" -m "$MODEL" -p "$SEED" -s "$SEQFILE" \ |
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| 142 | -N "$BOOTSTRAPS" \ |
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| 143 | -n BOOTSTRAP |
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| 144 | |
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| 145 | if [ -n "$MRE" ]; then |
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| 146 | # compute extended majority rule consensus tree |
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| 147 | $RAXML -J MRE -m "$MODEL" -z RAxML_bootstrap.BOOTSTRAP -n BOOTSTRAP_CONSENSUS |
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| 148 | fi |
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| 149 | } |
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| 150 | |
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| 151 | bootstrapAsyncIfRequested_and_wait() { |
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| 152 | if [ "$BOOTSTRAPS" != "no" ]; then |
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| 153 | if [ "$TRY_ASYNC" = "1" ]; then |
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| 154 | if [ $(($THREADS * 2)) -gt $CORES ]; then |
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| 155 | # wait for raxml (started by caller) to complete, |
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| 156 | # if we have not enough cores to run bootstrap search at the same time |
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| 157 | sleep 4 # just cosmetic (raxml output goes 1st) |
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| 158 | echo "Note: Not enough cores found ($CORES) to run ML search and" |
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| 159 | echo " BS in parallel with $THREADS threads. Waiting..." |
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| 160 | wait |
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| 161 | fi |
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| 162 | else |
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| 163 | # otherwise always sync silently |
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| 164 | wait |
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| 165 | fi |
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| 166 | bootstrap_and_consenseIfReq & |
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| 167 | fi |
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| 168 | wait # for all jobs |
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| 169 | } |
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| 170 | |
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| 171 | import_trees() { |
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| 172 | local TPREFIX="$1" |
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| 173 | local RUN="$2" |
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| 174 | local COMMENT="$3" |
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| 175 | |
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| 176 | local MAINTREE="${TPREFIX}.${RUN}" |
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| 177 | # imports tree MAINTREE |
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| 178 | # - with support values (if bootstrapping requested) |
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| 179 | # - else "as is" |
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| 180 | # imports MRE tree (if requested) |
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| 181 | |
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| 182 | if [ "$BOOTSTRAPS" != "no" ]; then |
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| 183 | # draw bipartition information |
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| 184 | $RAXML -f b -m "$MODEL" \ |
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| 185 | -t "${TPREFIX}.${RUN}" \ |
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| 186 | -z RAxML_bootstrap.BOOTSTRAP \ |
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| 187 | -n "${RUN}_WITH_SUPPORT" |
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| 188 | |
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| 189 | MAINTREE="RAxML_bipartitions.${RUN}_WITH_SUPPORT" |
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| 190 | COMMENT="${COMMENT} BOOTSTRAPS=${BOOTSTRAPS}" |
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| 191 | fi |
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| 192 | |
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| 193 | arb_read_tree "${TREENAME}" "${MAINTREE}" "${COMMENT}" |
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| 194 | |
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| 195 | if [ -n "$MRE" ]; then |
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| 196 | if [ "$BOOTSTRAPS" != "no" ]; then |
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| 197 | # otherwise no MRE tree possible |
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| 198 | arb_read_tree "${TREENAME}_mre" RAxML_MajorityRuleExtendedConsensusTree.BOOTSTRAP_CONSENSUS \ |
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| 199 | "PRG=RAxML8 MRE consensus tree of $BOOTSTRAPS bootstrap searches performed for species in ${TREENAME}" |
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| 200 | fi |
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| 201 | fi |
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| 202 | } |
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| 203 | |
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| 204 | # ------------------- |
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| 205 | # protocols |
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| 206 | |
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| 207 | dna_tree_thorough() { |
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| 208 | # do $REPEATS searches for best ML tree |
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| 209 | $RAXML -f d -m "$MODEL" -p "$SEED" -s "$SEQFILE" \ |
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| 210 | -N "$REPEATS" \ |
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| 211 | -n TREE_INFERENCE & |
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| 212 | |
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| 213 | bootstrapAsyncIfRequested_and_wait |
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| 214 | |
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| 215 | LIKELIHOOD=`extract_likelihood RAxML_info.TREE_INFERENCE 'Final\s*GAMMA-based\s*Score\s*of\s*best\s*tree'` |
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| 216 | import_trees RAxML_bestTree TREE_INFERENCE "PRG=RAxML8 FILTER=$FILTER DIST=$MODEL LIKELIHOOD=${LIKELIHOOD} PROTOCOL=thorough" |
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| 217 | } |
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| 218 | |
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| 219 | dna_tree_quick() { |
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| 220 | if [ "$BOOTSTRAPS" = "no" ]; then |
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| 221 | report_error You have to select the number of bootstraps to perform |
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| 222 | fi |
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| 223 | |
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| 224 | # run fast bootstraps |
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| 225 | $RAXML -f a -m "$MODEL" -p "$SEED" -x "$SEED" -s "$SEQFILE" \ |
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| 226 | -N "$BOOTSTRAPS" \ |
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| 227 | -n FAST_BS |
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| 228 | |
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| 229 | # import |
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| 230 | LIKELIHOOD=`extract_likelihood RAxML_info.FAST_BS 'Final\s*ML\s*Optimization\s*Likelihood:'` |
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| 231 | arb_read_tree ${TREENAME} RAxML_bipartitions.FAST_BS "PRG=RAxML8 FILTER=$FILTER DIST=$MODEL LIKELIHOOD=${LIKELIHOOD} PROTOCOL=quick" |
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| 232 | |
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| 233 | # create consensus tree |
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| 234 | if [ -n "$MRE" ]; then |
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| 235 | $RAXML -J MRE -m "$MODEL" -z RAxML_bootstrap.FAST_BS -n FAST_BS_MAJORITY |
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| 236 | # import |
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| 237 | arb_read_tree ${TREENAME}_mre RAxML_MajorityRuleExtendedConsensusTree.FAST_BS_MAJORITY \ |
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| 238 | "PRG=RAxML8 MRE consensus tree of $BOOTSTRAPS rapid-bootstraps performed while calculating ${TREENAME}" |
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| 239 | fi |
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| 240 | } |
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| 241 | |
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| 242 | dna_tree_add() { |
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| 243 | export_input_tree |
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| 244 | |
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| 245 | $RAXML -f d -m "$MODEL" -p "$SEED" -s "$SEQFILE" \ |
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| 246 | -g "$TREEFILE" \ |
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| 247 | -n ADD & |
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| 248 | |
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| 249 | bootstrapAsyncIfRequested_and_wait |
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| 250 | |
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| 251 | LIKELIHOOD=`extract_likelihood RAxML_info.ADD 'Final\s*GAMMA-based\s*Score\s*of\s*best\s*tree'` |
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| 252 | import_trees RAxML_bestTree ADD "PRG=RAxML8 FILTER=$FILTER DIST=$MODEL LIKELIHOOD=${LIKELIHOOD} PROTOCOL=add INPUTTREE=$INPUTTREE" |
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| 253 | } |
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| 254 | |
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| 255 | dna_tree_optimize() { |
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| 256 | export_input_tree |
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| 257 | |
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| 258 | $RAXML -f t -m "$MODEL" -p "$SEED" -s "$SEQFILE" \ |
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| 259 | -N "$REPEATS" \ |
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| 260 | -t "$TREEFILE" \ |
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| 261 | -n OPTIMIZE & |
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| 262 | |
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| 263 | bootstrapAsyncIfRequested_and_wait |
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| 264 | |
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| 265 | LIKELIHOOD=`extract_likelihood RAxML_info.OPTIMIZE 'Final\s*GAMMA-based\s*Score\s*of\s*best\s*tree'` |
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| 266 | import_trees RAxML_bestTree OPTIMIZE "PRG=RAxML8 FILTER=$FILTER DIST=$MODEL LIKELIHOOD=${LIKELIHOOD} PROTOCOL=optimize INPUTTREE=$INPUTTREE" |
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| 267 | } |
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| 268 | |
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| 269 | dna_tree_calcblen() { |
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| 270 | export_input_tree |
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| 271 | |
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| 272 | $RAXML -f e -m "$MODEL" -s "$SEQFILE" \ |
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| 273 | -t "$TREEFILE" \ |
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| 274 | -n CALCBLEN & |
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| 275 | |
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| 276 | bootstrapAsyncIfRequested_and_wait |
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| 277 | |
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| 278 | LIKELIHOOD=`extract_likelihood RAxML_info.CALCBLEN 'Final\s*GAMMA\s*likelihood:'` |
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| 279 | import_trees RAxML_result CALCBLEN "PRG=RAxML8 FILTER=$FILTER DIST=$MODEL LIKELIHOOD=${LIKELIHOOD} PROTOCOL=calcblen INPUTTREE=$INPUTTREE" |
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| 280 | } |
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| 281 | |
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| 282 | dna_tree_bootstrap() { |
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| 283 | if [ "$BOOTSTRAPS" = "no" ]; then |
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| 284 | report_error You have to select the number of bootstraps to perform |
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| 285 | fi |
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| 286 | |
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| 287 | export_input_tree |
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| 288 | bootstrapAsyncIfRequested_and_wait |
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| 289 | import_trees arb_export tree "PRG=RAxML8 FILTER=$FILTER DIST=$MODEL PROTOCOL=bootstrap INPUTTREE=$INPUTTREE" |
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| 290 | } |
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| 291 | |
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| 292 | dna_tree_score() { |
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| 293 | export_input_tree |
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| 294 | |
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| 295 | $RAXML -f n -m $MODEL -s "$SEQFILE" \ |
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| 296 | -z "$TREEFILE" \ |
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| 297 | -n SCORE |
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| 298 | |
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| 299 | RESULT=`extract_likelihood RAxML_info.SCORE 'Tree\s*0\s*Likelihood'` |
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| 300 | # RESULT contains sth like: -27819.642837 Tree-Length 6.899222 |
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| 301 | LIKELIHOOD=${RESULT/ Tree-Length */} |
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| 302 | TREELEN=${RESULT/* Tree-Length /} |
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| 303 | |
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| 304 | arb_write_tree_comment $INPUTTREE "RAxML8-score: FILTER=$FILTER DIST=$MODEL LIKELIHOOD=$LIKELIHOOD TREELEN=$TREELEN" |
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| 305 | } |
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| 306 | |
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| 307 | # -------------- |
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| 308 | # main |
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| 309 | |
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| 310 | MRE=Y |
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| 311 | TREENAME=raxml |
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| 312 | FILTER=unknown |
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| 313 | INPUTTREE= |
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| 314 | |
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| 315 | while [ -n "$1" ]; do |
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| 316 | case "$1" in |
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| 317 | -p) # protocol |
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| 318 | PROTOCOL="$2" |
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| 319 | shift |
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| 320 | ;; |
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| 321 | -m) # subst model |
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| 322 | MODEL="$2" |
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| 323 | shift |
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| 324 | ;; |
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| 325 | -s) # random seed |
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| 326 | SEED="$2" |
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| 327 | shift |
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| 328 | ;; |
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| 329 | -b) # bootstraps |
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| 330 | BOOTSTRAPS="$2" |
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| 331 | shift |
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| 332 | ;; |
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| 333 | -r) # number of tree searches |
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| 334 | REPEATS="$2" |
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| 335 | shift |
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| 336 | ;; |
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| 337 | -n) # tree name |
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| 338 | TREENAME="$2" |
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| 339 | shift |
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| 340 | ;; |
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| 341 | -nomre) # don't create mre tree |
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| 342 | MRE= |
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| 343 | ;; |
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| 344 | -nt) # seqtype dna |
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| 345 | SEQTYPE=N |
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| 346 | ;; |
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| 347 | -aa) # seqtype proto |
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| 348 | SEQTYPE=A |
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| 349 | ;; |
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| 350 | -f) # input file |
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| 351 | FILE="$2" |
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| 352 | shift |
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| 353 | ;; |
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| 354 | -t) # threads |
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| 355 | THREADS="$2" |
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| 356 | shift |
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| 357 | ;; |
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| 358 | -it) # inputtree |
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| 359 | INPUTTREE="$2" |
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| 360 | if [ "$INPUTTREE" = 'tree_?????' ]; then # has to match ../../TEMPLATES/arb_global_defs.h@NO_TREE_SELECTED |
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| 361 | INPUTTREE= |
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| 362 | fi |
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| 363 | shift |
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| 364 | ;; |
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| 365 | -fi) # filtername for comment |
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| 366 | FILTER="$2" |
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| 367 | shift |
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| 368 | ;; |
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| 369 | *) |
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| 370 | report_error argument not understood: "$1" |
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| 371 | ;; |
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| 372 | esac |
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| 373 | shift |
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| 374 | done |
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| 375 | |
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| 376 | # correct output treename (ensure prefix 'tree_', avoid things like 'tree_tree' etc) |
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| 377 | TREENAME="${TREENAME##tree}" |
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| 378 | TREENAME="${TREENAME#_}" |
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| 379 | TREENAME="${TREENAME#_}" |
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| 380 | TREENAME="tree_${TREENAME}" |
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| 381 | |
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| 382 | # use time as random SEED if empty |
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| 383 | if [ -z "$SEED" ]; then |
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| 384 | # seconds since 1970 |
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| 385 | SEED=`date +%s` |
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| 386 | fi |
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| 387 | |
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| 388 | # prepare data in tempdir |
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| 389 | DIR="`prepare_tmp_dir raxml`" |
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| 390 | SEQFILE="dna.phy" |
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| 391 | FULLSEQFILE="${DIR}/${SEQFILE}" |
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| 392 | |
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| 393 | arb_convert_aln --arb-notify -GenBank "$FILE" -phylip "${FULLSEQFILE}" 2>&1 |\ |
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| 394 | grep -v "^WARNING(14): LOCUS" || true # remove spurious warning |
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| 395 | rm "$FILE" |
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| 396 | |
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| 397 | cd "$DIR" |
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| 398 | |
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| 399 | # decide whether async execution of BS and main algo makes sense (ie. runtimes of both are expected similar) |
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| 400 | TRY_ASYNC=0 |
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| 401 | case "${PROTOCOL}" in |
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| 402 | (thorough|optimize) |
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| 403 | if [ "$BOOTSTRAPS" != "no" ]; then |
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| 404 | TRY_ASYNC=1 |
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| 405 | fi |
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| 406 | ;; |
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| 407 | esac |
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| 408 | |
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| 409 | # select RAxML binary |
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| 410 | if cpu_has_feature avx && can_run raxmlHPC8-AVX.PTHREADS; then |
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| 411 | RAXML=raxmlHPC8-AVX.PTHREADS |
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| 412 | elif cpu_has_feature sse3 && can_run raxmlHPC8-SSE3.PTHREADS; then |
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| 413 | RAXML=raxmlHPC8-SSE3.PTHREADS |
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| 414 | elif can_run raxmlHPC8-PTHREADS; then |
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| 415 | RAXML=raxmlHPC8-PTHREADS |
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| 416 | else |
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| 417 | report_error Could not find working RAxML binary. |
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| 418 | fi |
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| 419 | |
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| 420 | # get some numbers |
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| 421 | CORES=`cpu_get_cores` |
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| 422 | read NSEQS BP_ARB < <(head -n 1 $SEQFILE) |
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| 423 | |
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| 424 | # retrieve number of alignment patterns recognized by RAxML |
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| 425 | $RAXML -T 2 -f j -s "$SEQFILE" -b 123 -N 1 -m "$MODEL" -n PATTERNS |
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| 426 | BP=`extract_line_suffix RAxML_info.PATTERNS "Alignment Patterns:"` |
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| 427 | |
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| 428 | # warn if model is not recommended for given number of sequences |
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| 429 | BAD_PRACTICE="This is not considered good practice.\nPlease refer to the RAxML manual for details." |
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| 430 | if [ "$MODEL" == "GTRGAMMA" -a "$NSEQS" -gt 10000 ]; then |
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| 431 | arb_message "Using the GTRGAMMA model on more than 10,000 sequences.\n$BAD_PRACTICE" |
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| 432 | fi |
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| 433 | if [ "$MODEL" == "GTRCAT" -a "$NSEQS" -lt 150 ]; then |
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| 434 | arb_message "Using the GTRCAT model on less than 150 sequences.\n$BAD_PRACTICE" |
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| 435 | fi |
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| 436 | |
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| 437 | # ----------------------------------- |
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| 438 | # threads / cores detection |
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| 439 | |
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| 440 | CORES=$(( $CORES + 1 - 1 )) |
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| 441 | # calculate number of threads (if not passed) |
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| 442 | MAX_THREADS=$(( ( $BP - 1 ) / $BASES_PER_THREAD + 2)) |
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| 443 | # +1 is for master thread, |
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| 444 | # another +1 for the first $BASES_PER_THREAD (bash truncates); -1 to avoid extra thread if BP is divisible by BASES_PER_THREAD |
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| 445 | |
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| 446 | if [ "$CORES" -lt 1 ]; then |
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| 447 | # failed to detect CORES |
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| 448 | SETENVAR_HINT="set the environment variable PBS_NP to the number of cores available (before you start arb)" |
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| 449 | if [ -z "$THREADS" ]; then |
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| 450 | report_error "failed to detect number of cores.\nPlease specify 'CPU thread override' or\n${SETENVAR_HINT}." |
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| 451 | else |
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| 452 | CORES=$THREADS |
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| 453 | if [ "$TRY_ASYNC" = "1" ]; then |
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| 454 | echo "Warning: failed to detect number of cores (assuming ${CORES} from 'CPU thread override')" |
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| 455 | echo "Please ${SETENVAR_HINT}." |
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| 456 | else |
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| 457 | arb_message "Warning: failed to detect number of cores\n=> parallel bootstrapping disabled\nPlease ${SETENVAR_HINT} to avoid that." |
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| 458 | fi |
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| 459 | fi |
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| 460 | else |
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| 461 | MAX_TH_NOTE="maximum useful thread-count for alignment with ${BP} bp would be ${MAX_THREADS}" |
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| 462 | if [ -z "$THREADS" ]; then |
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| 463 | if [ "$CORES" -lt "$MAX_THREADS" ]; then |
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| 464 | echo "Note: Limiting threads to $CORES available cores (${MAX_TH_NOTE})" |
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| 465 | THREADS=$CORES |
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| 466 | else |
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| 467 | THREADS=$MAX_THREADS |
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| 468 | if [ "$TRY_ASYNC" = "1" ]; then |
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| 469 | if [ "$(($THREADS * 2))" -gt "$CORES" ]; then |
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| 470 | # split threads between BS and ML search |
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| 471 | if [ "$((($THREADS-1) * 2))" -le "$CORES" ]; then |
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| 472 | THREADS=$(($THREADS-1)) |
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| 473 | else |
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| 474 | if [ "$((($THREADS-2) * 2))" -le "$CORES" ]; then |
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| 475 | THREADS=$(($THREADS-2)) |
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| 476 | fi |
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| 477 | fi |
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| 478 | fi |
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| 479 | if [ "$THREADS" -lt "$MAX_THREADS" ]; then |
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| 480 | arb_message "Note: reduced threads to $THREADS to allow parallel execution of bootstrapping\nset 'CPU thread override' to ${MAX_THREADS} to avoid that" |
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| 481 | fi |
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| 482 | fi |
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| 483 | fi |
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| 484 | if [ "$THREADS" -lt 2 ]; then |
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| 485 | # use at least 2 threads (required by PTHREADS version) |
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| 486 | THREADS=2 |
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| 487 | fi |
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| 488 | else |
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| 489 | echo "Note: Threads forced to ${THREADS} (${MAX_TH_NOTE})" |
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| 490 | fi |
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| 491 | fi |
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| 492 | |
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| 493 | if [ "$CORES" -lt "$THREADS" ]; then |
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| 494 | arb_message "Performance-Warning: Using $THREADS threads on $CORES cores" |
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| 495 | fi |
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| 496 | |
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| 497 | RAXML="$RAXML -T $THREADS" |
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| 498 | |
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| 499 | case "${SEQTYPE}.${PROTOCOL}" in |
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| 500 | N.thorough) |
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| 501 | time dna_tree_thorough |
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| 502 | ;; |
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| 503 | N.quick) |
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| 504 | time dna_tree_quick |
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| 505 | ;; |
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| 506 | N.add) |
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| 507 | time dna_tree_add |
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| 508 | ;; |
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| 509 | N.optimize) |
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| 510 | time dna_tree_optimize |
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| 511 | ;; |
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| 512 | N.calcblen) |
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| 513 | time dna_tree_calcblen |
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| 514 | ;; |
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| 515 | N.bootstrap) |
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| 516 | time dna_tree_bootstrap |
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| 517 | ;; |
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| 518 | N.score) |
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| 519 | time dna_tree_score |
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| 520 | ;; |
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| 521 | *) |
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| 522 | report_error Unknown protocol "${SEQTYPE}.${PROTOCOL}" |
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| 523 | ;; |
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| 524 | esac |
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| 525 | |
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| 526 | # @@@ FIXME: cleanup temp dir |
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| 527 | |
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| 528 | exit |
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