Mercurial > repos > bcclaywell > argo_navis

annotate util.sh @ 0:d67268158946 draft

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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1 #!/bin/bash
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2
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3 extify() {
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4 local REQ_EXT=$1
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5 shift
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6
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7 local OUTPUT=""
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8 local FILE
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9 for FILE in $*; do
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10 local BASENAME=$(basename ${FILE})
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11 local EXT=${BASENAME##*.}
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12 if [[ ${EXT} != ${REQ_EXT} ]]; then
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13 local LINK="${BASENAME%%.*}.${REQ_EXT}"
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14 if [[ ! -f ${LINK} ]]; then
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15 ln -s ${FILE} ${LINK}
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16 fi
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17 FILE="${LINK}"
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18 fi
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19 OUTPUT="${OUTPUT} ${FILE}"
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20 done
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21
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22 echo ${OUTPUT}
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23 }
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24
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25 # from http://www.linuxjournal.com/content/use-date-command-measure-elapsed-time
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26 timer() {
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27 if [[ $# -eq 0 ]]; then
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28 echo $(date '+%s')
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29 else
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30 local stime=$1
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31 etime=$(date '+%s')
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32
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33 if [[ -z "$stime" ]]; then stime=$etime; fi
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34
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35 dt=$((etime - stime))
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36 ds=$((dt % 60))
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37 dm=$(((dt / 60) % 60))
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38 dh=$((dt / 3600))
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39 printf '%d:%02d:%02d' $dh $dm $ds
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40 fi
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41 }
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42
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43 on_exit() {
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44 echo "Elapsed time: $(timer ${START_TIME})"
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45 }
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46
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47 set -eux
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48
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49 START_TIME=$(timer)
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50 trap on_exit EXIT
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51
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52 # Custom to this tool; add the bin directory of the argo navis tool to path, and create an accessor for data
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53 # in it
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54 export ARGO_TOOL_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
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55 export PATH=$ARGO_TOOL_DIR/bin:$PATH