Mercurial > repos > bcclaywell > microbiome_pplacer_suite
annotate util.sh @ 7:b6ece07bec6a draft
planemo upload commit 45906ba522c7c319067e93d5cd5d7161223c3336
| author | bcclaywell |
|---|---|
| date | Mon, 12 Oct 2015 15:59:59 -0400 |
| parents | d4690e65afcd |
| children |
| rev | line source |
|---|---|
| 0 | 1 #!/bin/bash |
| 2 | |
| 3 extify() { | |
| 4 local REQ_EXT=$1 | |
| 5 shift | |
| 6 | |
| 7 local OUTPUT="" | |
| 8 local FILE | |
| 9 for FILE in $*; do | |
| 10 local BASENAME=$(basename ${FILE}) | |
| 11 local EXT=${BASENAME##*.} | |
| 12 if [[ ${EXT} != ${REQ_EXT} ]]; then | |
| 13 local LINK="${BASENAME%%.*}.${REQ_EXT}" | |
| 14 if [[ ! -f ${LINK} ]]; then | |
| 15 ln -s ${FILE} ${LINK} | |
| 16 fi | |
| 17 FILE="${LINK}" | |
| 18 fi | |
| 19 OUTPUT="${OUTPUT} ${FILE}" | |
| 20 done | |
| 21 | |
| 22 echo ${OUTPUT} | |
| 23 } | |
| 24 | |
| 25 # from http://www.linuxjournal.com/content/use-date-command-measure-elapsed-time | |
| 26 timer() { | |
| 27 if [[ $# -eq 0 ]]; then | |
| 28 echo $(date '+%s') | |
| 29 else | |
| 30 local stime=$1 | |
| 31 etime=$(date '+%s') | |
| 32 | |
| 33 if [[ -z "$stime" ]]; then stime=$etime; fi | |
| 34 | |
| 35 dt=$((etime - stime)) | |
| 36 ds=$((dt % 60)) | |
| 37 dm=$(((dt / 60) % 60)) | |
| 38 dh=$((dt / 3600)) | |
| 39 printf '%d:%02d:%02d' $dh $dm $ds | |
| 40 fi | |
| 41 } | |
| 42 | |
| 43 on_exit() { | |
| 44 echo "Elapsed time: $(timer ${START_TIME})" | |
| 45 } | |
| 46 | |
| 47 set -eux | |
| 48 | |
|
7
b6ece07bec6a
planemo upload commit 45906ba522c7c319067e93d5cd5d7161223c3336
bcclaywell
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|
49 env > env.log |
| 0 | 50 |
| 51 START_TIME=$(timer) | |
| 52 trap on_exit EXIT |