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bash-wrapper-gcp.txt
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bash-wrapper-gcp.txt
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#!/bin/bash
# NEXTFLOW TASK: Hello 1
set -e
set -u
NXF_DEBUG=${NXF_DEBUG:=0}; [[ $NXF_DEBUG > 1 ]] && set -x
NXF_ENTRY=${1:-nxf_main}
# bash helper functions
nxf_cp_retry() {
local max_attempts=1
local timeout=10
local attempt=0
local exitCode=0
while (( $attempt < $max_attempts ))
do
if "$@"
then
return 0
else
exitCode=$?
fi
if [[ $exitCode == 0 ]]
then
break
fi
nxf_sleep $timeout
attempt=$(( attempt + 1 ))
timeout=$(( timeout * 2 ))
done
}
nxf_parallel() {
IFS=$'\n'
local cmd=("$@")
local cpus=$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
local max=$(if (( cpus>4 )); then echo 4; else echo $cpus; fi)
local i=0
local pid=()
(
set +u
while ((i<${#cmd[@]})); do
local copy=()
for x in "${pid[@]}"; do
[[ -e /proc/$x ]] && copy+=($x)
done
pid=("${copy[@]}")
if ((${#pid[@]}>=$max)); then
nxf_sleep 0.2
else
eval "${cmd[$i]}" &
pid+=($!)
((i+=1))
fi
done
for p in "${pid[@]}"; do
wait $p
done
)
unset IFS
}
# google storage helper
gs_opts=('-q' '-m' '-o' 'GSUtil:parallel_thread_count=1' '-o' 'GSUtil:sliced_object_download_max_components=8')
nxf_gs_download() {
local source=$1
local target=$2
local project=$3
local basedir=$(dirname $2)
local ret
local opts=("${gs_opts[@]}")
if [[ $project ]]; then
opts+=('-u' "$project")
fi
## download assuming it's a file download
mkdir -p $basedir
ret=$(gsutil ${opts[@]} cp "$source" "$target" 2>&1) || {
## if fails check if it was trying to download a directory
mkdir $target
gsutil ${opts[@]} cp -R "$source/*" "$target" || {
rm -rf $target
>&2 echo "Unable to download path: $source"
exit 1
}
}
}
nxf_gs_upload() {
local name=$1
local target=$2
gsutil ${gs_opts[@]} cp -R "$name" "$target/$name"
}
nxf_sleep() {
sleep $1 2>/dev/null || sleep 1;
}
nxf_date() {
local ts=$(date +%s%3N);
if [[ ${#ts} == 10 ]]; then echo ${ts}000
elif [[ $ts == *%3N ]]; then echo ${ts/\%3N/000}
elif [[ $ts == *3N ]]; then echo ${ts/3N/000}
elif [[ ${#ts} == 13 ]]; then echo $ts
else echo "Unexpected timestamp value: $ts"; exit 1
fi
}
nxf_env() {
echo '============= task environment ============='
env | sort | sed "s/\(.*\)AWS\(.*\)=\(.\{6\}\).*/\1AWS\2=\3xxxxxxxxxxxxx/"
echo '============= task output =================='
}
nxf_kill() {
declare -a children
while read P PP;do
children[$PP]+=" $P"
done < <(ps -e -o pid= -o ppid=)
kill_all() {
[[ $1 != $$ ]] && kill $1 2>/dev/null || true
for i in ${children[$1]:=}; do kill_all $i; done
}
kill_all $1
}
nxf_mktemp() {
local base=${1:-/tmp}
if [[ $(uname) = Darwin ]]; then mktemp -d $base/nxf.XXXXXXXXXX
else TMPDIR="$base" mktemp -d -t nxf.XXXXXXXXXX
fi
}
on_exit() {
exit_status=${nxf_main_ret:=$?}
printf $exit_status > {{folder}}/.exitcode
set +u
[[ "$tee1" ]] && kill $tee1 2>/dev/null
[[ "$tee2" ]] && kill $tee2 2>/dev/null
[[ "$ctmp" ]] && rm -rf $ctmp || true
exit $exit_status
}
on_term() {
set +e
[[ "$pid" ]] && nxf_kill $pid
}
nxf_launch() {
/bin/bash -ue {{folder}}/.command.sh
}
nxf_stage() {
true
# stage input files
echo start | gsutil -q cp -c - gs://bucket/work/dir/.command.begin
downloads=()
downloads+=("nxf_gs_download gs://bucket/work/dir/.command.sh .command.sh ")
nxf_parallel "${downloads[@]}"
}
nxf_unstage() {
true
gsutil -m -q cp -R .command.out gs://bucket/work/dir/.command.out || true
gsutil -m -q cp -R .command.err gs://bucket/work/dir/.command.err || true
gsutil -m -q cp -R .exitcode gs://bucket/work/dir/.exitcode || true
[[ ${nxf_main_ret:=0} != 0 ]] && return
}
nxf_main() {
trap on_exit EXIT
trap on_term TERM INT USR2
trap '' USR1
[[ "${NXF_CHDIR:-}" ]] && cd "$NXF_CHDIR"
NXF_SCRATCH={{folder}}
[[ $NXF_DEBUG > 0 ]] && nxf_env
set +u
set -u
[[ $NXF_SCRATCH ]] && echo "nxf-scratch-dir $HOSTNAME:$NXF_SCRATCH" && cd $NXF_SCRATCH
set +e
local ctmp=$(set +u; nxf_mktemp /dev/shm 2>/dev/null || nxf_mktemp $TMPDIR)
local cout=$ctmp/.command.out; mkfifo $cout
local cerr=$ctmp/.command.err; mkfifo $cerr
tee .command.out < $cout &
tee1=$!
tee .command.err < $cerr >&2 &
tee2=$!
( nxf_launch ) >$cout 2>$cerr &
pid=$!
wait $pid || nxf_main_ret=$?
wait $tee1 $tee2
}
$NXF_ENTRY