entrypoint-aws-batch

#!/bin/bash
set -euo pipefail

# Show what we're running for the benefit of the logs.
if [[ "${NEXTSTRAIN_AWS_BATCH_VERBOSE:=1}"!= 0 ]];then
set -x
fi

# Download the working dir.
case"$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL"in
 s3://*.zip)
 aws s3 cp --no-progress "$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL""$PWD.zip"

fordirin /nextstrain/{augur,auspice,fauna};do
 relative_dir="$(realpath "$dir" --relative-to="$PWD")"/

if zipinfo -1 "$PWD.zip""$relative_dir"&>/dev/null;then
echo"removing $dir because workdir ZIP contains $relative_dir overlay"
 rm -rf "$dir"
fi
done

 unzip -: -o "$PWD.zip"
 ;;
 s3://*)
# Note that this doesn't preserve file permissions/modes.
 aws s3 sync --no-progress "$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL".
 ;;
*)
echo"entrypoint-aws-batch: No handler for NEXTSTRAIN_AWS_BATCH_WORKDIR_URL <$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL>">&2
exit 1
 ;;
esac

# Run the passed command, with the effect of "set -e" temporarily disabled,
# saving the exit status for later.
"$@"&& exited=0 || exited=$?

# Upload the new workdir state with results.
#
# XXX TODO: In the future this may want to be separate from the initial workdir
# state instead of overwriting it. That would let us hash the local workdir
# before uploading and re-use previously uploaded initial workdirs.
# -trs, 13 Sept 2018
case"$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL"in
 s3://*.zip)
succeed-when-nothing-to-update() {
local zipstatus="$1"
if [[ $zipstatus-eq 12 ]];then
return 0
else
return"$zipstatus"
fi
 }
 zip -u "$PWD.zip" -r . --exclude ".snakemake/*"|| succeed-when-nothing-to-update $?
 zip -u "$PWD.zip" -r . --include ".snakemake/log/*"".snakemake/metadata/*"|| succeed-when-nothing-to-update $?
 aws s3 cp --no-progress "$PWD.zip""$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL"
 ;;
 s3://*)
 aws s3 sync --no-progress ."$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL" --exclude ".snakemake/*" --include ".snakemake/log/*"
 ;;
*)
echo"entrypoint-aws-batch: No handler for NEXTSTRAIN_AWS_BATCH_WORKDIR_URL <$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL>">&2
exit 1
 ;;
esac

# Exit with the same status as the passed command.
exit"$exited"