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remove jq dependency and fix some shellcheck issues #4761

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merged 2 commits into from Jun 29, 2018
Merged

remove jq dependency and fix some shellcheck issues #4761

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e7f8d54
remove jq dependency and fix some shellcheck issues
martinpeck Jun 14, 2018
067f20a
bump the dateUpdated for the NextFlow sample
martinpeck Jun 14, 2018
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2 changes: 1 addition & 1 deletion nextflow-genomics-cluster-ubuntu/metadata.json
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Expand Up @@ -3,5 +3,5 @@
"description": "This template deploys a scalable Nextflow cluster with a Jumpbox, n cluster nodes, docker support and shared storage.",
"summary": "This deploys a Nextflow cluster for running scalable and reproducible scientific workflows using software containers.",
"githubUsername": "lawrencegripper",
"dateUpdated": "2018-01-22"
"dateUpdated": "2018-06-14"
}
15 changes: 7 additions & 8 deletions nextflow-genomics-cluster-ubuntu/scripts/init.sh
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Expand Up @@ -19,7 +19,7 @@ ADDITIONAL_INSTALL_SCRIPT_ARGUMENT=${10}
log () {
echo "-------------------------" | tee -a "$2"
date -Is | tee -a "$2"
echo $1 | tee -a "$2"
echo "$1" | tee -a "$2"
echo "-------------------------" | tee -a "$2"
}

Expand Down Expand Up @@ -128,13 +128,12 @@ setupNfs() {
copyLogsToCifsShareForDebugging() {
log "Get machine metadata and copy logs to share"

apt-get install jq curl -y | tee -a /tmp/nfinstall.log
apt-get install curl -y | tee -a /tmp/nfinstall.log

#Write instance details into share log folder for debugging
METADATA=$(curl -H Metadata:true http://169.254.169.254/metadata/instance?api-version=2017-04-02)
# shellcheck disable=SC2116
# shellcheck disable=SC2086
NODENAME=$(echo $METADATA | jq -r '.compute.name')
#Get node name and other instance metadata and write details into share log folder for debugging
#see https://docs.microsoft.com/en-us/azure/virtual-machines/windows/instance-metadata-service
METADATA=$(curl -H Metadata:true "http://169.254.169.254/metadata/instance?api-version=2017-04-02")
NODENAME=$(curl -H Metadata:true "http://169.254.169.254/metadata/instance/compute/name?api-version=2017-04-02&format=text")

#Create a log folder for each node
mkdir -p "$CIFS_SHAREPATH/logs/$NODENAME" | tee -a /tmp/nfinstall.log
Expand Down Expand Up @@ -198,7 +197,7 @@ setNextflowEnvironmentVars() {
echo export "NXF_AZ_NFSPATH=$NFS_SHAREPATH"
} >> /etc/environment

#Use asure epherical instance drive for tmp
#Use azure epherical instance drive for tmp
mkdir -p /mnt/nextflow_temp
echo export NXF_TEMP=/mnt/nextflow_temp >> /etc/environment

Expand Down