enh: added kubernetes files

Author: akeshavan

kubernetes/delete_cluster.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+gcloud container clusters delete dmriprep --zone=us-west1-a

kubernetes/delete_job.sh

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+#!/bin/bash
+kubectl delete -f run_dmriprep.yml

kubernetes/docker/build_tag_push.sh

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+#!/bin/bash
+docker build -t dmriprep:kube1 -f dockerfile-dmriprep-kube1 .
+docker tag dmriprep:kube1 gcr.io/dmriprep/dmriprep:kube1
+docker push gcr.io/dmriprep/dmriprep:kube1

kubernetes/docker/dmriprep_all.sh

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+#!/bin/bash
+mkdir inputs
+mkdir outputs
+dmriprep-data --subject $1 $PWD/inputs/
+dmriprep $PWD/inputs $PWD/outputs
+dmriprep-upload --access_key $2 --secret_key $3 $PWD/outputs preafq-hbn 

kubernetes/docker/dockerfile-dmriprep-kube

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+FROM dmriprep:prod
+COPY dmriprep_all.sh /dmriprep_all.sh
+CMD ["/neurodocker/startup.sh", "dmriprep_all.sh"]

kubernetes/run_dmriprep.yml

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+apiVersion: batch/v1
+kind: Job
+metadata:
+  name: dmriprep0
+spec:
+  template:
+    spec:
+      containers:
+      - name: dmriprep-subject
+        image: gcr.io/dmriprep/dmriprep:kube1
+        command: ["/neurodocker/startup.sh", "./dmriprep_all.sh",  "sub-NDARED632KNG", "{{access_key}}", "{{secret_key}}"]
+      restartPolicy: Never
+  backoffLimit: 1

kubernetes/run_job.sh

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+#!/bin/bash
+kubectl apply -f run_dmriprep.yml

kubernetes/setup_gcp_kubernetes_dmriprep.sh

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+#!/bin/bash
+
+# login
+gcloud auth login [email protected]
+
+# set the project to dmriprep
+gcloud config set project dmriprep
+
+# some variables
+ZONE=us-west1-a
+MAX_NODES=4
+CLUSTERNAME=dmriprep
+
+# set the default compute zone
+gcloud config set compute/zone $ZONE
+
+# start the cluster!
+gcloud beta container clusters create $CLUSTERNAME --machine-type n1-highmem-4 --enable-autoscaling --max-nodes=$MAX_NODES --num-nodes 2 --cluster-version latest --node-labels dmriprep/node-purpose=core