I would like to run a command within the yaml file for kubernetes:
Here is the part of the yaml file that i use The idea is to calculate a precent value based on mapped and unmapped values. mapped and unmapped are set properly but the percent line fails I think the problem comes from the single quotes in the BEGIN statement of the awk command which i guess need to escape ???
If mapped=8 and unmapped=7992 Then percent is (8/(8+7992)*100) = 0.1%
command: ["/bin/sh","-c"]
args: ['
...
echo "Executing command" &&
map=${grep -c "^@" outfile.mapped.fq} &&
unmap=${grep -c "^@" outfile.unmapped.fq} &&
percent=$(awk -v CONVFMT="%.10g" -v map="$map" -v unmap="$unmap" "BEGIN { print ((map/(unmap+map))*100)}") &&
echo "finished"
']
Thanks to the community comments: Ed Morton & david
For those files with data, please create configmap:
outfile.mapped.fq
outfile.unmapped.fq
kubectl create configmap config-volume --from-file=/path_to_directory_with_files/Create pod:
apiVersion: v1
kind: Pod
metadata:
name: awk-ubu
spec:
containers:
- name: awk-ubuntu
image: ubuntu
workingDir: /test
command: [ "/bin/sh", "-c" ]
args:
- echo Executing_command;
map=$(grep -c "^@" outfile.mapped.fq);
unmap=$(grep -c "^@" outfile.unmapped.fq);
percent=$(awk -v CONVFMT="%.10g" -v map="$map" -v unmap="$unmap" "BEGIN { print ((map/(unmap+map))*100)}");
echo $percent;
echo Finished;
volumeMounts:
- name: special-config
mountPath: /test
volumes:
- name: special-config
configMap:
# Provide the name of the ConfigMap containing the files you want
# to add to the container
name: config-volume
restartPolicy: NeverOnce completed verify the result:
kubectl logs awk-ubu
Executing_command
53.3333
Finished