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Commit 6e759f3c authored by Jasper Koehorst's avatar Jasper Koehorst
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added eggmapper

parent 5135e6fa
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...@@ -12,7 +12,7 @@ LABEL documentation="NA" ...@@ -12,7 +12,7 @@ LABEL documentation="NA"
LABEL license="NA" LABEL license="NA"
LABEL tags="Base" LABEL tags="Base"
# ARG cwltool_version=3.0.20200720165847 # ARG cwltool_version=3.1.20211004060744
ENV DEBIAN_FRONTEND=noninteractive LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LANGUAGE=en_US.UTF-8 ENV DEBIAN_FRONTEND=noninteractive LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LANGUAGE=en_US.UTF-8
...@@ -30,7 +30,7 @@ RUN python3 -m pip install python-irodsclient --upgrade && \ ...@@ -30,7 +30,7 @@ RUN python3 -m pip install python-irodsclient --upgrade && \
apt-get update && \ apt-get update && \
wget -qO - https://packages.irods.org/irods-signing-key.asc | apt-key add - && \ wget -qO - https://packages.irods.org/irods-signing-key.asc | apt-key add - && \
echo "# /etc/apt/sources.list.d/renci-irods.list" | tee -a /etc/apt/sources.list.d/renci-irods.list && \ echo "# /etc/apt/sources.list.d/renci-irods.list" | tee -a /etc/apt/sources.list.d/renci-irods.list && \
echo "deb [arch=amd64] https://packages.irods.org/apt/ xenial main" | tee -a /etc/apt/sources.list.d/renci-irods.list && \ echo "deb [arch=amd64] https://packages.irods.org/apt/ bionic main" | tee -a /etc/apt/sources.list.d/renci-irods.list && \
apt-get update && apt-get install --no-install-recommends --yes irods-icommands apt-get update && apt-get install --no-install-recommends --yes irods-icommands
# Couple shell to bash # Couple shell to bash
...@@ -87,6 +87,9 @@ RUN source /root/miniconda/bin/activate && \ ...@@ -87,6 +87,9 @@ RUN source /root/miniconda/bin/activate && \
# conda clean && \ # conda clean && \
rm /picrust2_env.yml /v2.4.1.tar.gz rm /picrust2_env.yml /v2.4.1.tar.gz
## eggmapper
RUN pip install eggnog-mapper
## HUMAnN meta-omics ## HUMAnN meta-omics
RUN python3 -m pip install humann --no-binary :all: && \ RUN python3 -m pip install humann --no-binary :all: && \
python3 -m pip install metaphlan --no-binary :all: && \ python3 -m pip install metaphlan --no-binary :all: && \
......
kubectl apply -f instance.yaml #!/bin/bash
\ No newline at end of file #============================================================================
#title :Instance creation for unlock nodes
#description :Creates an sleeping instance on each of the unlock nodes
#author :Jasper Koehorst & Bart Nijsse
#date :2021
#version :0.0.2
#============================================================================
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
# Clean up finished sync pods
kubectl get pods --namespace='unlock' | grep munlock-instance | grep Completed | awk '{print "kubectl -n unlock delete pod "$1}' | sh
# Get all possible nodes
kubectl get nodes -l node-role.kubernetes.io/worker=true | grep -v "SchedulingDisabled" | awk '{print $1}' | grep -v NAME > $DIR/nodes.txt
while read node; do
sed "s/HOSTNAME/$node/g" $DIR/template_instance.yaml > $DIR/$node\_instance.yaml
kubectl apply -f $DIR/$node\_instance.yaml
rm $DIR/$node\_instance.yaml
done < $DIR/nodes.txt
\ No newline at end of file
apiVersion: v1
kind: Pod
metadata:
name: munlock-instance
namespace: unlock
labels:
purpose: live-instance
spec:
containers:
- name: munlock-instance
image: docker-registry.wur.nl/unlock/docker:kubernetes
# Just spin & wait forever
command: [ "/bin/sh", "-c", "--" ]
args: [ "apt-get install -y screen; while true; do sleep 30; done;" ]
envFrom:
- configMapRef:
name: path
env:
- name: irodsHost
valueFrom:
secretKeyRef:
name: unlock-secret
key: irodsHost
- name: irodsPort
valueFrom:
secretKeyRef:
name: unlock-secret
key: irodsPort
- name: irodsUserName
valueFrom:
secretKeyRef:
name: unlock-secret
key: irodsUserName
- name: irodsZone
valueFrom:
secretKeyRef:
name: unlock-secret
key: irodsZone
- name: irodsAuthScheme
valueFrom:
secretKeyRef:
name: unlock-secret
key: irodsAuthScheme
- name: irodsHome
valueFrom:
secretKeyRef:
name: unlock-secret
key: irodsHome
- name: irodsCwd
valueFrom:
secretKeyRef:
name: unlock-secret
key: irodsCwd
- name: irodsPassword
valueFrom:
secretKeyRef:
name: unlock-secret
key: irodsPassword
- name: irodsSSL
valueFrom:
secretKeyRef:
name: unlock-secret
key: irodsSSL
resources:
limits:
cpu: '2'
memory: 20000Mi
requests:
cpu: '2'
memory: 20000Mi
volumeMounts:
- mountPath: /unlock
name: unlock
restartPolicy: OnFailure
volumes:
- name: unlock
persistentVolumeClaim:
claimName: unlock
nodeSelector:
kubernetes.io/hostname: ichibi
\ No newline at end of file
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