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m-unlock
docker
Commits
6e759f3c
Commit
6e759f3c
authored
3 years ago
by
Jasper Koehorst
Browse files
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added eggmapper
parent
5135e6fa
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Changes
3
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3 changed files
kubernetes/Dockerfile
+5
-2
5 additions, 2 deletions
kubernetes/Dockerfile
kubernetes/kube_instance/deploy.sh
+20
-1
20 additions, 1 deletion
kubernetes/kube_instance/deploy.sh
kubernetes/kube_instance/instance.yaml
+0
-80
0 additions, 80 deletions
kubernetes/kube_instance/instance.yaml
with
25 additions
and
83 deletions
kubernetes/Dockerfile
+
5
−
2
View file @
6e759f3c
...
@@ -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
.202
00720165847
# ARG cwltool_version=3.
1
.202
11004060744
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: && \
...
...
This diff is collapsed.
Click to expand it.
kubernetes/kube_instance/deploy.sh
+
20
−
1
View file @
6e759f3c
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
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kubernetes/kube_instance/instance.yaml
deleted
100644 → 0
+
0
−
80
View file @
5135e6fa
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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