cytomine installation

I have today installed the Cytomine version 3 from cytomine.org Here I will explain in detail the different steps needed to install the software.

Firstly I installed a Linux Ubuntu 18.04LTS with 16VCPU’s and 64GB memory in the Norwegian UH OpenStack nrec.no cloud.

Then I installed the Docker-CE with following bash commands:

#!/bin/bash

# ubuntu packages, nice to have
apt -y install mailutils
apt -y install htop
apt -y install unzip
apt -y install mailutils


# docker ce
apt-get -y install apt-transport-https \
    ca-certificates \
    curl \
    software-properties-common

curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
sudo apt-key fingerprint 0EBFCD88
sudo add-apt-repository \
    "deb [arch=amd64] https://download.docker.com/linux/ubuntu \
    $(lsb_release -cs) \
    stable"
sudo apt-get -y update
sudo apt-get -y install docker-ce

The docker service is started with:

service docker start

Next I read the documentation:

https://doc.cytomine.org/How-to-install-Cytomine?structure=Admins

The next bash commands are:

mkdir Cytomine_bootstrap/
cd Cytomine_bootstrap/
wget https://github.com/cytomine/Cytomine-bootstrap/archive/v3.0.0.zip -O bootstrap.zip
unzip bootstrap.zip
mv Cytomine-bootstrap-3.0.0/* .
rm -rf bootstrap.zip Cytomine-bootstrap-3.0.0/

Then the configuration.sh file needed to be edited to fit our setup:

nano configuration.sh

Or if you prefer vim:

vim configuration.sh

The main changes in our configuration.sh file were:

CORE_URL=cytomine3-core.app.uib.no
IMS_URL1=cytomine3-ims.app.uib.no
IMS_URL2=cytomine3-ims2.app.uib.no
UPLOAD_URL=cytomine3-upload.app.uib.no

IMS_STORAGE_PATH=/data/www/images
IMS_BUFFER_PATH=/data/www/images/_buffer
BACKUP_PATH=/data/www/backup
ALGO_PATH=/data/www/algo/

the 4 domain names were then added to our DNS server.

Then I ran the init.sh script:

bash init.sh

Which produced the following start_deploy.sh file:

#!/bin/bash

#
# Copyright (c) 2009-2020. Authors: see NOTICE file.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#      http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#

docker create --name memcached \
--restart=unless-stopped \
cytomine/memcached:v1.1.2 > /dev/null

docker cp $PWD/configs/memcached/memcached.conf memcached:/etc/memcached.conf
docker start memcached


docker create --name rabbitmq \
-p 5672:5672 -p 15672:15672 \
-e RABBITMQ_PASS=$RABBITMQ_PASS \
--restart=unless-stopped \
cytomine/rabbitmq:v1.1.2 > /dev/null

docker start rabbitmq


docker volume create --name postgis_data > /dev/null
# create database docker
docker run -d -m 8g --name postgresql -v postgis_data:/var/lib/postgresql \
--restart=unless-stopped \
cytomine/postgis:v2.0.0 > /dev/null

docker volume create --name mongodb_data > /dev/null
# create mongodb docker
docker run -d --name mongodb -v mongodb_data:/data/db \
--restart=unless-stopped \
cytomine/mongodb:v1.1.2 > /dev/null


if [ ! -e $PWD/configs/software_router/keys/ssh_key ]
then
    echo "ssh keys for software_router must exists !"
    echo "generate them and put them in the $PWD/configs/software_router/keys folder "
    exit 1
fi


docker volume create --name slurm_data > /dev/null
# create slurm docker
docker create --name slurm \
--privileged \
-h cytomine-slurm \
-v slurm_data:/var/lib/mysql \
-v singularity_images:/data/softwares/images \
-v /etc/localtime:/etc/localtime \
cytomine/slurm:v1.0.0 > /dev/null

docker cp $PWD/configs/software_router/keys/ssh_key.pub slurm:/home/cytomine/.ssh/authorized_keys
docker cp $PWD/hosts/slurm/addHosts.sh slurm:/tmp/addHosts.sh
docker start slurm


docker create --name iipOff \
--link memcached:memcached \
-v /data/www/images:/data/www/images \
--privileged -e NB_IIP_PROCESS=10 \
--restart=unless-stopped \
cytomine/iipofficial:v1.2.0 > /dev/null

docker cp $PWD/configs/iipOff/nginx.conf.sample iipOff:/tmp/nginx.conf.sample
docker start iipOff


docker create --name iipCyto \
--link memcached:memcached \
-v /data/www/images:/data/www/images \
--privileged -e NB_IIP_PROCESS=10 \
--restart=unless-stopped \
cytomine/iipcyto:v1.2.1 > /dev/null

docker cp $PWD/configs/iipCyto/nginx.conf.sample iipCyto:/tmp/nginx.conf.sample
docker start iipCyto


docker create --name bioformat \
-v /data/www/images:/data/www/images \
-e BIOFORMAT_PORT=4321 \
--restart=unless-stopped \
cytomine/bioformat:v1.1.2 > /dev/null

docker start bioformat


docker create --name ims \
--link bioformat:bioformat \
-e IMS_STORAGE_PATH=/data/www/images \
-v /data/www/images:/data/www/images \
-v /data/www/images/_buffer:/tmp/uploaded \
--restart=unless-stopped \
cytomine/ims:v1.2.3 > /dev/null

docker cp $PWD/configs/ims/imageserverconfig.properties ims:/usr/share/tomcat7/.grails/imageserverconfig.properties
docker cp $PWD/hosts/ims/addHosts.sh ims:/tmp/addHosts.sh
docker start ims


docker create --name core \
--link postgresql:postgresql \
--link mongodb:mongodb \
--link rabbitmq:rabbitmq \
-v /etc/localtime:/etc/localtime \
-v /data/softwares/code:/data/softwares/code \
--restart=unless-stopped \
cytomine/core:v3.0.0 > /dev/null

docker cp $PWD/configs/core/cytomineconfig.groovy core:/usr/share/tomcat7/.grails/cytomineconfig.groovy
docker cp $PWD/hosts/core/addHosts.sh core:/tmp/addHosts.sh
docker start core


docker create --name web_UI \
-v /etc/localtime:/etc/localtime \
--restart=unless-stopped \
cytomine/web_ui:v1.2.0 > /dev/null

docker cp "${PWD}/configs/web_ui/configuration.json" web_UI:/app/configuration.json
docker cp "${PWD}/configs/web_ui/nginx.conf" web_UI:/etc/nginx/nginx.conf
docker start web_UI


docker create --name nginx \
--link ims:ims \
--link iipCyto:iipCyto \
--link core:core \
--link iipOff:iipOff \
--link web_UI:web_UI \
-v /data/www/images/_buffer:/tmp/uploaded \
-p 80:80 \
--restart=unless-stopped \
cytomine/nginx:v1.2.0 > /dev/null

docker cp $PWD/configs/nginx/nginx.conf nginx:/usr/local/nginx/conf/nginx.conf
docker start nginx


docker create --name software_router \
-v singularity_images:/data/softwares/images \
-v /var/run/docker.sock:/var/run/docker.sock \
--privileged \
--link rabbitmq:rabbitmq \
--link slurm:slurm \
--restart=unless-stopped \
cytomine/software_router:v2.0.0 > /dev/null

docker cp $PWD/hosts/software_router/addHosts.sh software_router:/tmp/addHosts.sh
docker cp $PWD/configs/software_router/config.groovy software_router:/software_router/config.groovy
docker cp $PWD/configs/software_router/keys/ssh_key software_router:/root/.ssh/id_rsa
docker start software_router

Then the next bash command for deploying Cytomine were:

sudo sh restart.sh

Which produced these lines:

clean containers
Error response from daemon: No such container: memcached
Error: No such container: memcached
Error response from daemon: No such container: rabbitmq
Error: No such container: rabbitmq
Error response from daemon: No such container: mongodb
Error: No such container: mongodb
Error response from daemon: No such container: postgresql
Error: No such container: postgresql
Error response from daemon: No such container: backup_mongo
Error: No such container: backup_mongo
Error response from daemon: No such container: backup_postgis
Error: No such container: backup_postgis
Error response from daemon: No such container: slurm
Error: No such container: slurm
Error response from daemon: No such container: iipOff
Error: No such container: iipOff
Error response from daemon: No such container: iipCyto
Error: No such container: iipCyto
Error response from daemon: No such container: bioformat
Error: No such container: bioformat
Error response from daemon: No such container: ims
Error: No such container: ims
Error response from daemon: No such container: core
Error: No such container: core
Error response from daemon: No such container: web_UI
Error: No such container: web_UI
Error response from daemon: No such container: nginx
Error: No such container: nginx
Error response from daemon: No such container: software_router
Error: No such container: software_router
launch new containers
Unable to find image 'cytomine/memcached:v1.1.2' locally
v1.1.2: Pulling from cytomine/memcached
3b37166ec614: Pulling fs layer
ba077e1ddb3a: Pulling fs layer
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84b69b6e4743: Waiting
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Digest: sha256:f0c96bc02dd3d52da3b8db5099bc67292f1d2c6ca12cfde90b9442cd3bac6901
Status: Downloaded newer image for cytomine/memcached:v1.1.2
memcached
Unable to find image 'cytomine/rabbitmq:v1.1.2' locally
v1.1.2: Pulling from cytomine/rabbitmq
3b37166ec614: Already exists
ba077e1ddb3a: Already exists
34c83d2bc656: Already exists
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606c90c8c9bf: Waiting
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d304f9b0a677: Verifying Checksum
80f792bfec4b: Verifying Checksum
80f792bfec4b: Download complete
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Digest: sha256:bc15b5a4995eb42f0dc047047645a5f9c81319d294784d50472b2910b444729f
Status: Downloaded newer image for cytomine/rabbitmq:v1.1.2
rabbitmq
Unable to find image 'cytomine/postgis:v2.0.0' locally
v2.0.0: Pulling from cytomine/postgis
3b37166ec614: Already exists
ba077e1ddb3a: Already exists
34c83d2bc656: Already exists
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Digest: sha256:2d41589d471b4d0dbfe41c02d3fa2820df337e0bbfe292463bc12e47a456ced2
Status: Downloaded newer image for cytomine/postgis:v2.0.0
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Unable to find image 'cytomine/mongodb:v1.1.2' locally
v1.1.2: Pulling from cytomine/mongodb
3b37166ec614: Already exists
ba077e1ddb3a: Already exists
34c83d2bc656: Already exists
84b69b6e4743: Already exists
0f72e97e1f61: Already exists
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Digest: sha256:38686e1a2c68833babffa3a724400781d1b970742c55a104dd40578b848d4342
Status: Downloaded newer image for cytomine/mongodb:v1.1.2
Unable to find image 'cytomine/slurm:v1.0.0' locally
v1.0.0: Pulling from cytomine/slurm
840caab23da4: Pulling fs layer
c9b33345e712: Pulling fs layer
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Digest: sha256:98ffe0793e399d80e6fbf8d52c7cb1e242f253723b1cd46c2e97f8e853b326e1
Status: Downloaded newer image for cytomine/slurm:v1.0.0

slurm
Unable to find image 'cytomine/iipofficial:v1.2.0' locally
v1.2.0: Pulling from cytomine/iipofficial
3b37166ec614: Already exists
ba077e1ddb3a: Already exists
34c83d2bc656: Already exists
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043cec74afc6: Download complete
959192421a03: Download complete
d780fd775ac0: Verifying Checksum
d780fd775ac0: Download complete
1064d3045cb3: Download complete
9cbd4f92df51: Verifying Checksum
9cbd4f92df51: Download complete
ca9fbb9c3f37: Verifying Checksum
ca9fbb9c3f37: Download complete
bda42567b063: Verifying Checksum
bda42567b063: Download complete
d3b20500281b: Verifying Checksum
d3b20500281b: Download complete
6a84d7b204a7: Verifying Checksum
6a84d7b204a7: Download complete
2a6dd82d1642: Verifying Checksum
2a6dd82d1642: Download complete
7309828131dd: Verifying Checksum
7309828131dd: Download complete
f987232076f5: Verifying Checksum
f987232076f5: Download complete
dc0c25ef1a48: Verifying Checksum
dc0c25ef1a48: Download complete
165c1eefd1a9: Download complete
b0045e737456: Verifying Checksum
b0045e737456: Download complete
94735b9221c1: Pull complete
64aad079aa2e: Pull complete
f00d61d640ec: Pull complete
462b1abf5663: Pull complete
fc917f87e3d6: Pull complete
28125f36460d: Pull complete
043cec74afc6: Pull complete
d780fd775ac0: Pull complete
959192421a03: Pull complete
1064d3045cb3: Pull complete
ca9fbb9c3f37: Pull complete
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bda42567b063: Pull complete
2a6dd82d1642: Pull complete
d3b20500281b: Pull complete
6a84d7b204a7: Pull complete
7309828131dd: Pull complete
f987232076f5: Pull complete
dc0c25ef1a48: Pull complete
165c1eefd1a9: Pull complete
b0045e737456: Pull complete
Digest: sha256:34aac6e94a4a302a88b3e1d46471a30e3f9727094fc1d8eb286a9ceb00adf638
Status: Downloaded newer image for cytomine/iipofficial:v1.2.0
iipOff
Unable to find image 'cytomine/iipcyto:v1.2.1' locally
v1.2.1: Pulling from cytomine/iipcyto
3b37166ec614: Already exists
ba077e1ddb3a: Already exists
34c83d2bc656: Already exists
84b69b6e4743: Already exists
0f72e97e1f61: Already exists
d36e74c1cf32: Already exists
0d0dfd4ddd77: Already exists
94735b9221c1: Already exists
64aad079aa2e: Already exists
f00d61d640ec: Already exists
462b1abf5663: Already exists
fc917f87e3d6: Already exists
28125f36460d: Already exists
043cec74afc6: Already exists
d780fd775ac0: Already exists
959192421a03: Already exists
1064d3045cb3: Already exists
ca9fbb9c3f37: Already exists
9cbd4f92df51: Already exists
bda42567b063: Already exists
2a6dd82d1642: Already exists
d3b20500281b: Already exists
6a84d7b204a7: Already exists
82a0d3bc920e: Pulling fs layer
408df44a5b6d: Pulling fs layer
5163890db256: Pulling fs layer
1ee28e537faf: Pulling fs layer
11f7d8ced79e: Pulling fs layer
4feb1471087d: Pulling fs layer
fc4cd05a9de9: Pulling fs layer
3026c397467b: Pulling fs layer
11f7d8ced79e: Waiting
4feb1471087d: Waiting
fc4cd05a9de9: Waiting
3026c397467b: Waiting
1ee28e537faf: Waiting
82a0d3bc920e: Verifying Checksum
82a0d3bc920e: Download complete
82a0d3bc920e: Pull complete
408df44a5b6d: Verifying Checksum
408df44a5b6d: Download complete
408df44a5b6d: Pull complete
5163890db256: Download complete
5163890db256: Pull complete
4feb1471087d: Verifying Checksum
4feb1471087d: Download complete
1ee28e537faf: Verifying Checksum
1ee28e537faf: Download complete
1ee28e537faf: Pull complete
11f7d8ced79e: Download complete
3026c397467b: Verifying Checksum
3026c397467b: Download complete
11f7d8ced79e: Pull complete
fc4cd05a9de9: Verifying Checksum
fc4cd05a9de9: Download complete
4feb1471087d: Pull complete
fc4cd05a9de9: Pull complete
3026c397467b: Pull complete
Digest: sha256:1aeafb17a239365c68798429aac64c7f41c858032915ea465fe5686f447d765c
Status: Downloaded newer image for cytomine/iipcyto:v1.2.1
iipCyto
Unable to find image 'cytomine/bioformat:v1.1.2' locally
v1.1.2: Pulling from cytomine/bioformat
3b37166ec614: Already exists
ba077e1ddb3a: Already exists
34c83d2bc656: Already exists
84b69b6e4743: Already exists
0f72e97e1f61: Already exists
35ef24d18073: Already exists
143f7824e502: Pulling fs layer
564dc6ae2dec: Pulling fs layer
911e1bdff49d: Pulling fs layer
f1248f5c25db: Pulling fs layer
9f90171f5e74: Pulling fs layer
dd2d5f61560b: Pulling fs layer
e94e315fab4c: Pulling fs layer
c122c56ba0de: Pulling fs layer
f1248f5c25db: Waiting
9f90171f5e74: Waiting
dd2d5f61560b: Waiting
e94e315fab4c: Waiting
564dc6ae2dec: Verifying Checksum
564dc6ae2dec: Download complete
143f7824e502: Verifying Checksum
143f7824e502: Download complete
143f7824e502: Pull complete
564dc6ae2dec: Pull complete
f1248f5c25db: Verifying Checksum
f1248f5c25db: Download complete
9f90171f5e74: Verifying Checksum
9f90171f5e74: Download complete
dd2d5f61560b: Verifying Checksum
dd2d5f61560b: Download complete
e94e315fab4c: Download complete
c122c56ba0de: Verifying Checksum
c122c56ba0de: Download complete
911e1bdff49d: Verifying Checksum
911e1bdff49d: Download complete
911e1bdff49d: Pull complete
f1248f5c25db: Pull complete
9f90171f5e74: Pull complete
dd2d5f61560b: Pull complete
e94e315fab4c: Pull complete
c122c56ba0de: Pull complete
Digest: sha256:de33ba2b60c0ed11d5b13febe00207be0749430c57d8aa27bfb3170023924acf
Status: Downloaded newer image for cytomine/bioformat:v1.1.2
bioformat
Unable to find image 'cytomine/ims:v1.2.3' locally
v1.2.3: Pulling from cytomine/ims
3b37166ec614: Already exists
ba077e1ddb3a: Already exists
34c83d2bc656: Already exists
84b69b6e4743: Already exists
0f72e97e1f61: Already exists
d36e74c1cf32: Already exists
0d0dfd4ddd77: Already exists
c5ac6bc5ad2c: Pulling fs layer
ad7fbf42b480: Pulling fs layer
27f375d9c24b: Pulling fs layer
e71a31b0ac80: Pulling fs layer
37f18f37a79a: Pulling fs layer
6937fe223926: Pulling fs layer
75ff364d641c: Pulling fs layer
a71d44a4eacc: Pulling fs layer
9d95b26a91bb: Pulling fs layer
a1a740fb42dc: Pulling fs layer
b9ac151f0c77: Pulling fs layer
f9f977660c81: Pulling fs layer
4773cb49a1f7: Pulling fs layer
359360017c9b: Pulling fs layer
cf1f2f821649: Pulling fs layer
45867cc3ad1b: Pulling fs layer
585a23faf3df: Pulling fs layer
953275c394f9: Pulling fs layer
1b3642773408: Pulling fs layer
23a46414423f: Pulling fs layer
cb0c0d0fc633: Pulling fs layer
6cd40541e30d: Pulling fs layer
33e36e4c8614: Pulling fs layer
4a9f0aa2614c: Pulling fs layer
48a581a5e378: Pulling fs layer
b68ac48c1c39: Pulling fs layer
c64263df9c38: Pulling fs layer
e71a31b0ac80: Waiting
37f18f37a79a: Waiting
4773cb49a1f7: Waiting
6937fe223926: Waiting
359360017c9b: Waiting
75ff364d641c: Waiting
cf1f2f821649: Waiting
a71d44a4eacc: Waiting
45867cc3ad1b: Waiting
9d95b26a91bb: Waiting
33e36e4c8614: Waiting
585a23faf3df: Waiting
953275c394f9: Waiting
4a9f0aa2614c: Waiting
48a581a5e378: Waiting
23a46414423f: Waiting
a1a740fb42dc: Waiting
cb0c0d0fc633: Waiting
b9ac151f0c77: Waiting
c64263df9c38: Waiting
f9f977660c81: Waiting
6cd40541e30d: Waiting
ad7fbf42b480: Verifying Checksum
ad7fbf42b480: Download complete
c5ac6bc5ad2c: Download complete
c5ac6bc5ad2c: Pull complete
ad7fbf42b480: Pull complete
37f18f37a79a: Verifying Checksum
37f18f37a79a: Download complete
6937fe223926: Verifying Checksum
75ff364d641c: Download complete
e71a31b0ac80: Verifying Checksum
e71a31b0ac80: Download complete
a71d44a4eacc: Verifying Checksum
a71d44a4eacc: Download complete
9d95b26a91bb: Verifying Checksum
9d95b26a91bb: Download complete
27f375d9c24b: Verifying Checksum
27f375d9c24b: Download complete
a1a740fb42dc: Verifying Checksum
a1a740fb42dc: Download complete
f9f977660c81: Verifying Checksum
f9f977660c81: Download complete
4773cb49a1f7: Verifying Checksum
4773cb49a1f7: Download complete
359360017c9b: Verifying Checksum
359360017c9b: Download complete
45867cc3ad1b: Download complete
27f375d9c24b: Pull complete
e71a31b0ac80: Pull complete
37f18f37a79a: Pull complete
6937fe223926: Pull complete
585a23faf3df: Verifying Checksum
585a23faf3df: Download complete
75ff364d641c: Pull complete
a71d44a4eacc: Pull complete
9d95b26a91bb: Pull complete
a1a740fb42dc: Pull complete
953275c394f9: Verifying Checksum
953275c394f9: Download complete
1b3642773408: Verifying Checksum
1b3642773408: Download complete
cf1f2f821649: Verifying Checksum
cf1f2f821649: Download complete
cb0c0d0fc633: Download complete
6cd40541e30d: Download complete
33e36e4c8614: Verifying Checksum
33e36e4c8614: Download complete
4a9f0aa2614c: Verifying Checksum
23a46414423f: Verifying Checksum
23a46414423f: Download complete
48a581a5e378: Verifying Checksum
48a581a5e378: Download complete
b68ac48c1c39: Verifying Checksum
b68ac48c1c39: Download complete
c64263df9c38: Download complete
b9ac151f0c77: Verifying Checksum
b9ac151f0c77: Download complete
b9ac151f0c77: Pull complete
f9f977660c81: Pull complete
4773cb49a1f7: Pull complete
359360017c9b: Pull complete
cf1f2f821649: Pull complete
45867cc3ad1b: Pull complete
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1b3642773408: Pull complete
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cb0c0d0fc633: Pull complete
6cd40541e30d: Pull complete
33e36e4c8614: Pull complete
4a9f0aa2614c: Pull complete
48a581a5e378: Pull complete
b68ac48c1c39: Pull complete
c64263df9c38: Pull complete
Digest: sha256:ec1ba4fb080255e188e8272597155fe2925e808155473e1593b4b0df9aecae24
Status: Downloaded newer image for cytomine/ims:v1.2.3
ims
Unable to find image 'cytomine/core:v3.0.0' locally
v3.0.0: Pulling from cytomine/core
3b37166ec614: Already exists
ba077e1ddb3a: Already exists
34c83d2bc656: Already exists
84b69b6e4743: Already exists
0f72e97e1f61: Already exists
d36e74c1cf32: Already exists
0d0dfd4ddd77: Already exists
c5ac6bc5ad2c: Already exists
ad7fbf42b480: Already exists
27f375d9c24b: Already exists
e71a31b0ac80: Already exists
37f18f37a79a: Already exists
6937fe223926: Already exists
75ff364d641c: Already exists
a71d44a4eacc: Already exists
9d95b26a91bb: Already exists
a1a740fb42dc: Already exists
76064578fc41: Pulling fs layer
032233f2ae0e: Pulling fs layer
f0fab090ab0c: Pulling fs layer
9ab859ed9888: Pulling fs layer
22561a5bfcec: Pulling fs layer
8f94c9f39791: Pulling fs layer
ee257a8fcbda: Pulling fs layer
88fb5e860648: Pulling fs layer
9ab859ed9888: Waiting
22561a5bfcec: Waiting
8f94c9f39791: Waiting
ee257a8fcbda: Waiting
88fb5e860648: Waiting
f0fab090ab0c: Verifying Checksum
f0fab090ab0c: Download complete
032233f2ae0e: Verifying Checksum
032233f2ae0e: Download complete
9ab859ed9888: Verifying Checksum
9ab859ed9888: Download complete
22561a5bfcec: Verifying Checksum
22561a5bfcec: Download complete
8f94c9f39791: Verifying Checksum
8f94c9f39791: Download complete
ee257a8fcbda: Verifying Checksum
ee257a8fcbda: Download complete
88fb5e860648: Verifying Checksum
88fb5e860648: Download complete
76064578fc41: Download complete
76064578fc41: Pull complete
032233f2ae0e: Pull complete
f0fab090ab0c: Pull complete
9ab859ed9888: Pull complete
22561a5bfcec: Pull complete
8f94c9f39791: Pull complete
ee257a8fcbda: Pull complete
88fb5e860648: Pull complete
Digest: sha256:4a9293c87922b5334424a98cb58dd2097ea1d32050eeba2bd6ec70e49fcd4860
Status: Downloaded newer image for cytomine/core:v3.0.0
core
Unable to find image 'cytomine/web_ui:v1.2.0' locally
v1.2.0: Pulling from cytomine/web_ui
54fec2fa59d0: Pulling fs layer
4ede6f09aefe: Pulling fs layer
f9dc69acb465: Pulling fs layer
8bc1c953c518: Pulling fs layer
db7028f8e9f4: Pulling fs layer
6ae45564280a: Pulling fs layer
8bc1c953c518: Waiting
db7028f8e9f4: Waiting
6ae45564280a: Waiting
f9dc69acb465: Verifying Checksum
f9dc69acb465: Download complete
4ede6f09aefe: Verifying Checksum
4ede6f09aefe: Download complete
54fec2fa59d0: Verifying Checksum
54fec2fa59d0: Download complete
8bc1c953c518: Verifying Checksum
6ae45564280a: Verifying Checksum
6ae45564280a: Download complete
54fec2fa59d0: Pull complete
db7028f8e9f4: Verifying Checksum
db7028f8e9f4: Download complete
4ede6f09aefe: Pull complete
f9dc69acb465: Pull complete
8bc1c953c518: Pull complete
db7028f8e9f4: Pull complete
6ae45564280a: Pull complete
Digest: sha256:bf94e6a963db5b363c9a0ed8fe7073689191ff0a8349e4f3e7588ea1f93fc555
Status: Downloaded newer image for cytomine/web_ui:v1.2.0
web_UI
Unable to find image 'cytomine/nginx:v1.2.0' locally
v1.2.0: Pulling from cytomine/nginx
3b37166ec614: Already exists
ba077e1ddb3a: Already exists
34c83d2bc656: Already exists
84b69b6e4743: Already exists
0f72e97e1f61: Already exists
d36e74c1cf32: Already exists
0d0dfd4ddd77: Already exists
b6579bbee20e: Pulling fs layer
e145d5f6493f: Pulling fs layer
0ba2afb41647: Pulling fs layer
2cb8192f0994: Pulling fs layer
9f14803d55c5: Pulling fs layer
f5e9e4ceeccb: Pulling fs layer
8c61e7d21b1c: Pulling fs layer
ddb306922432: Pulling fs layer
b8652ea10723: Pulling fs layer
2cb8192f0994: Waiting
9f14803d55c5: Waiting
f5e9e4ceeccb: Waiting
b8652ea10723: Waiting
8c61e7d21b1c: Waiting
ddb306922432: Waiting
e145d5f6493f: Verifying Checksum
e145d5f6493f: Download complete
0ba2afb41647: Download complete
2cb8192f0994: Verifying Checksum
2cb8192f0994: Download complete
f5e9e4ceeccb: Verifying Checksum
f5e9e4ceeccb: Download complete
9f14803d55c5: Download complete
8c61e7d21b1c: Verifying Checksum
8c61e7d21b1c: Download complete
b6579bbee20e: Verifying Checksum
b6579bbee20e: Download complete
b8652ea10723: Verifying Checksum
b8652ea10723: Download complete
b6579bbee20e: Pull complete
e145d5f6493f: Pull complete
0ba2afb41647: Pull complete
ddb306922432: Verifying Checksum
ddb306922432: Download complete
2cb8192f0994: Pull complete
9f14803d55c5: Pull complete
f5e9e4ceeccb: Pull complete
8c61e7d21b1c: Pull complete
ddb306922432: Pull complete
b8652ea10723: Pull complete
Digest: sha256:b5e4807007ff946f8e8742110a0107fc58eeccff79707292db0b87d06d60330f
Status: Downloaded newer image for cytomine/nginx:v1.2.0
nginx
Unable to find image 'cytomine/software_router:v2.0.0' locally
v2.0.0: Pulling from cytomine/software_router
3b37166ec614: Already exists
ba077e1ddb3a: Already exists
34c83d2bc656: Already exists
84b69b6e4743: Already exists
0f72e97e1f61: Already exists
d36e74c1cf32: Already exists
0d0dfd4ddd77: Already exists
c5ac6bc5ad2c: Already exists
ad7fbf42b480: Already exists
27f375d9c24b: Already exists
ffb980851c66: Pulling fs layer
468ae2160788: Pulling fs layer
da21caf34d1a: Pulling fs layer
e43cb66b6500: Pulling fs layer
b56986f4080c: Pulling fs layer
bbabf3b87d4b: Pulling fs layer
241863c00ea3: Pulling fs layer
e43cb66b6500: Waiting
bbabf3b87d4b: Waiting
c40609e86e45: Pulling fs layer
241863c00ea3: Waiting
c40609e86e45: Waiting
1cfffebec7d5: Pulling fs layer
b70282cab766: Pulling fs layer
78e86bc61603: Pulling fs layer
1cfffebec7d5: Waiting
e1ca411352b1: Pulling fs layer
da21caf34d1a: Verifying Checksum
da21caf34d1a: Download complete
ffb980851c66: Download complete
ffb980851c66: Pull complete
e43cb66b6500: Verifying Checksum
e43cb66b6500: Download complete
b56986f4080c: Verifying Checksum
b56986f4080c: Download complete
bbabf3b87d4b: Verifying Checksum
bbabf3b87d4b: Download complete
c40609e86e45: Verifying Checksum
c40609e86e45: Download complete
1cfffebec7d5: Verifying Checksum
1cfffebec7d5: Download complete
241863c00ea3: Verifying Checksum
241863c00ea3: Download complete
b70282cab766: Download complete
78e86bc61603: Verifying Checksum
78e86bc61603: Download complete
468ae2160788: Verifying Checksum
468ae2160788: Download complete
e1ca411352b1: Download complete
468ae2160788: Pull complete
da21caf34d1a: Pull complete
e43cb66b6500: Pull complete
b56986f4080c: Pull complete
bbabf3b87d4b: Pull complete
241863c00ea3: Pull complete
c40609e86e45: Pull complete
1cfffebec7d5: Pull complete
b70282cab766: Pull complete
78e86bc61603: Pull complete
e1ca411352b1: Pull complete
Digest: sha256:0e69e19e9b57b3454227627b966b06c0fc38f342415ac423143f86af2a3f973f
Status: Downloaded newer image for cytomine/software_router:v2.0.0
software_router

In order to grab the Admin password, I ran this command:

cat configs/core/cytomineconfig.groovy | grep adminPassword

And Voilá:

http://cytomine3-core.app.uib.no/

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