Category: Open source

cytomine installation

Helge on

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
34c83d2bc656: Pulling fs layer
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8e1c1b7407ec: Pulling fs layer
84b69b6e4743: Waiting
35ef24d18073: Waiting
75a8bc04c91d: Waiting
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34c83d2bc656: Download complete
ba077e1ddb3a: Verifying Checksum
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8e1c1b7407ec: Pull complete
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
84b69b6e4743: Already exists
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8bf154095d84: Pulling fs layer
606c90c8c9bf: Waiting
8bf154095d84: Waiting
cc852daf3515: Waiting
d304f9b0a677: Verifying Checksum
80f792bfec4b: Verifying Checksum
80f792bfec4b: Download complete
d304f9b0a677: Pull complete
7a352f869d3a: Verifying Checksum
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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
84b69b6e4743: Already exists
0f72e97e1f61: Already exists
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b7b3f29f15a4: Pulling fs layer
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91575c9c3c9b: Pulling fs layer
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2fc250d09202: Waiting
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f7efc699e07b: Pull complete
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
d36e74c1cf32: Pulling fs layer
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00a7dc437f3b: Waiting
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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
846127e02907: Pulling fs layer
a6a68821583f: Pulling fs layer
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846127e02907: Download complete
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79517d1acdda: Verifying Checksum
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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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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
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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
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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
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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
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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
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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
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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
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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/

Analysing gigapixel images online is possible with Cytomine

Helge on

We have a collaborating project between Norway, Moldova, Armenia and Belarus in Oral Pathology. In order to view slides online we installed a software called Cytomine. This software, or multiple combined software/applications, is developed in Belgium by a cooperating team. All about Cytomine can be read here: https://cytomine.coop/

This is an open source software. It is installed on a Linux Ubuntu 16.04 LTE server with Docker CE. The server has 96GB memory, 2TB storage and 24 VCPU’s. It is located in University of Bergen, hosted by the UH-Iaas project group (http://iaas.readthedocs.io/en/latest/getting_started/index.html)

This application gives the user to view slides (pictures) of multiple gigabyte online and almost without any download time. For instance we have tested it with a 5GB large slide, and it could be viewed immidiately online through a 4G mobile phone in Yerevan, Armenia through the Internet with the servers located in Norway, Bergen.

The Cytomine software can be used by students, teachers, pathologist for viewing, annotating, discussing tissue slides (or any picture actually).

Our server is located here:

https://cytomine-core.app.uib.no

In order to install Cytomine you need to have a basic understanding of Linux Ubuntu, bash scripting, Docker and general web-server technology.

I have created a short video that shows how the software works:

Open Archive

Helge on

Open AccessHere at the University of Bergen (UiB) we have an archive that we call Bergen Open Research Archive, short: BORA
The adress is: https://bora.uib.no

It is run with DSpace in a Tomcat context, with Apache frontend with reverse proxy, and backend database Postgresql. Everything on a Redhat Enterprise Linux Redhat 6 server. More about DSpace here at the University of Bergen can be read here: http://wiki.uib.no/dok/index.php/DSpace (sorry, norwegian only at the moment).

More about BORA at UiB:

http://www.uib.no/en/ub/79538/bergen-open-research-archive

There is also on archive at HiB:

http://bora.hib.no/nb/

and, “jaggu meg”, there seems to be something called NORA (Norwegian Open Research Archives) as well:

http://www.ub.uio.no/nora/search.html