Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/dpwrussell/omero-hydration-docker

Docker build for OMERO hydration
https://github.com/dpwrussell/omero-hydration-docker

Last synced: about 1 month ago
JSON representation

Docker build for OMERO hydration

Awesome Lists containing this project

README 

        
AWS

---



Deploy a local setup using docker



```bash

# Quickstart

docker-compose up

```



To customize the configuration either edit `docker-compose.yml` or run the

docker container's manually like this:



```bash



docker run \

  -d \

  --name postgres \

  -e POSTGRES_PASSWORD=postgres

  postgres:9.4



docker run \

  -d \

  --name omero-master \

  --link postgres:db \

  -e DBNAME=postgres \

  -e DBPASS=postgres \

  -e DBUSER=postgres \

  -e PUBLIC_GROUP=public-group \

  -e ROOTPASS=omero \

  -p 4063:4063 \

  -p 4064:4064 \

  dpwrussell/omero-hydration



docker run \

  -d \

  --name omero-web \

  --link omero-master:master \

  -e PUBLIC_GROUP=public-group \

  -p 8080:8080 \

  dpwrussell/omero-grid-web

```



Note: It takes a few minutes for the containers to start and as they have to

start and stop services during configuration so it may appear to be working

then offline, then working again.



Now the OMERO infrastructure is up and running normal importing using Insight

can be commenced on localhost, standard OMERO ports (unless changed in the

above examples). The web client will also be operational on port 8080 (again,

unless changed in the above examples).



In-place

--------



It is also possible to do in-place importing. This is a good way of creating

an archive without losing the original file-structure of the data. This is

useful if the data archive is multipurpose, being accessed through OMERO, but

also directly, thus preserving the original filesystem structure can be

desirable.



When running the docker container for `omero-master`, include an additional

setting `-v :/mnt/ `, adding a local directory to the

container.



```bash



docker run \

  -d \

  --name omero-master \

  --link postgres:db \

  -e DBNAME=postgres \

  -e DBPASS=postgres \

  -e DBUSER=postgres \

  -e PUBLIC_GROUP=public-group \

  -p 4063:4063 \

  -p 4064:4064 \

  -v /TestData:/mnt/TestData \

  dpwrussell/omero-hydration

```



Then log into the omero container through docker:



```bash

docker exec -it --user omero omero-master /bin/bash

```



Once logged in, create a symlink from the mounted data directory to a directory

in `/OMERO`, like this:



```bash

ln -s /mnt/TestData/project1 /OMERO/inplace

```



Warning: When dehydrating this OMERO instance, everything in the symlinked

directory will be uploaded to S3. In the above example this would be everything

in the `/mnt/TestData/project1` via the `/OMERO/inplace` symlink. This is an

intentional effort to retain the files from the original structure which may

or may not be relevant to OMERO.



We can now do an in-place imports of anything in `/OMERO/inplace`, in this

example we will import everything:



```bash

~/OMERO.server/bin/omero import -- --transfer=ln_s /OMERO/inplace/

```



Dehydrate

---------



Once an archive is built, it can be "dehydrated" into S3. First, generate

some temporary credentials to use inside the omero-master container. Do this

on whatever machine you have configured to communicate with AWS.



```bash

aws sts get-session-token

```



Then login to omero-master through docker.



```bash

docker exec -it --user omero omero-master /bin/bash

```



Create a bucket in S3 to dehydrate the archive into. This can be done on the

AWS console or through the CLI like this (In this case I make it publicly

readable to anyone, and in the us-east-1 region):



```bash

EXPORT BUCKETNAME=""

aws s3api create-bucket --bucket ${BUCKETNAME} --acl public-read --region us-east-1

echo "{ \"Version\" : \"2012-10-17\", \"Statement\" : [ { \"Effect\" : \"Allow\", \"Principal\" : \"*\", \"Resource\" : [ \"arn:aws:s3:::ionewfioewn9023/*\" ], \"Sid\" : \"PublicReadGetObject\", \"Action\" : [ \"s3:GetObject\" ] } ] }" > s3_public.json

aws s3api put-bucket-policy --bucket ${BUCKETNAME} --policy file://s3_public.json --region us-east-1

```



Stop the server and begin the dehydration using the `~/dehydrate.sh` script and the temporary

AWS credentials.



```bash

~/OMERO.server/bin/omero admin stop

~/dehydrate    

```



This may take some time depending on the size of the repository to upload.