wormbase-architecture

This repository is a set of code that can be used to setup the various WormBase environments.

The main provisioning tool that is used in the repostitory is Ansible.

Getting started - install Ansible

First you will need to install docker and other dependencies on your host machine.

mount devices

Follow instructions for mounting volumes.

eg. `sudo mkfs -t xfs /dev/xvdf; sudo mount /dev/xvdf /datastore;`

start datomic transactor

sudo ~/datomic/bin/transactor \
     ~/datomic_configs/free-transactor.properties

Command 1

ansible-playbook -i inventory install.yml

Command 2

ansible-playbook -i inventory site.yml

Result

When you run docker images you should now see the image "wormbase-datomic" listed as a docker image.

Loading data into acedb

foreach acefile (ls /datastore/acedb/raw-data/WS250/*.ace) tace <<quit parse $acefile quit end

Using Containers

General

Identify running docker containers

docker ps -a

To figure out the docker containers ip address

docker inspect  (look for NetworkSettings -> IPAddress )

To connect to machine and inspect the container with bash

docker exec -it <container-id | container-name> bash

Database (postgresql)

This database could be used in stead of the free storage protocol with Datomic.

Data is stored in /var/log/postresql/data.

Log in from remote host

psql -U postgres -h <postgres-container-ip-addr>

Start Container

ansible-playbook -i inventory postgresql.yml;

Datomic

Datomic will already be running you will be able to connect with it either through port 4334 or through ssh

To shell into the container

docker exec -it wombase-datatomic /bin/bash

Datomic API

docker run -d -P \
   --name wormbase-datomic-api \
   --link wormbase-datomic:wormbase-datomic \
          wormbase-datomic-api \
   /bin/bash

##Running lein

I am following the docker links to make a connection to the datomic database. To do the host needs to be modified to

(def uri "datomic:free://WORMBASE_DATOMIC_PORT_4224_TCP/wb250-imp1

In the script on the following page:

https://github.com/WormBase/db/wiki/Timestamp-Importer