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Dockerised setup

Making it even easier to set up a custom Ensembl

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Work in Progress

Having just released Lepbase v4, we're actively working on reorganising all our code and documentation and testing for/fixing any bugs. If you would like to set up your own Lepbase-style GenomeHub then you may like to try out the tutorials on genomehubs.org.

Dockerised setup allows you to set up a complete site like lepbase, including blast and downloads services using a set of five Docker containers. Lepbase-specific Docker images are available at hub.docker.com/u/lepbase

A set of slides from a presentation at PAG XXV describing this setup is available, which may be useful to fill in the gaps in this draft documentation.

For the example commands that follow, a straightforward directory structure is used to simplify versioning and backup, with subdirectories for most components containing configuration and data files.

lepbase/
├── v4
│   ├── blast
│   │   ├── blastdbs
│   │   └── conf
│   ├── download
│   │   ├── conf
│   │   └── data
│   ├── ensembl
│   │   ├── conf
│   │   └── logs
│   └── import
│       ├── conf
│       └── data
└── mysql

The main exception is the ensembl directory, used for the EasyMirror docker container, which lacks a data subdirectory as it is linked to the mysql database container when used.

mySQL

docker run -d \
           --name lb-mysql \
           -v ~/lepbase/mysql:/var/lib/mysql \
           -e MYSQL_RANDOM_ROOT_PASSWORD=yes \
           -e MYSQL_ROOT_HOST='172.17.0.0/255.255.0.0' \
           mysql/mysql-server:5.5

# run a container
           # call it lb-mysql
           # mount the mySQL directory
           # set environment variables
           # using this mysql container image

Then update the root password using docker exec -it lb-mysql bash and logging in to mysql using the GENERATED_ROOT_PASSWORD which can be found by running docker logs lb-mysql

EasyMirror

nano ~/lepbase/v4/ensembl/conf/database.ini

# set passwords for database users

# specify Ensembl/EnsemblGenomes databases to download and 
  host locally (DB_HOST should be lb-mysql)

nano /home/ubuntu/lepbase/v4/ensembl/conf/setup.ini

# specify database connection settings

# specify Ensembl plugins to use

# specify species/comparative databases to use

docker run -d \
           --name lb-ensembl \
           -v ~/lepbase/v4/ensembl/conf:/ensembl/conf \
           -v ~/lepbase/v4/ensembl/logs:/ensembl/logs \
           --link lb-mysql:mysql/mysql-server \
           -p 8011:8080 \
          lepbase/easy-mirror

# run a container
           # call it lb-ensembl
           # mount conf and logs directories
           # link to the lb-mysql container
           # map port for the website
           # using the lepbase easy-mirror container image

EasyImport

EasyImport is used to export files and index databases when setting up a mirror site. To use for new data import, additional flags will be required.

nano ~/lepbase/v4/import/conf/hmel2_core_32_85_1.ini

# specify database connection settings

docker run -d \
           --name lb-import-hmel2 \
           --link lb-mysql:mysql/mysql-server \
           -v ~/lepbase/v4/import/conf:/import/conf \
           -v ~/lepbase/v4/import/data:/import/data \
           -v ~/lepbase/v4/download/data:/import/download \
           -v ~/lepbase/v4/blast/blastdbs:/import/blast \
           -e DATABASE=hmel2_core_32_85_1 \
           -e FLAGS="-e -j -i" \
           lepbase/easy-import

# run a container
           # call it lb-import-hmel2
           # link to the lb-mysql container
           # mount some directories
           # set some environment variables
           # using the lepbase easy-import container image

Downloads

docker run -d \
           --name lb-download \
           -v ~/lepbase/v4/download/conf:/conf \
           -v ~/lepbase/v4/download/data:/var/www/v4 \
           -p 8012:80 \
           lepbase/h5ai

# run a container
           # call it lb-download
           # mount some directories
           # map the port
           # using the lepbase h5ai image

BLAST

docker run -d \
           --name lb-blast \
           -v ~/lepbase/v4/blast/conf:/conf \
           -v ~/lepbase/v4/blast/blastdbs:/dbs \
           -p 8013:4567 \
           lepbase/sequenceserver

# run a container
           # call it lb-blast
           # mount some directories
           # map the port
           # using the lepbase sequenceserver image

Updated less than a minute ago