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HelloModules

Before you begin

This project is an example of a BioLockJ module.

To build it, or even just to use it, you must have successfully installed and tested BioLockJ.

biolockj --version
biolockj ${BLJ}/templates/myFirstPipeline/myFirstPipeline.properties

For more information about how to create BioLockJ modules and for other examples, see the BioLockJ external modules resource repository

Use this module

See the userguide pages for the modules in this project.

Download the jar file to your external modules folder (mods), which you point to with the --external-modules argument. In your config file, reference the Hello_World module in your module run order using the #BioModule keyword.

Minimalist example:

PROJ=HelloModules
URL=https://github.com/BioLockJ-Dev-Team/HelloModules/releases/latest/download
CONFIG=sayHello.config

mkdir ${PROJ}_Example
cd ${PROJ}_Example
wget $URL/${PROJ}.jar -P $PWD/mods
wget $URL/demo.zip
unzip demo.zip && rm demo.zip 
biolockj --external-modules $PWD/mods ./demo/$CONFIG

The example above will create a minimalist pipeline demonstrating the use of the Hello_World module from the HelloModules project.

Add the #BioModule line for the Hello_World module to any other pipeline.

Build this module

Download the source code:

wget https://github.com/BioLockJ-Dev-Team/HelloModules/archive/refs/heads/main.zip 
unzip main.zip && rm main.zip && mv HelloModules-main HelloModules

Alternatively, use git:

# git clone https://github.com/BioLockJ-Dev-Team/HelloModules.git

Note: The build file references the BioLockJ project using the $BLJ variable. There is an option to use a relative path instead, see commented lines in the build.xml.

Run the ant command from the project root directory.

cd HelloModules
ant

If you encounter build difficulties, try using the docker build process below.

Test that BioLockJ recognizes the module.

biolockj-api listModules --external-modules $PWD/dist

The output list should include "com.github.fodorlab.hello_world.Hello_World".

Run a demo pipeline.

biolockj --external-modules $PWD/dist ./demo/sayHello.config

See more in the demo folder.

Build the project and its documentation using docker

Confirm docker is running:

docker run --rm hello-world

Note: the code block below references this project directory as $PWD.

cd HelloModules

This is the standard build process for BioLockJ modules.

docker run --rm \
  -v $PWD:/project \
  -v $BLJ:/BioLockJ \
  -e BLJ=/BioLockJ \
  -w /project \
  biolockjdevteam/build_and_deploy \
  ant userguide

This process produces the jar file and the standardized userguide pages for the modules in this project.