Arteria bcl2fastq

A self contained (Tornado) REST service for running Illuminas bcl2fastq.

Trying it out

The easiest way to try out arteria-bcl2fastq is to run it in the provided Vagrant box.

# get the vagrant environment running
# Please note that starting this vm requires 4 GB or RAM (since bcl2fastq requires alot of memory to run)
vagrant up

# ssh into it
vagrant ssh

# move into the vagrant working directory
cd /vagrant

# create a virtual environment and activate it
virtualenv venv && source venv/bin/activate

# update pip (unfortunately the installed verison is to old)
pip install --upgrade pip    

# install bcl2fastq (with -e for "editable" to make development easier)
pip install -r requirements/dev .

Now you can try running it:

 bcl2fastq-ws --config config/ --port 8888

And then you can find a simple api documentation by opening up an additional terminal by running going to:

curl http://localhost:8888/api | python -m json.tool

To try things out a bit more, you need to setup a path to watch and place some runfolders there, e.g.

# Create the following folders under the /vagrant directory (or anywhere you like, but then
# you need to make the corresponding changes in the `config/app.config`).
mkdir ./bcl2fastq_logs ./runfolder_output

# Clone a directory with test data
git clone https://github.com/roryk/tiny-test-data.git

# Start the service again
bcl2fastq-ws --config config/ --port 8888

# And now you can kick of running bcl2fastq on the small runfolder by:
curl -X POST --data '{"additional_args": "--ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls"}' http://localhost:8888/api/1.0/start/flowcell

# You can poll its status on the returned link, or you can poll
curl http://localhost:8888/api/1.0/status/