Instructions on auto-deploying BBMRI BIOS pipeline using ansible, conda and biopet framework.

BBMRI BIOS pipeline

The RNAseq pipeline that can be deployed using this Ansible script is the exact replication of the RNAseq pipeline used by this Nature Genetics paper (www.nature.com/ng/journal/v49/n1/full/ng.3737.html). For more background information, please read its method section.

Prerequisite

• Please read the general introduction of Ansible first: http://docs.ansible.com/ansible/latest/intro_getting_started.html#
• A basic understanding of (Bio-)Conda is good to have, but not really required if you just want to deploy this BBMRI BIOS pipeline.
• On the managing computer, Ansible 2.0 or higher is required to run the playbook.
• On the managed computer/VM, Ubuntu (tested on 14.04) with SSH and a user account (sudo is not necessary) is required.

• Gcc and libxrender should be installed already.

Test with Vagrant

To run this playbook within vagrant the following requirements are needed:

• Anisble installed
• VirtualBox installed
• Vagrant installed (version 1.5.x and above)

If the machine is not up yet run the follow command withing this directory:

vagrant up

If this is the first time provision, ansible will start automatically. To manually start provision when the VM is already up please use:

vagrant provision

Deploy pipeline and all its dependency on a remote server/VM

In the [invertory.yml] file the nodes where to install this pipeline are listed. Here you can also define a user account to use on the remote machine. In the [playbook.yml] file, you should specify "data_dir" in "vars".

To execute the playbook run the following command on the managing computer:

ansible-playbook -i inventory.yml playbook.yml

Run pipeline with tested dataset

Define samples in samples.yml:

samples:
  sample1:
    libraries:
      lib1:
        R1: <Path to R1 fq>
        R2: <Path to R2 fq>
  sample2:
    libraries:
      lib1:
        R1: <Path to R1 fq>
        R2: <Path to R2 fq>

Running a dry run of the pipeline:

bios-pipeline -config <samples.yml> -cv output_dir=<output_dir>

Running the pipeline with:

bios-pipeline -config <samples.yml> -cv output_dir=<output_dir> -run

Running multiple jobs in parallel:

bios-pipeline -config <samples.yml> -cv output_dir=<output_dir> -maxConcurrentRun 10  -jobRunner ParallelShell -run