Roslin-variant

Roslin-variant is a reproducible and reusable workflow for Cancer Genomic Sequencing Analysis

Prerequisites

To build, deploy, and use Roslin, you will need:

• Python 3
• Python3-dev
• Singularity 3.3.0+
• MongoDB 3.0.15+ (optional)

Most testing of Roslin has been done with the specific versions above on hosts running CentOS 7.6. If you run into problems, search through the issues for related solutions. If you cannot solve the problem without our help, then please create a new issue with detailed information on how to reproduce your problem.

Installation

Clone the repo, switch to the current branch, init and update submodules:

git clone --branch 2.6.x --recurse-submodules https://github.com/mskcc/roslin-variant.git

Enter the repo and edit the configuration files as appropriate for your host/environment. At minimum, enter your MongoDB admin user/password in core/config.core.yaml:

cd roslin-variant
vi core/config.core.yaml
vi config.variant.yaml

Users of the Juno cluster at MSKCC, can simply copy sample-juno-config.yaml instead:

cp sample-juno-config.yaml config.variant.yaml

1. Add the root with the path where you want to install the pipeline
2. Modify TOIL_LSF_ARGS within both root and test env's as appropriate

You can use TOIL_LSF_ARGS to run all your jobs under a SLA or increase walltime. For example:

TOIL_LSF_ARGS: '-sla jvSC -W 168:00'

Here is a table containing the description of important keys in core/config.core.yaml:

Key	Description
root	The path to install roslin core, or an existing installation of roslin core
mongo	All the information needed to connect to the mongo database

Here is a table containing the description of important keys in config.variant.yaml:

Key	Description
root	The path to install roslin pipeline
binding.extra	All the paths in the host system that needs to be mounted
env	Envirornment variables to set before running the pipeline
dependencies.singularity	Location of singularity binary files
build.installCore	Option to either install core or use an existing installation
test.tempDir	Path to test tempdir
test.runArgs	Path to test run arguments

Here is how to use the source key under dependencies in config.variant.yaml:

Type	Example	Description	Dependency Supported
path	path:/usr/local/bin/singularity	Path to binary or source files	singularity, cmo, toil
module	module:singularity	Module name with the version key representing the module version	singularity
github	github:https://github.com/dataBiosphere/toil	Github repo with the version key representing the branch/tag	toil, cmo

For installation, simply run this script. Make sure it has internet access:

./build-pipeline.sh

After installation is completed you should see a message like this:

 ______     ______     ______     __         __     __   __
/\  == \   /\  __ \   /\  ___\   /\ \       /\ \   /\ "-.\ \
\ \  __<   \ \ \/\ \  \ \___  \  \ \ \____  \ \ \  \ \ \-.  \
 \ \_\ \_\  \ \_____\  \/\_____\  \ \_____\  \ \_\  \ \_\\"\_\
  \/_/ /_/   \/_____/   \/_____/   \/_____/   \/_/   \/_/ \/_/
 ______   __     ______   ______     __         __     __   __     ______
/\  == \ /\ \   /\  == \ /\  ___\   /\ \       /\ \   /\ "-.\ \   /\  ___\
\ \  _-/ \ \ \  \ \  _-/ \ \  __\   \ \ \____  \ \ \  \ \ \-.  \  \ \  __\
 \ \_\    \ \_\  \ \_\    \ \_____\  \ \_____\  \ \_\  \ \_\\"\_\  \ \_____\
  \/_/     \/_/   \/_/     \/_____/   \/_____/   \/_/   \/_/ \/_/   \/_____/

Roslin Pipeline

Your workspace: /home/vagrant/roslin-pipelines/variant/2.6.0/workspace/vagrant-3.10

Add the following line to your .profile or .bashrc if not already added:

source /home/vagrant/roslin-core/2.1.2/config/settings.sh

This message has two important pieces of information:

1. The location of your workspace in the pipeline
2. The settings.sh file that sets your env to operate the pipeline

Make sure to source the settings.sh in your ~/.bashrc or some other appropriate startup dotfile.

Test an example

Source the settings.sh, enter a folder with sample data, and run the bash wrapper around roslin_request_to_yaml.py and roslin_submit.py:

source [your settings.sh file path]
cd [your workspace path]/examples/SampleWorkflow
./run-example.sh

Add a user

If another user wants to run your deployment of Roslin, they can setup their own workspace by running:

source [your settings.sh file path]
roslin_workspace_init.py --name [your pipeline name] --version [your pipeline version]