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https://github.com/mskcc/roslin-variant
Roslin is a reproducible and reusable workflow for Cancer Genomic Sequencing Analysis
https://github.com/mskcc/roslin-variant
pipeline prism
Last synced: about 1 month ago
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Roslin is a reproducible and reusable workflow for Cancer Genomic Sequencing Analysis
- Host: GitHub
- URL: https://github.com/mskcc/roslin-variant
- Owner: mskcc
- Created: 2017-03-14T14:49:44.000Z (almost 8 years ago)
- Default Branch: 2.6.x
- Last Pushed: 2021-06-15T21:49:48.000Z (over 3 years ago)
- Last Synced: 2023-10-20T21:55:37.062Z (about 1 year ago)
- Topics: pipeline, prism
- Language: Python
- Homepage:
- Size: 793 MB
- Stars: 15
- Watchers: 31
- Forks: 7
- Open Issues: 11
-
Metadata Files:
- Readme: README.md
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README
# 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](https://packages.ubuntu.com/bionic/python3)
- [Python3-dev](https://packages.ubuntu.com/bionic/python3-dev)
- [Singularity 3.3.0+](https://sylabs.io/guides/3.0/user-guide/installation.html#distribution-packages-of-singularity)
- [MongoDB 3.0.15+](https://docs.openstack.org/project-install-guide/meter/newton/database/environment-nosql-database-rdo.html) (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](../../issues) for related solutions. If you cannot solve the problem without our help, then please create a [new issue](../../issues/new) 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](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]
```