INSTALL.md

Installation

This small tutorial will explain to you how to install and run CAW on a small sample test data on any POSIX compatible system (Linux, Solaris, OS X, etc).

To use this pipeline, you need to have a working version of Nextflow installed, Reference files and Docker or Singularity to facilitate the use of other tools. You can use a small reference genome as testing

• See the Install Nextflow documentation
• See the Reference files documentation
• See the Install Docker documentation
• See the Install Singularity documentation

Installation

This workflow itself needs little installation.

Nextflow will automatically fetch CAW from GitHub when launched if SciLifeLab/CAW is specified as the workflow name.

CAW use Singularity containers to package all the different tools.

If you plan to use the automatic pull of Singularity images, you can use the singularity.config configuration file. You can also set up the Nextflow environnement variable NXF_SINGULARITY_CACHEDIR to choose where to store them.

For example

export NXF_SINGULARITY_CACHEDIR=$HOME/.singularity

Docker can also be used as a container technology.

Test CAW with small dataset and small reference

The following tutorial explain how to run CAW on a small dataset using a small reference.

# Connect to your system
> ssh -AX [USER]@[system]
# Or just open a terminal

# Install Nextflow
> curl -s https://get.nextflow.io | bash

# Move Nextflow into your $PATH
> mv nextflow $HOME/bin

# Set up the cache directory for Singularity Images if needed
> export NXF_SINGULARITY_CACHEDIR=$HOME/.singularity

# make a test directory
> mkdir test_CAW
> cd test_CAW

# Download and build the smallGRCh37 reference using Singularity
> nextflow run SciLifeLab/CAW/buildReferences.nf --download --genome smallGRCh37 -profile singularity

# Or download and build the smallGRCh37 reference using Docker
> nextflow run SciLifeLab/CAW/buildReferences.nf --download --genome smallGRCh37 -profile docker

# Test CAW on a test tiny set using Singularity
> nextflow run SciLifeLab/CAW --test --genome smallGRCh37 --noReports -profile singularity

# Or test CAW on a test tiny set using Docker
> nextflow run SciLifeLab/CAW --test --genome smallGRCh37 --noReports -profile docker

Update

To update CAW, it's also very simple:

# Connect to your system
> ssh -AX [USER]@[system]REFERENCES
# Or just open a terminal

# Update CAW
> nextflow pull SciLifeLab/CAW

Run CAW on real data

Follow the references documentation on how to download/build the references files.

Follow the configuration and profile documentation on how to modify and use the configuration files and profiles.

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