SYSUCC-RNAseqPipe installation

1 Install NextFlow

Nextflow runs on most POSIX systems (Linux, Mac OSX etc). It can be installed by running the following commands:

# Make sure that Java v8+ is installed
java -version
# Install Nextflow
curl -fsSL get.nextflow.io | bash
# Add Nextflow binary to your PATH:
mv nextflow ~/bin/
# OR system-wide installation:
# sudo mv nextflow /usr/local/bin

See nextflow.io for further instructions on how to install and configure Nextflow.

2 Install the pipeline

2.1 Get project code

The whole pipeline is hosted in github. To install, you’ll need to download and transfer the pipeline files manually:

# create directory
mkdir -p ~/my-pipelines/
# clone project code
git clone https://github.com/likelet/RNAseqPipe.git
# Run analysis with test
cd ~/my_data/
nextflow run ~/my-pipelines/RNAseqPipe -profile test

To stop nextflow from looking for updates online, you can tell it to run in offline mode by specifying the following environment variable in your ~/.bashrc file:

export NXF_OFFLINE='TRUE'

2.2 Development

If you would like to make changes to the pipeline, it’s best to make a fork on GitHub and then clone the files. Once cloned you can run the pipeline directly as above.

3 Pipeline configuration

By default, the pipeline runs with the standard configuration profile. This uses a number of sensible defaults for process requirements and is suitable for running on a simple (if powerful!) basic server. You can see this configuration in [conf/base.config](../conf/base.config).

Be warned of two important points about this default configuration:

  1. The default profile uses the local executor
    • All jobs are run in the login session. If you’re using a simple server, this may be fine. If you’re using a compute cluster, this is bad as all jobs will run on the head node.
    • See the `nextflow docs <https://www.nextflow.io/docs/latest/executor.html`_ for information about running with other hardware backends. Most job scheduler systems are natively supported.
  2. Nextflow will expect all software to be installed and available on the PATH

3.1 Software deps: Docker

First, install docker on your system: Docker Installation Instructions

Then, running the pipeline with the option -profile standard,docker tells Nextflow to enable Docker for this run. An image containing all of the software requirements will be automatically fetched and used from dockerhub (https://hub.docker.com/r/likelet/RNAseqPipe/).

3.2 Software deps: Singularity

If you’re not able to use Docker then Singularity is a great alternative. The process is very similar: running the pipeline with the option -profile standard,singularity tells Nextflow to enable singularity for this run. An image containing all of the software requirements will be automatically fetched and used from singularity hub.

If running offline with Singularity, you’ll need to download and transfer the Singularity image first:

singularity pull --name RNAseqPipe.simg shub://likelet/RNAseqPipe

Once transferred, use -with-singularity and specify the path to the image file:

nextflow run /path/to/circPipe -with-singularity circPipe.simg

Remember to pull updated versions of the singularity image if you update the pipeline.

3.3 Software deps: conda

If you’re not able to use Docker _or_ Singularity, you can instead use conda to manage the software requirements. This is slower and less reproducible than the above, but is still better than having to install all requirements yourself! The pipeline ships with a conda environment file and nextflow has built-in support for this. To use it first ensure that you have conda installed (we recommend `miniconda<https://conda.io/miniconda.html>`_, then follow the same pattern as above and use the flag -profile standard,conda

Note

When using conda profile, users should preinstalled DAtools in your system and specify the path in config files. To get the DAtools plz using the following command:

curl http://cancerbio.info/pub/DATOOLS/DAtools_v2.7.4.jar
chmod 777 DAtools_v2.7.4.jar
mv DAtools_v2.7.4.jar /opt/