Skip to content

Latest commit

 

History

History
49 lines (35 loc) · 1.67 KB

installation.md

File metadata and controls

49 lines (35 loc) · 1.67 KB
Raw

ICGC-FeatureCounts Installation

To start using the ICGC-FeatureCounts pipeline, there are three steps described below:

  1. Install Nextflow
  2. Install the pipeline
  3. Configure the pipeline

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 v7+ 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

You need NextFlow version >= 0.30.2 to run this pipeline.

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

2) Install the Pipeline

This pipeline itself needs no installation - NextFlow will automatically fetch it from GitHub if ICGC-FeatureCounts is specified as the pipeline name.

Offline use

If you need to run the pipeline on a system with no internet connection, you will need to download the files yourself from GitHub and run them directly:

wget https://github.com/ICGC-FeatureCounts/archive/master.zip
unzip master.zip -d /my-pipelines/
cd /my_data/
nextflow run /my-pipelines/icgc-featurecounts-master

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'