To start using the uct-cbio/16S-rDNA-dada2-pipeline, follow the steps below:
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#From your home directory on hex install nextflow
curl -fsSL get.nextflow.io | bash
#Add the following to ~/.bashrc:
JAVA_HOME=/opt/exp_soft/java/jdk1.8.0_31/
JAVA_CMD=/opt/exp_soft/java/jdk1.8.0_31/bin/java
#Do not run nextflow from the headnode, it requires substantial memory to run java. Please therefore first start an interactive job as follows:
qsub -I -q UCTlong -l nodes=1:series600:ppn=1 -d `pwd`
You need NextFlow version >= 0.24 to run this pipeline.
See nextflow.io and NGI-NextflowDocs for further instructions on how to install and configure Nextflow.
This pipeline itself needs no installation - NextFlow will automatically fetch it from GitHub if uct-cbio/16S-rDNA-dada2-pipeline is specified as the pipeline name when executing nextflow run uct-cbio/16S-rDNA-dada2-pipeline. If for some reason you need to use the development branch, this can be specified as nextflow run uct-cbio/16S-rDNA-dada2-pipeline -r dev
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/uct-cbio/16S-rDNA-dada2-pipeline/archive/master.zip
unzip master.zip -d /my-pipelines/
cd /my_data/
nextflow run /my-pipelines/16S-rDNA-dada2-pipeline-master