Skill Tracer
Skills › Knowledge Work Plugins › nextflow-development › installation.md

installation.md

96 lines · bio-research/skills/nextflow-development/references/installation.md at 2574e29

Open on GitHub
1# Installation
2

Installation

Raw lines 1 to 2
3## Contents
4- [Quick install](#quick-install)
5- [Docker setup](#docker-setup)
6- [Singularity setup (HPC)](#singularity-setup-hpc)
7- [nf-core tools (optional)](#nf-core-tools-optional)
8- [Verify installation](#verify-installation)
9- [Common issues](#common-issues)

Contents

  • Quick install
  • Docker setup
  • Singularity setup (HPC)
  • nf-core tools (optional)
  • Verify installation
  • Common issues
Raw lines 3 to 10
11## Quick install
13```bash
14# Nextflow
15curl -s https://get.nextflow.io | bash
16mv nextflow ~/bin/
17export PATH="$HOME/bin:$PATH"
19# Verify
20nextflow -version
21java -version # Requires 11+
22```

Quick install

# Nextflow
curl -s https://get.nextflow.io | bash
mv nextflow ~/bin/
export PATH="$HOME/bin:$PATH"

# Verify
nextflow -version
java -version  # Requires 11+
Raw lines 11 to 23
24## Docker setup

Docker setup

Raw lines 24 to 25
26### Linux
27```bash
28sudo apt-get update && sudo apt-get install docker.io
29sudo systemctl enable --now docker
30sudo usermod -aG docker $USER
31# Log out and back in
32```

Linux

sudo apt-get update && sudo apt-get install docker.io
sudo systemctl enable --now docker
sudo usermod -aG docker $USER
# Log out and back in
Raw lines 26 to 33
34### macOS
35Download Docker Desktop: https://docker.com/products/docker-desktop

macOS

Download Docker Desktop: https://docker.com/products/docker-desktop

Raw lines 34 to 36
37### Verify
38```bash
39docker run hello-world
40```

Verify

docker run hello-world
Raw lines 37 to 41
42## Singularity setup (HPC)
44```bash
45# Ubuntu/Debian
46sudo apt-get install singularity-container
48# Or via conda
49conda install -c conda-forge singularity
50```

Singularity setup (HPC)

# Ubuntu/Debian
sudo apt-get install singularity-container

# Or via conda
conda install -c conda-forge singularity
Raw lines 42 to 51
52### Configure cache
53```bash
54export NXF_SINGULARITY_CACHEDIR="$HOME/.singularity/cache"
55mkdir -p $NXF_SINGULARITY_CACHEDIR
56echo 'export NXF_SINGULARITY_CACHEDIR="$HOME/.singularity/cache"' >> ~/.bashrc
57```

Configure cache

export NXF_SINGULARITY_CACHEDIR="$HOME/.singularity/cache"
mkdir -p $NXF_SINGULARITY_CACHEDIR
echo 'export NXF_SINGULARITY_CACHEDIR="$HOME/.singularity/cache"' >> ~/.bashrc
Raw lines 52 to 58
59## nf-core tools (optional)
61```bash
62pip install nf-core
63```
65Useful commands:
66```bash
67nf-core list # Available pipelines
68nf-core launch rnaseq # Interactive parameter selection
69nf-core download rnaseq -r 3.14.0 # Download for offline use
70```

nf-core tools (optional)

pip install nf-core

Useful commands:

nf-core list                    # Available pipelines
nf-core launch rnaseq           # Interactive parameter selection
nf-core download rnaseq -r 3.14.0  # Download for offline use
Raw lines 59 to 71
72## Verify installation
74```bash
75nextflow run nf-core/demo -profile test,docker --outdir test_demo
76ls test_demo/
77```

Verify installation

nextflow run nf-core/demo -profile test,docker --outdir test_demo
ls test_demo/
Raw lines 72 to 78
79## Common issues
81**Java version wrong:**
82```bash
83export JAVA_HOME=/path/to/java11
84```
86**Docker permission denied:**
87```bash
88sudo usermod -aG docker $USER
89# Log out and back in
90```
92**Nextflow not found:**
93```bash
94echo 'export PATH="$HOME/bin:$PATH"' >> ~/.bashrc
95source ~/.bashrc
96```

Common issues

Java version wrong:

export JAVA_HOME=/path/to/java11

Docker permission denied:

sudo usermod -aG docker $USER
# Log out and back in

Nextflow not found:

echo 'export PATH="$HOME/bin:$PATH"' >> ~/.bashrc
source ~/.bashrc
Raw lines 79 to 96