Setup and Installation

This guide will walk you through the process of setting up and installing the RNAchrom Nextflow pipeline.

Prerequisites

Before you begin, ensure you have the following installed on your system:

Java 8 or later
Nextflow (version 20.04.0 or later)
Anaconda

The pipeline uses Conda environments specified in envs/ directory . Ensure you have Conda installed on your system.

Installing Nextflow

To install Nextflow, run the following commands:

$ curl -s https://get.nextflow.io | bash
$ mv nextflow ~/bin/

Make sure ~/bin is in your PATH.

Cloning the Repository Clone the RNAchrom repository:

$ git clone https://github.com/your-repo/rnachrom.git
$ cd rnachrom

Pipeline Dependencies

The pipeline automatically installs several tools during execution. These include:

RnaChromATA
Bitap
StereoGene
fastq-dupaway

Installation Process

The PrepareSoftware process in the pipeline handles the installation of these tools:

RnaChromATA

Installed from the bin/RnaChromATA/setup.py file in the project directory.

Bitap

Cloned from the GitHub repository and compiled:

$ git clone https://github.com/ikm4rkov/RawReadsProcessor.git

StereoGene

Cloned from GitHub and compiled:

$ git clone https://github.com/favorov/stereogene.git
$ cd stereogene/src
$ make

fastq-dupaway

Cloned from GitHub and compiled:

$ git clone https://github.com/AndrewSigorskih/fastq-dupaway.git
$ cd fastq-dupaway
$ make

Running the Pipeline

Before running pipeline with real data, try running the pipeline in test mode. Thus, all required tools and conda environments will be installed.

To run the pipeline:

$ nextflow run main.nf --input samples.csv --outdir results

Troubleshooting

If you encounter issues during installation or execution:

Ensure all prerequisites are correctly installed. Check the log files in the work directory for error messages. Verify that all required input files are present and correctly formatted. For more detailed information, refer to the pipeline documentation or open an issue on the GitHub repository.