pyrpipe: python rna-seq pipeliner

Introduction

pyrpipe (Pronounced as "pyre-pipe") is a python package to easily develop RNA-Seq analyses workflow by integrating popular RNA-Seq analysis programs in an object oriented manner. pyrpipe can be used on local computers or on HPC environments to manage analysis of RNA-Seq data. Users can use the easy-to-use APIs to popular bioinformatic tools provided with pyrpipe, or can use the methods provided in the pyrpipe_engine module to integrate any other third-party program in their pipeline.

What it does

Allows fast and easy development of bioinformatics pipelines in python by providing

• a high level api to popular bioinformatics tools
• a general api to execute any linux command from python (using the subprocess module)
• comprehensive logging features to log all the commands, output and their return status
• report generating features for easy sharing, reproducing, benchmarking and debugging

Prerequisites

• python 3.6 or higher
• OS: Linux, Mac

pyrpipe provides API to:

Read the documentation here

Installation

Please follow these instruction:

To create a new Conda environment (optional):

1. Download and install Conda
2. conda create -n pyrpipe python=3.7
3. conda activate pyrpipe

Install latest stable version

pip install pyrpipe --upgrade

If above command fails due to dependency issues, try:

1. Download the requirements.txt
2. pip install -r requirements.txt
3. pip install pyrpipe

To run tests:

1. Download the test set (direct link)
2. pip install pytest
3. To build test_environment (This will download tools):

cd tests 
. ./build_test_env.sh

4. Go one directory above (use same terminal used for build_test_env.sh) tests and run py.test tests/test_*

Install current developer version

git clone https://github.com/urmi-21/pyrpipe.git
pip install -r pyrpipe/requirements.txt
pip install -e path_to/pyrpipe

#Running tests; From pyrpipe root perform
#To build test_environment (This will download tools): 
cd tests ; . ./build_test_env.sh
#in same terminal
py.test tests/test_*

Setting NCBI SRA Toolkit

Use vdb-config -i to configure SRA Toolkit. Make sure that:

• Under the TOOLS tab, prefetch downloads to is set to public user-repository
• Under the CACHE tab, location of public user-repository is not empty