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pyrpipe: python rna-seq pipeliner


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


  • python 3.6 or higher
  • OS: Linux, Mac

pyrpipe provides API to:

Tool Purpose
SRA Tools (v. 2.9.6 or higher) SRA access
Trimgalore QC
Hisat2 Alignment
STAR Alignment
Bowtie2 Alignment
Kallisto Quant
Salmon Quant
Stringtie Transcript Assembly
Cufflinks Transcript Assembly
Trinity Transcript Assembly
Samtools Tools
Portcullis Tools
Mikado Tools

Read the documentation here


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 
. ./
  1. Go one directory above (use same terminal used for tests and run py.test tests/test_*

Install current developer version

git clone
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 ; . ./
#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

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