pyrpipe
Project description
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.
Preprint is available here
Note: pyrpipe version 0.0.4 and above is not compatible with lower versions due to changes in the API design.
What it does
Allows fast and easy development of bioinformatics pipelines in python by providing
- a high level api to popular bioinformatics tools
- optimizes program parameters based on the data
- 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:
Tool | Purpose |
---|---|
SRA Tools (v. 2.9.6 or higher) | SRA access |
Trimgalore | QC |
BBDuk | 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
Installation
Please follow these instruction:
To create a new Conda environment (optional):
- Download and install Conda
conda create -n pyrpipe python=3.7
conda activate pyrpipe
NOTE: You need to install the third-party tools to work with pyrpipe. We recomend installing these through bioconda where possible. A recommended environment file, using python 3.7, is given here. It is best to share your conda environment files with pyrpipe scripts to ensure reproducibility.
Install latest stable version
pip install pyrpipe --upgrade
If above command fails due to dependency issues, try:
- Download the requirements.txt
pip install -r requirements.txt
pip install pyrpipe
To run tests:
- Download the test set (direct link)
pip install pytest
- To build test_environment. Please READ THIS
- From pyrpipe root directory, 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
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