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.
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:
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
Install latest stable version
pip install pyrpipe
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 (This will download tools):
cd tests && . ./build_test_env.sh
- Go one directory above
tests
and runpy.test tests/
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
py.test tests/
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
Project details
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