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
Read the docs here
Note: pyrpipe version 0.0.4 and above is not compatible with lower versions due to changes in the API design.
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
- python 3.6 or higher
- OS: Linux, Mac
| 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
Please follow these instruction:
- Download and install Conda
conda create -n pyrpipe python=3.7conda 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.
conda install -c bioconda pyrpipe
pip install pyrpipe --upgrade
If above command fails due to dependency issues, try:
- Download the requirements.txt
pip install -r requirements.txtpip 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_*
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_*
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