pyrpipe 0.0.0

pyrpipe

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

Installation

Please follow these instruction

Install latest stable version

pip install pyrpipe

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

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