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Releases: urmi-21/pyrpipe

Version 0.0.5

18 Jan 22:29
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0.0.5
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Version 0.0.5 Latest
Latest

Major changes in v 0.0.5

  • Implemented the Runnable class responsible for execution of all the tools
  • Runnable allows integrity checks and resume-able pipelines
  • pyrpipe now logs md5 checksums and create script backups
  • Enable auto-loading of yaml parameters
  • Added pyrpipe options such as dry-run safe-mode threads mem
  • Moved, refactored, and improved pyrpipe_diagnostic command
  • Added simple test command to test sratools integration
  • Removed some tools API
  • Better integration with workflow systems
  • Updated colors via colorama
  • Multiple bug fixes
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Version 0.0.4

23 Mar 20:22
@urmi-21 urmi-21
0.0.4
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Version 0.0.4

Version 0.0.4

  • Version 0.0.4 is not compatible with lower versions
  • Major changes in the API implementation
  • The constructors (for class representing tools) do not take **kwargs any more
  • **kwargs arguments can be passed to API functions
  • Case_study examples are updated to use version 0.0.4
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Version 0.0.3

17 Feb 21:10
@urmi-21 urmi-21
0.0.3
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Version 0.0.3
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Version 0.0.2

17 Feb 20:45
@urmi-21 urmi-21
0.0.2
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Version 0.0.2

pyrpipe v 0.0.2

  • Added Diamond
  • Added Transdecoder
  • Multiple refactor
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version 0.0.1

29 Jan 23:14
@urmi-21 urmi-21
0.0.1
56a2b08
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version 0.0.1

First release

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
Assets 2
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