Metadata-Version: 1.1
Name: cgatshowcase
Version: 0.1.7
Summary: cgatshowcase : the Computational Genomics Analysis Toolkit example pipeline/workflow
Home-page: https://github.com/cgat-developers/cgat-showcase
Author: Adam Cribbs
Author-email: adam.cribbs@imm.ox.ac.uk
License: MIT
Description: # cgat-showcase
        
        cgat-showcase is a repository containing an example pipeline constructed to demonstrate how the [cgat-core](https://github.com/cgat-developers/cgat-core) workflow management system can be used to create common workflows required in bioinformatics analysis.
        
        Within this repository is an example [pipeline](https://github.com/cgat-developers/cgat-showcase/blob/master/cgatshowcase/pipeline_transdiffexprs.py) `pipeline_transdiffexprs.py` that performs pseudoalignment of fastq files
        with [kallisto](https://pachterlab.github.io/kallisto/about.html) and differential expression using [DESeq2](https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html). It can be run locally on your own machine or distributed across a cluster depending on your requirements.
        
        Documentation on how to run this pipeline can be found [here](https://cgat-showcase.readthedocs.io/en/latest/) and documentation on how
        to build your own custom workflow from scratch can be found [here](https://cgat-core.readthedocs.io/en/latest/defining_workflow/Tutorial.html).
        
        Installation
        ------------
        
        The following sections describe how to install the cgat-showcase pipeline.
        
        We recommend installing using conda and the steps are described below::
        
           `conda install -c cgat cgatshowcase`
        
        Alternatively, the pipeline can be installed using pip::
        
           `pip install cgatshowcase`
        
        However, you will require certain software to run the pipeline. More detail on installation can be found on the [Installation](https://cgat-showcase.readthedocs.io/en/latest/getting_started/Installation.html) documentation.
        
Keywords: computational genomics
Platform: any
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved
Classifier: Programming Language :: Python
Classifier: Topic :: Software Development
Classifier: Topic :: Scientific/Engineering
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Operating System :: MacOS
