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        "author": "Adam Cribbs",
        "author_email": "adam.cribbs@imm.ox.ac.uk",
        "bugtrack_url": null,
        "classifiers": [
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved",
            "Operating System :: MacOS",
            "Operating System :: POSIX",
            "Operating System :: Unix",
            "Programming Language :: Python",
            "Topic :: Scientific/Engineering",
            "Topic :: Software Development"
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        "description": "# cgat-showcase\n\ncgat-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.\n\nWithin 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\nwith [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.\n\nDocumentation on how to run this pipeline can be found [here](https://cgat-showcase.readthedocs.io/en/latest/) and documentation on how\nto build your own custom workflow from scratch can be found [here](https://cgat-core.readthedocs.io/en/latest/defining_workflow/Tutorial.html).\n\nInstallation\n------------\n\nThe following sections describe how to install the cgat-showcase pipeline.\n\nWe recommend installing using conda and the steps are described below::\n\n   `conda install -c cgat cgatshowcase`\n\nAlternatively, the pipeline can be installed using pip::\n\n   `pip install cgatshowcase`\n\nHowever, 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.\n",
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