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    "info": {
        "author": "Soumitra Pal",
        "author_email": "soumitrakp@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "License :: OSI Approved :: MIT License",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 3"
        ],
        "description": "# JUDI - Bioinformatics Pipeline: *Just Do It*\n\n*judi* comes from the idea of bringing the power and efficiency of *doit* to\nexecute any kind of task under many combinations of parameter settings.\n\n\n## Sample Code\n\nSnippet from [tutorial](https://judi.readthedocs.io/tutorial_1.html), save it as ``dodo.py``.\n\n```python\nfrom judi import File, Task, add_param, combine_csvs\n\nadd_param('100 101 102 103'.split(), 'sample')\nadd_param('1 2'.split(), 'group')\n\nREF = 'hg_refs/hg19.fa'\npath_gen = lambda x: '{}_{}.fq'.format(x['sample'],x['group'])\n\nclass AlignFastq(Task):\n  inputs = {'reads': File('orig_fastq', path = path_gen)}\n  targets = {'sai': File('aln.sai')}\n  actions = [('bwa aln {} {} > {}', [REF,'$reads','$sai'])]\n\nclass CreateBam(Task):\n  mask = ['group']\n  inputs = {'reads': AlignFastq.inputs['reads'],\n             'sai': AlignFastq.targets['sai']}\n  targets = {'bam': File('aln.bam', mask = mask)}\n  actions = [('bwa sampe {} {} {} | samtools view -Sbh - | samtools sort - > {}', [REF,'$sai','$reads','$bam'])]\n\nclass GetCoverage(Task):\n  mask = ['group']\n  inputs = {'bam': CreateBam.targets['bam']}\n  targets = {'cov': File('cov.csv', mask = mask)}\n  actions = [('(echo val; samtools rmdup {} - | samtools mpileup - | cut -f4) > {}', ['$bam','$cov'])]\n\nclass CombineCoverage(Task):\n  mask = ['group', 'sample']\n  inputs = {'cov': GetCoverage.targets['cov']}\n  targets = {'csv': File('combined.csv', mask = mask),\n             'pdf': File('pltcov.pdf', mask = mask, root = '.')}\n  actions = [(combine_csvs, ['#cov', '#csv']),\n             (\"\"\"echo \"library(ggplot2); pdf('{}')\n              ggplot(read.csv('{}'), aes(x = val)) +\n              geom_density(aes(color = factor(sample)))\"\\\n              | R --vanilla\"\"\", ['$pdf','$csv'])]\n```\nRun from terminal:\n\n```console\n$ doit list\nAlignFastq\nCombineCoverage\nCreateBam\nGetCoverage\n$ doit\n. AlignFastq:group~1,sample~100\n. AlignFastq:group~2,sample~100\n. AlignFastq:group~1,sample~101\n. AlignFastq:group~2,sample~101\n. AlignFastq:group~1,sample~102\n. AlignFastq:group~2,sample~102\n. AlignFastq:group~1,sample~103\n. AlignFastq:group~2,sample~103\n. CreateBam:sample~100\n. CreateBam:sample~102\n. CreateBam:sample~103\n. CreateBam:sample~101\n. GetCoverage:sample~100\n. GetCoverage:sample~102\n. GetCoverage:sample~103\n. GetCoverage:sample~101\n. CombineCoverage:\n```\n\n## Project Details\n\n - Website & docs - [https://pyjudi.readthedocs.io](https://pyjudi.readthedocs.io)\n - Project management on github - [https://github.com/ncbi/JUDI](https://github.com/ncbi/JUDI)\n\n## License\n\nThe MIT License\nCopyright (c) 2019-2020 Soumitra Pal\n\nsee LICENSE file\n\n\n## Install\n\n*judi* is tested on python 3.6.\n\n```console\n$ pip install judi\n```\n\n## Dependencies\n\n- doit\n\n## Documentation\n\n``docs`` folder contains ReST documentation based on Sphinx.\n\n```console\n$ make html\n```\n\n## Contributing\n\nOn github create pull requests using a named feature branch.\n\n\n",
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        "summary": "A Software Workflow Management System Based on DoIt",
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