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        "author": "Brent Pedersen, Joe Brown",
        "author_email": "bpederse@gmail.com",
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            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 3",
            "Topic :: Utilities"
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        "description": "bsub\n====\n\npython wrapper to submit jobs to bsub (and later qsub)\n\nAuthors\n------\n@brentp, @brwnj\n\n\nExample\n-------\n\n```python\n>>> from bsub import bsub\n>>> sub = bsub(\"some_job\", R=\"rusage[mem=1]\", verbose=True)\n\n# submit a job via call'ing the sub object with the command to run.\n# the return value is the numeric job id.\n>>> print sub(\"date\").job_id.isdigit()\nTrue\n\n# 2nd argument can be a shell script, in which case\n# the call() is empty.\n#>>> bsub(\"somejob\", \"run.sh\", verbose=True)()\n\n# dependencies:\n>>> job_id = bsub(\"sleeper\", verbose=True)(\"sleep 2\").job_id\n>>> bsub.poll(job_id)\nTrue\n\n```\n\nSugar\n-----\n\nFor file jobs, we can emulate shell syntax:\n\n```Python\n\njob = bsub('my-job') < 'run.sh'\n```\n\nSame for text commands:\n\n```Python\n\n\"echo hello\" | bsub('other-job')\n\n```\n\nChaining\n--------\n\nIt's possible to specify dependencies to LSF using a flag like:\n\n   bsub -w 'done(\"other-name\")' < myjob\n\nWe make this more pythonic with:\n\n```Python\n\n>>> j = sub('sleep 1').then('sleep 2')\n\n```\nwhich will wait for the first job `sleep 1` to complete\nbefore running the second job `sleep 2`. These can be chained as:\n\n```Python\n\nj = sub('myjob')\nj2 = j('sleep 1')\nj3 = j2.then('echo \"hello\"')\nj4 = j3.then('echo \"world\"')\nj5 = j4.then('my scripts.p')\n\n# or:\n\nj('sleep 1').then('echo \"hello\"').then('echo \"world\"')\n\n```\nWhere each job in `.then()` is not run until the preceding job\nis `done()` according to LSF.\n\n\nBioinformatics example of chaining:\n\nThis would submit jobs for positive and negative strand coverage in parallel.\nEach strand submitting jobs that run serially.\n\n```Python\n\nfrom bsub import bsub\n\nsubmit = bsub(\"bam2bg\", verbose=verbose)\n\n# convert bam to stranded bg then bw\nsample = \"subject_1\"\nchrom_sizes = \"chrom_sizes.txt\"\n\n#  submit jobs by strand for parallel processing\nfor symbol, strand in zip([\"+\", \"-\"], [\"pos\", \"neg\"]):\n\n    bigwig = \"%s_%s.bw\" % (sample, strand)\n    bedgraph = \"%s_%s.bedgraph\" % (sample, strand)\n\n    bam_to_bg = (\"bedtools genomecov -strand %s -bg \"\n                    \"-ibam %s | bedtools sort -i - > %s\") % (symbol, bam, bedgraph)\n    bg_to_bw = \"bedGraphToBigWig %s %s %s\" % (bedgraph, chrom_sizes, bigwig)\n    gzip_bg = \"gzip -f %s\" % bedgraph\n\n    # process strand-based steps serially\n    # submit first 2 jobs to default queue; final job to 'gzip' queue\n    submit(bam_to_bg).then(bg_to_bw, job_name=\"bg2bw\").then(gzip_bg, \"gzipbg\", q='gzip')\n\n```\n\n\nCommand-Line\n------------\n\nuse the command-line to run jobs with auto-specified err and log files:\n\n\n```Shell\necho \"hello\" | python -m bsub -J \"fake\" \nbsub  -J fake -e fake.%J.err -o fake.%J.out < /tmp/tmp3vFDwn.sh\n```\nIf a log/ directory exists, the logs will be placed there.\n\nthe shell script is automatically created and cleaned up after use.",
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