run

#!/data/users/astar/gis/rpd/apps/miniconda3/bin/python
"""Convenience wrapper to pipelines for users

This is the only place where the interpreter needs to be set for a
release.

Could be used to set other env vars but then things get
tricky (needed for example in Snakefile etc).
"""


import subprocess
import os
import sys
from collections import namedtuple


Pipeline = namedtuple('Pipeline', ['cat', 'script'])

disabled_pipeline_cfg = os.path.join(os.path.dirname(os.path.realpath(__file__)), 
                                     ".disabled-pipelines.txt")
disabled_pipelines = []
if os.path.exists(disabled_pipeline_cfg):
    with open(disabled_pipeline_cfg) as fh:
        for line in fh:
            disabled_pipelines.append(line.strip())
#sys.stderr.write("DEBUG disabled = {}\n".format(disabled_pipelines))

SCRIPTS = ['chromatin-profiling/atacseq/atacseq.py',
           'chromatin-profiling/chipseq/chipseq.py',
           'custom/SG10K/SG10K.py',
           'germs/vipr/vipr.py',
           'mapping/BWA-MEM/BWA-MEM.py',
           'metagenomics/essential-genes/essential-genes.py',
           'metagenomics/shotgun-metagenomics/shotgun-metagenomics.py',
           'rnaseq/fluidigm-ht-c1-rnaseq/fluidigm-ht-c1-rnaseq.py',
           'rnaseq/star-rsem/star-rsem.py',
           'rnaseq/wafergen-scrna/wafergen-scrna.py',
           'somatic/lofreq-somatic/lofreq-somatic.py',
           'somatic/mutect/mutect.py',
           'variant-calling/gatk/gatk.py',
           'variant-calling/lacer-lofreq/lacer-lofreq.py'
       ]

SCRIPTS = [s for s in SCRIPTS if s not in disabled_pipelines]

def usage(fh, pipeline_map):
    """print usage info"""
    myname = os.path.abspath(sys.argv[0])
    fh.write("Usage: {} name options\n".format(myname))
    fh.write(" e.g.: {} gatk --help\n\n".format(myname))
    fh.write("Please chose a pipeline from the following list:\n")
    for cat in sorted(set([pipeline.cat for pipeline in pipeline_map.values()])):
        fh.write("# category: {}\n".format(cat))
        # this is stupid
        for k, p in sorted(pipeline_map.items()):
            if p.cat == cat:
                fh.write("{}\n".format(k))


def main():
    """main function"""
    python = sys.executable
    root_path = os.path.dirname(os.path.abspath(
        os.path.realpath(sys.argv[0])))
    # set PYTHONPATH, used within wrappers and Snakefiles though
    #python_path = sys.path
    #python_path.insert(0, os.path.join(root_path, "lib"))

    pipeline_map = dict()
    for script in SCRIPTS:
        key = os.path.basename(os.path.splitext(script)[0])
        cat = os.path.dirname(script).split(os.sep)[0]
        script = os.path.join(root_path, script)
        pipeline_map[key] = Pipeline(cat, script)

    if len(sys.argv) > 1:
        name = sys.argv[1]
    else:
        name = None
    if name not in pipeline_map or not name:
        if name is None:
            sys.stderr.write("ERROR: Need pipeline name as first argument.\n")
            usage(sys.stderr, pipeline_map)
        elif name not in pipeline_map:
            sys.stderr.write("FATAL: unknown pipeline '{}'\n".format(name))
            usage(sys.stderr, pipeline_map)
        sys.exit(1)
    pipeline_args = sys.argv[2:]

    pipeline = pipeline_map[name]
    #cmd = "PYTHONPATH={} {} {}".format(':'.join(python_path), python, pipeline.script)
    cmd = "{} {} {}".format(python, pipeline.script, ' '.join(pipeline_args))
    subprocess.call(cmd, shell=True)

if __name__ == "__main__":
    main()