<reponame>pwwang/biopipen<gh_stars>1-10
#!/usr/bin/env python
"""Using PyPPL to distribute and run commands."""
import sys
from os import path
from pyppl import PyPPL, Proc, Diot
from bioprocs import params
from tempfile import gettempdir

params._prefix     = '-'
params._hbald      = False
params.cmds.desc   = 'The cmd list. If not provided, STDIN will be used.'
params.runner      = 'local'
params.runner.desc = 'The runner.'
params.intype      = 'stdin' # or file, stdin, or cmds (pass cmds directly)
params.intype.desc = 'Type of option `cmds`, cmds or file?'
params.cache       = False
params.cache.desc  = 'Cache the jobs or not?'
params.ppldir      = path.join(gettempdir(), 'bioprocs.workdir')
params.ppldir.desc = 'The ppldir to save the pipeline data.'
params.forks       = 1
params.forks.desc  = 'How many jobs to run simultaneously.'

def main():
	opts = params._parse(dict_wrapper = Diot)

	if not isinstance(opts.cmds, list):
		if opts.intype == 'cmds':
			opts.cmds = opts.cmds.splitlines()
		elif opts.intype == 'file':
			with open(opts.cmds) as f:
				opts.cmds = f.read().splitlines()
		else:
			opts.cmds = []
			for line in sys.stdin:
				opts.cmds.append(line.strip())

	pCmdRunner        = Proc(desc = 'Using PyPPL to distribute and run commands.')
	pCmdRunner.runner = opts.get('runner', 'local')
	pCmdRunner.cache  = opts.cache
	pCmdRunner.errhow = 'halt'
	pCmdRunner.forks  = int(opts.get('forks', 1))
	pCmdRunner.input  = {'cmd': opts.cmds}
	pCmdRunner.script = '{{i.cmd}}'

	config = {'_log': {'file': None}, 'default': {'ppldir': opts.ppldir}}
	PyPPL(config).start(pCmdRunner).run()

if __name__ == "__main__":
	main()

#!/usr/bin/env python
"""Using PyPPL to distribute and run commands."""
import sys
from os import path
from pyppl import PyPPL, Proc, Diot
from bioprocs import params
from tempfile import gettempdir

params._prefix     = '-'
params._hbald      = False
params.cmds.desc   = 'The cmd list. If not provided, STDIN will be used.'
params.runner      = 'local'
params.runner.desc = 'The runner.'
params.intype      = 'stdin' # or file, stdin, or cmds (pass cmds directly)
params.intype.desc = 'Type of option `cmds`, cmds or file?'
params.cache       = False
params.cache.desc  = 'Cache the jobs or not?'
params.ppldir      = path.join(gettempdir(), 'bioprocs.workdir')
params.ppldir.desc = 'The ppldir to save the pipeline data.'
params.forks       = 1
params.forks.desc  = 'How many jobs to run simultaneously.'

def main():
	opts = params._parse(dict_wrapper = Diot)

	if not isinstance(opts.cmds, list):
		if opts.intype == 'cmds':
			opts.cmds = opts.cmds.splitlines()
		elif opts.intype == 'file':
			with open(opts.cmds) as f:
				opts.cmds = f.read().splitlines()
		else:
			opts.cmds = []
			for line in sys.stdin:
				opts.cmds.append(line.strip())

	pCmdRunner        = Proc(desc = 'Using PyPPL to distribute and run commands.')
	pCmdRunner.runner = opts.get('runner', 'local')
	pCmdRunner.cache  = opts.cache
	pCmdRunner.errhow = 'halt'
	pCmdRunner.forks  = int(opts.get('forks', 1))
	pCmdRunner.input  = {'cmd': opts.cmds}
	pCmdRunner.script = '{{i.cmd}}'

	config = {'_log': {'file': None}, 'default': {'ppldir': opts.ppldir}}
	PyPPL(config).start(pCmdRunner).run()

if __name__ == "__main__":
	main()
#!/usr/bin/env python Using PyPPL to distribute and run commands. # or file, stdin, or cmds (pass cmds directly)