def __init__(self, callbaack_url, scratch):
self.callback_url = callbaack_url
self.scratch = scratch
self.file_util = FU(callbaack_url)
self.special = special(self.callback_url)
self.report = report(self.callback_url, scratch)
self.wdl_file = '/kb/module/jgi_meta_spades.wdl'
def __init__(self, callbaack_url, scratch, wdl='../../metaAssembly/'):
self.callback_url = callbaack_url
self.scratch = scratch
self.special = special(self.callback_url)
self.ru = ReadsUtils(self.callback_url)
self.au = AssemblyUtil(self.callback_url)
self.report = KBaseReport(self.callback_url)
self.wdl_base = wdl
def _test_slurm(self, token):
print("Submitting SLURM")
sr = special(self.callback_url, token=token)
with open('./work/tmp/slurm.sl', 'w') as f:
f.write('#/bin/sh')
f.write('echo hello')
p = {'submit_script': 'slurm.sl'}
res = sr.slurm(p)
print('slurm' + str(res))
def wdl(callback_url, token, params):
sr = special(callback_url, token=token)
src = '/kb/module/workflow.wdl'
wdl_file = 'workflow.wdl'
shutil.copy(src, '/kb/module/work/tmp/' + wdl_file)
input_file = 'inputs.json'
ins = {'name': 'KBase'}
with open('/kb/module/work/tmp/' + input_file, 'w') as f:
f.write(json.dumps(ins))
p = {'workflow': wdl_file, 'inputs': input_file}
res = sr.wdl(p)
print('wdl: ' + str(res))