def __init__(self, source, dest=None):
# Basic #
self.source = FASTQ(source)
self.dest = DirectoryPath(dest)
# Default case #
if dest is None:
self.dest = DirectoryPath(self.source.prefix_path + '.fastqc')
def __init__(self,
command,
language='python',
base_dir=os.path.abspath(os.getcwd()),
modules=None,
**kwargs):
# Check the modules variable is a list #
if modules is None: self.modules = []
elif not isinstance(modules, list): self.modules = list(modules)
else: self.modules = modules
# Check command type #
if not isinstance(command, list): command = [command]
# Log directory #
for i in range(30):
now = datetime.datetime.now(dateutil.tz.tzlocal())
log_name = now.strftime("%Y-%m-%da%Hh%Mm%Ss%Z%z")
base_dir = DirectoryPath(base_dir + log_name + '/')
if not base_dir.exists:
base_dir.create()
break
else:
time.sleep(2)
continue
else:
base_dir.create()
# Modules directory #
modules_dir = DirectoryPath(base_dir + "modules/")
modules_dir.create()
# The script to be sent #
script = []
# Copy modules to the log directory #
for module in self.modules:
module_dir = os.path.dirname(module.__file__)
module_name = module.__name__
repos_dir = os.path.abspath(module_dir + '/../')
project_name = os.path.basename(repos_dir)
static_module_dir = modules_dir + project_name + '/'
module_version = module.__version__ + ' ' + get_git_tag(repos_dir)
# Copy #
print "Making static copy of module '%s' for SLURM job..." % module_name
sh.cp('-R', repos_dir, static_module_dir)
# Make script #
script.insert(0, "sys.path.insert(0, '%s')" % static_module_dir)
script += ["import %s" % module_name]
script += [
"print 'Using static copy of module %s version %s'" %
(module_name, module_version)
]
# Prepend to the script to be sent #
script.insert(0, "import os, sys")
# Add the user's command to the script #
script += command
# Super #
JobSLURM.__init__(self, script, language, base_dir, **kwargs)
def set_paths(self, base_dir, script_path):
"""Set the directory, the script path and the outfile path"""
# Make absolute paths #
if 'change_dir' in self.kwargs:
self.kwargs['change_dir'] = DirectoryPath(
os.path.abspath(self.kwargs['change_dir']))
if 'out_file' in self.kwargs:
self.kwargs['out_file'] = FilePath(
os.path.abspath(self.kwargs['out_file']))
# In case there is a base directory #
if base_dir is not None:
self.base_dir = DirectoryPath(os.path.abspath(base_dir))
self.script_path = FilePath(base_dir + "run." +
self.extensions[self.language])
self.kwargs['change_dir'] = base_dir
self.kwargs['out_file'] = FilePath(base_dir + "run.out")
# Other cases #
if base_dir is None and script_path is None:
self.script_path = FilePath(new_temp_path())
if script_path is not None:
self.script_path = FilePath(os.path.abspath(script_path))
