Commit f5cc1b8e authored by Gerald Salin's avatar Gerald Salin

add print in run.py in process_raw_files to add some info in the stdout,

easier to debug
in weaver.function.py, give back the /usr/bin/env {0} line instead of
the absolute path to python, which help us to begin with migration to
slurm
parent 6e272c00
......@@ -34,7 +34,6 @@ from ng6.config_reader import NG6ConfigReader
from ng6.utils import Utils
from ng6.exceptions import UnsavedRunError
class Run(object):
"""
Class Run: Define a nG6 run object
......@@ -98,6 +97,7 @@ class Run(object):
"""
nb_seq, full_size = 0, 0
for file in self.raw_files:
print("run process_raw_files " + file)
# Get nb_seq and full_size values
reader = seqio.SequenceReader(file)
for id, desc, seq, qualities in reader:
......
......@@ -210,7 +210,7 @@ class PythonFunction(ScriptFunction):
- `cmd_format` -- String template used to generate command string.
"""
PYTHON_VERSION = 'python{0}.{1}'.format(sys.version_info[0], sys.version_info[1])
PYTHON_TEMPLATE = '''#!/tools/python/3.4.3/bin/python3.4
PYTHON_TEMPLATE = '''#!/usr/bin/env {0}
import pickle
import {{0}}
......
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