Optitype crashes with python2.7.17 due to configparser

[naumenko-sa]

Hello OptiType developers!

Thanks for developing and supporting OptiType!

In a fresh 1.2.0 bcbio installation variant calling with hlacaller: optitype fails at

https://github.com/FRED-2/OptiType/blob/master/OptiTypePipeline.py#L231

A fresh one has python 2.7.17 in python2 environment and a backported module configparser:

>>> import os
>>> import configparser
>>> config = configparser.SafeConfigParser(os.environ)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/path/bcbio120/anaconda/envs/python2/lib/python2.7/site-packages/backports/configparser/__init__.py", line 1264, in __init__
    super(SafeConfigParser, self).__init__(*args, **kwargs)
  File "/path/bcbio120/anaconda/envs/python2/lib/python2.7/site-packages/backports/configparser/__init__.py", line 637, in __init__
    self._read_defaults(defaults)
  File "/path/bcbio120/anaconda/envs/python2/lib/python2.7/site-packages/backports/configparser/__init__.py", line 1255, in _read_defaults
    self.read_dict({self.default_section: defaults})
  File "/path/bcbio120/anaconda/envs/python2/lib/python2.7/site-packages/backports/configparser/__init__.py", line 750, in read_dict
    raise DuplicateOptionError(section, key, source)
backports.configparser.DuplicateOptionError: While reading from u'<dict>': option u'http_proxy' in section u'DEFAULT' already exists

A less fresh one with python 2.7.15 does not have it and works fine:

>>> import os
>>> import configparser
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named configparser
>>> import ConfigParser as configparser
>>> config = configparser.SafeConfigParser(os.environ)

Andras @andras86, would it be possible to fix this on the Optitype side?

Sergey

[koujiaodahan]

my conda python: 2.7.16 ;has similar errors~~~~~~``` Log : % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed ^M 0 0 0 0 0 697 0 421k --:--:-- --:--:-- --:--:-- 421k^M888 191 191 191 0 697 8983 32781 --:--:-- --:--:-- --:--:-- 0 [M::bam2fq_mainloop] processed 645126 reads [M::bam2fq_mainloop] processed 208 reads [M::bam2fq_mainloop] processed 206 reads Traceback (most recent call last): File "OptiType-master/OptiTypePipeline.py", line 231, in config = configparser.SafeConfigParser(os.environ) File "anaconda2/lib/python2.7/site-packages/backports/configparser/init.py", line 1332, in init super(SafeConfigParser, self).init(*args, **kwargs) File "anaconda2/lib/python2.7/site-packages/backports/configparser/init.py", line 710, in init self._read_defaults(defaults) File "anaconda2/lib/python2.7/site-packages/backports/configparser/init.py", line 1323, in _read_defaults self.read_dict({self.default_section: defaults}) File /anaconda2/lib/python2.7/site-packages/backports/configparser/init.py", line 823, in read_dict raise DuplicateOptionError(section, key, source) backports.configparser.DuplicateOptionError: While reading from u'': option u'runlevel' in section u'DEFAULT' already exists

[koujiaodahan]

I try to use in 2.7.15,but errors as follows : $sh test15_run_optitye_xin2.sh Traceback (most recent call last): File "/OptiTypePipeline.py", line 129, in from model import OptiType File "/share/optitype-1.3.2-3/model.py", line 19, in from pyomo.environ import ConcreteModel, Set, Param, Var, Binary, Objective, Constraint, ConstraintList, maximize File "/lib/python2.7/site-packages/pyomo/environ/init.py", line 13, in import pyomo.core File "/python2.7/site-packages/pyomo/core/init.py", line 10, in from pyomo.util.plugin import PluginGlobals File "lib/python2.7/site-packages/pyomo/util/init.py", line 10, in from pyomo.util._task import pyomo_api, PyomoAPIData, PyomoAPIFactory File "/lib/python2.7/site-packages/pyomo/util/_task.py", line 22, in from pyomo.util import plugin File "test_python7.15/lib/python2.7/site-packages/Pyomo-5.6.10.dev0-py2.7-linux-x86_64.egg/pyomo/init.py", line 11, in from . import common File "/lib/python2.7/site-packages/Pyomo-5.6.10.dev0-py2.7-linux-x86_64.egg/pyomo/common/init.py", line 13, in from . import log ImportError: cannot import name log