Installation on CPU (linux)

[tpentim]

Hi Dr Rasse,

Thanks a lot for wrapping up the best segmentation tools and providing upstream and downstream analyses, it's great!

I have successfully installed Opsef 3 using the yaml file with a small tweak (I had to comment out python-graphviz and install it separately later).

I've run the configure notebook without problems however when I try to run the 'OpSeF_IV_Run_001' notebook I'm stuck at importing packages with the following error. It happens when I import cellpose, mxnet and tensorflow later.

Is this linked to OpSeF requiring a GPU? Is a CPU installation avaliable?

Thanks in advance for your help.

Best,
Tancredi

---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
<ipython-input-7-825adcf56a6e> in <module>
     41 
     42 # for cellpose
---> 43 from cellpose import models as cp_models
     44 from cellpose import utils as cp_utils
     45 from cellpose import plot, transforms

~/miniconda3/envs/opsef003/lib/python3.6/site-packages/cellpose/models.py in <module>
      9 import cv2
     10 
---> 11 from mxnet import gluon, nd
     12 from mxnet.gluon import nn
     13 import mxnet as mx

~/miniconda3/envs/opsef003/lib/python3.6/site-packages/mxnet/__init__.py in <module>
     22 from __future__ import absolute_import
     23 
---> 24 from .context import Context, current_context, cpu, gpu, cpu_pinned
     25 from . import engine
     26 from .base import MXNetError

~/miniconda3/envs/opsef003/lib/python3.6/site-packages/mxnet/context.py in <module>
     22 import warnings
     23 import ctypes
---> 24 from .base import classproperty, with_metaclass, _MXClassPropertyMetaClass
     25 from .base import _LIB
     26 from .base import check_call

~/miniconda3/envs/opsef003/lib/python3.6/site-packages/mxnet/base.py in <module>
    211 __version__ = libinfo.__version__
    212 # library instance of mxnet
--> 213 _LIB = _load_lib()
    214 
    215 # type definitions

~/miniconda3/envs/opsef003/lib/python3.6/site-packages/mxnet/base.py in _load_lib()
    202     """Load library by searching possible path."""
    203     lib_path = libinfo.find_lib_path()
--> 204     lib = ctypes.CDLL(lib_path[0], ctypes.RTLD_LOCAL)
    205     # DMatrix functions
    206     lib.MXGetLastError.restype = ctypes.c_char_p

~/miniconda3/envs/opsef003/lib/python3.6/ctypes/__init__.py in __init__(self, name, mode, handle, use_errno, use_last_error)
    346 
    347         if handle is None:
--> 348             self._handle = _dlopen(self._name, mode)
    349         else:
    350             self._handle = handle

OSError: libcudart.so.10.0: cannot open shared object file: No such file or directory