Cellprofiler environment can't find python-bioformats but it's installed

Hi,

I’m trying to install Cellprofiler using conda environment with the .yml as follows:

# run: conda env create -f environment.yml
# run: conda env update -f environment.yml
# run: conda env remove -n cellprofiler
name: cellprofiler
# in order of priority: highest (top) to lowest (bottom)
channels:
  - anaconda
  - goodman # mysql-python for mac
  - bioconda
  - cyclus # java-jdk for windows
  - conda-forge # libxml2 for windows
  - daf # wxpython for linux
# - BjornFJohansson # wxpython for linux not longer available
dependencies:
  - appdirs
  - boto3
  - cython
  - h5py
  - ipywidgets
  - java-jdk
  - joblib
  - jupyter
  - libtiff
  - libxml2
  - libxslt
  - lxml
  - packaging
  - pillow
  - pip
  - python=2.7
  - pyzmq=15.3.0
  - mahotas
  - matplotlib!=2.1.0,>2.0.0
  - mysqlclient
  - numpy
  - raven
  - requests
  - scikit-image>=0.13
  - scikit-learn
  - scipy
  - sphinx
  - tifffile
  - wxpython=3.0.2.0
  - pip:
    - cellh5
    - centrosome
    - inflect
    - prokaryote==2.4.0
    - javabridge==1.0.15
    - python-bioformats==1.4.0
    - git+https://github.com/CellProfiler/CellProfiler.git@v3.1.9

But I get the error:

(cellprofiler) gema@Mint-G:~/miniconda2/envs$ cellprofiler
Traceback (most recent call last):
  File "/home/gema/.local/bin/cellprofiler", line 6, in <module>
    from pkg_resources import load_entry_point
  File "/home/gema/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3251, in <module>
    @_call_aside
  File "/home/gema/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3235, in _call_aside
    f(*args, **kwargs)
  File "/home/gema/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3264, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/home/gema/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 583, in _build_master
    ws.require(__requires__)
  File "/home/gema/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 900, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/home/gema/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 786, in resolve
    raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'python-bioformats==1.4.0' distribution was not found and is required by CellProfiler

However, pip freeze shows that the proper version of python-bioformats is installed:

alabaster==0.7.12
appdirs==1.4.3
arrow==0.15.5
asn1crypto==1.3.0
attrs==19.3.0
Babel==2.8.0
backports-abc==0.5
backports.functools-lru-cache==1.6.1
backports.shutil-get-terminal-size==1.0.0
binaryornot==0.4.4
bleach==3.1.0
boto3==1.11.6
botocore==1.14.6
cellh5==1.3.0
CellProfiler==3.1.9
centrosome==1.1.6
certifi==2019.11.28
cffi==1.13.2
chardet==3.0.4
Click==7.0
cloudpickle==1.2.2
configparser==4.0.2
contextlib2==0.6.0.post1
cookiecutter==1.7.0
cryptography==2.8
cycler==0.10.0
Cython==0.29.14
cytoolz==0.10.1
dask==1.2.2
decorator==4.4.2
defusedxml==0.6.0
deprecation==2.0.7
dnspython==1.16.0
docutils==0.15.2
entrypoints==0.3
enum34==1.1.6
functools32==3.2.3.post2
future==0.18.2
futures==3.3.0
gitdb2==2.0.6
GitPython==2.1.14
h5py==2.7.0
hmmlearn==0.2.2
idna==2.8
imagecodecs-lite==2019.12.3
imageio==2.6.1
imagesize==1.2.0
importlib-metadata==1.4.0
inflect==3.0.2
ipaddress==1.0.23
ipykernel==4.10.0
ipython==5.8.0
ipython-genutils==0.2.0
ipywidgets==7.5.1
javabridge==1.0.15
Jinja2==2.10.3
jinja2-time==0.2.0
jmespath==0.9.4
joblib==0.14.1
jsonschema==3.2.0
jupyter==1.0.0
jupyter-client==6.0.0
jupyter-console==5.2.0
jupyter-core==4.6.1
kiwisolver==1.1.0
linecache2==1.0.0
lxml==4.4.2
mahotas==1.4.9
MarkupSafe==1.1.1
matplotlib==2.2.4
mistune==0.8.4
mkl-fft==1.0.15
mkl-random==1.1.0
mkl-service==2.3.0
more-itertools==5.0.0
mysql-connector-python==8.0.19
MySQL-python==1.2.5
mysqlclient==1.4.6
nbconvert==5.6.1
nbformat==4.4.0
networkx==2.2
nf-core==1.7
notebook==5.4.1
numpy==1.15.4
olefile==0.46
packaging==20.0
pandas==0.24.2
pandocfilters==1.4.2
pathlib==1.0.1
pathlib2==2.3.5
pexpect==4.7.0
pickleshare==0.7.5
Pillow==6.2.2
poyo==0.5.0
prokaryote==2.4.0
prompt-toolkit==1.0.15
protobuf==3.6.1
ptyprocess==0.6.0
pycparser==2.20
Pygments==2.5.2
pyOpenSSL==19.1.0
pyparsing==2.4.6
pyrsistent==0.15.7
PySocks==1.7.1
python-bioformats==1.4.0
python-dateutil==2.8.1
pytz==2019.3
PyWavelets==1.0.3
PyYAML==5.3
pyzmq==15.3.0
qtconsole==4.7.2
QtPy==1.9.0
raven==6.10.0
requests==2.22.0
requests-cache==0.5.2
s3transfer==0.3.1
scandir==1.10.0
scikit-image==0.14.0
scikit-learn==0.20.4
scipy==1.1.0
Send2Trash==1.5.0
simplegeneric==0.8.1
singledispatch==3.4.0.3
sip==4.19.13
six==1.14.0
smmap2==2.0.5
snowballstemmer==2.0.0
Sphinx==1.8.5
sphinxcontrib-websupport==1.2.1
subprocess32==3.5.4
tabulate==0.8.6
terminado==0.8.3
testpath==0.4.4
tifffile==2019.7.26.2
toolz==0.10.0
tornado==5.1.1
traceback2==1.4.0
traitlets==4.3.3
typing==3.7.4.1
unittest2==1.1.0
urllib3==1.25.7
wcwidth==0.1.9
webencodings==0.5.1
whichcraft==0.6.1
widgetsnbextension==3.5.1
wxPython==3.0.2.0
wxPython-common==3.0.2.0
zipp==1.0.0

I tried to manually install the python-bioformats version within the environment using conda install -p cellprofiler -c bioconda python-bioformats==1.4.0 but still the same.

I also tried to install cellprofiler v.3.1.8 but I get the same error.

Any ideas?

Thank you in advance
Gema