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I download the Albacore wheel from Oxford Nanopore.

I activated my conda environment that has Python 3 as the default python version.

I tried to install Albacore with

pip3 install ont_albacore-2.1.10-cp36-cp36m-macosx_10_11_x86_64.whl

but got the following error:

ont_albacore-2.1.10-cp36-cp36m-macosx_10_11_x86_64.whl is not a supported wheel on this platform.
You are using pip version 8.1.2, however version 9.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.`

I then upgraded my pip with:

pip install --upgrade pip
Requirement already up-to-date: pip in /Users/.../anaconda3/envs/python3env/lib/python3.6/site-packages`

So it seems that my pip was already up to date. I do not understand why it complains about my pip if I am using pip3 anyways. I tried to install Albacore again but I got the same message as before.

Can anyone help me install Albacore on my Mac El Capitan laptop, please?

Update based on Wouter's suggestion:

python -m pip install ont_albacore-2.1.10-cp36-cp36m-macosx_10_11_x86_64.whl
Processing ./ont_albacore-2.1.10-cp36-cp36m-macosx_10_11_x86_64.whl
Requirement already satisfied: python-dateutil in /Users/userName/anaconda3/lib/python3.6/site-packages (from ont-albacore==2.1.10)
Requirement already satisfied: setuptools in /Users/userName/anaconda3/lib/python3.6/site-packages (from ont-albacore==2.1.10)
Requirement already satisfied: h5py in /Users/userName/anaconda3/lib/python3.6/site-packages (from ont-albacore==2.1.10)
Collecting progressbar33 (from ont-albacore==2.1.10)
Requirement already satisfied: numpy>=1.12.1 in /Users/userName/anaconda3/lib/python3.6/site-packages (from ont-albacore==2.1.10)
Collecting ont-fast5-api>=0.4.1 (from ont-albacore==2.1.10)
  Using cached ont_fast5_api-0.4.1-py2.py3-none-any.whl
Requirement already satisfied: six>=1.5 in /Users/userName/anaconda3/lib/python3.6/site-packages (from python-dateutil->ont-albacore==2.1.10)
Installing collected packages: progressbar33, ont-fast5-api, ont-albacore
Successfully installed ont-albacore-2.1.10 ont-fast5-api-0.4.1 progressbar33-2.4

At first sight, it looks like Albacore was successfully installed but if I run: read_fast5_basecaller.py --help

I get:

Traceback (most recent call last):
  File "/Users/userName/anaconda3/bin/read_fast5_basecaller.py", line 69, in <module>
    from albacore.input_utils import list_input_files
  File "/Users/userName/anaconda3/lib/python3.6/site-packages/albacore/input_utils.py", line 7, in <module>
    from albacore import log_utils
  File "/Users/userName/anaconda3/lib/python3.6/site-packages/albacore/log_utils.py", line 5, in <module>
    from albacore.pipeline_core import get_debug_level
ImportError: dlopen(/Users/userName/anaconda3/lib/python3.6/site-packages/albacore/pipeline_core.cpython-36m-darwin.so, 2): Library not loaded: /usr/local/opt/python3/Frameworks/Python.framework/Versions/3.6/Python
  Referenced from: /Users/userName/anaconda3/lib/python3.6/site-packages/albacore/pipeline_core.cpython-36m-darwin.so
  Reason: image not found

Is there a library missing?

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  • 1
    $\begingroup$ Are you using a 32bit kernel by any chance? $\endgroup$
    – terdon
    Feb 22 '18 at 14:53
  • 1
    $\begingroup$ Which python version? python --version You are using a wheel for python3.6 $\endgroup$ Feb 22 '18 at 15:22
  • $\begingroup$ RELEASE_X86_64 x86_64, so 64 bit kernel $\endgroup$ Feb 22 '18 at 18:06
  • $\begingroup$ and Python version 3.6 python --version Python 3.6.4 :: Anaconda, Inc. $\endgroup$ Feb 22 '18 at 18:06
  • $\begingroup$ could you try python -m pip install ont_albacore-2.1.10-cp36-cp36m-macosx_10_11_x86_64.whl $\endgroup$ Feb 23 '18 at 13:21
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Not sure about conda as I don't use it, but I can highly recommend pipenv which is the python.org recommended package management system for python.

I have tested the following on my Mac and it worked like a dream

mkdir albacore && cd albacore
mv ../ont_albacore-2.1.10-cp36-cp36m-macosx_10_11_x86_64.whl .

# install pipenv if you don't have it
brew install pipenv  # or pip3 install pipenv

# the following will create a virtual environment and install albacore into it
pipenv install ont_albacore-2.1.10-cp36-cp36m-macosx_10_11_x86_64.whl

# activate the virtual environment
pipenv shell

read_fast5_basecaller.py -h

And that should bring up the albacore help menu and you're ready to go.

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