<p>Not sure about <code>conda</code> as I don't use it, but I can highly recommend <a href="https://pipenv.readthedocs.io/en/latest/" rel="nofollow noreferrer"><code>pipenv</code></a> which is the python.org recommended package management system for python.  </p>

<p>I have tested the following on my Mac and it worked like a dream  </p>

<pre><code>mkdir albacore &amp;&amp; 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
</code></pre>

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

CC BY-SA 3.0
2018-02-24T11:42:26.237Z
2018-02-26T08:45:44.387Z
2018-02-26T08:45:44.387Z
Michael Hall
<p>I download the <a href="https://mirror.oxfordnanoportal.com/software/analysis/ont_albacore-2.1.10-cp36-cp36m-macosx_10_11_x86_64.whl" rel="nofollow noreferrer">Albacore wheel</a> from Oxford Nanopore.</p>

<p>I activated my conda environment that has Python 3 as the default python version.</p>

<p>I tried to install Albacore with </p>

<pre><code>pip3 install ont_albacore-2.1.10-cp36-cp36m-macosx_10_11_x86_64.whl
</code></pre>

<p>but got the following error:</p>

<pre><code>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.`
</code></pre>

<p>I then upgraded my <code>pip</code> with:</p>

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

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

<p>Can anyone help me install Albacore on my Mac El Capitan laptop, please?</p>

<p>Update based on Wouter's suggestion: </p>

<pre><code>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&gt;=1.12.1 in /Users/userName/anaconda3/lib/python3.6/site-packages (from ont-albacore==2.1.10)
Collecting ont-fast5-api&gt;=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&gt;=1.5 in /Users/userName/anaconda3/lib/python3.6/site-packages (from python-dateutil-&gt;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
</code></pre>

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

<p>I get: </p>

<pre><code>Traceback (most recent call last):
  File "/Users/userName/anaconda3/bin/read_fast5_basecaller.py", line 69, in &lt;module&gt;
    from albacore.input_utils import list_input_files
  File "/Users/userName/anaconda3/lib/python3.6/site-packages/albacore/input_utils.py", line 7, in &lt;module&gt;
    from albacore import log_utils
  File "/Users/userName/anaconda3/lib/python3.6/site-packages/albacore/log_utils.py", line 5, in &lt;module&gt;
    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
</code></pre>

<p>Is there a library missing?</p>

CC BY-SA 4.0
2024-04-19T13:24:15.810Z
Is this a pip / conda conflict per chance?  At one time there was severe conflict between them that this procedure was unusable. Thus the suggestion by @MichaelHall would be correct. I'd maybe look at updating conda first.
M__
CC BY-SA 3.0
2018-02-22T14:53:06.123Z
Are you [using a 32bit kernel](https://discussions.apple.com/thread/3200553) by any chance?
terdon
CC BY-SA 3.0
2018-02-22T15:22:36.033Z
Which python version?
`python --version`

You are using a wheel for python3.6
Wouter De Coster
CC BY-SA 3.0
2018-02-22T18:06:03.113Z
RELEASE_X86_64 x86_64, so 64 bit kernel
Biomagician
CC BY-SA 3.0
2018-02-22T18:06:33.003Z
and Python version 3.6 python --version
Python 3.6.4 :: Anaconda, Inc.
Biomagician
CC BY-SA 3.0
2018-02-23T13:21:41.230Z
could you try `python -m pip install ont_albacore-2.1.10-cp36-cp36m-macosx_10_11_x86_64.whl`
Wouter De Coster
<nanopore><minion><software-installation><albacore>
Albacore wheel not supported on this platform (Mac OS X El Capitan)
# Albacore wheel not supported on this platform (Mac OS X El Capitan)

(Asked by: username_0 on 2018-02-22)

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 
    from albacore.input_utils import list_input_files
  File "/Users/userName/anaconda3/lib/python3.6/site-packages/albacore/input_utils.py", line 7, in 
    from albacore import log_utils
  File "/Users/userName/anaconda3/lib/python3.6/site-packages/albacore/log_utils.py", line 5, in 
    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?

**Tags:** nanopore, minion, software-installation, albacore
> **Comments:**
> **username_2**: Are you [using a 32bit kernel](https://discussions.apple.com/thread/3200553) by any chance?  
> **username_3**: Which python version? `python --version`  You are using a wheel for python3.6  
> **username_0**: RELEASE_X86_64 x86_64, so 64 bit kernel  
> **username_0**: and Python version 3.6 python --version Python 3.6.4 :: Anaconda, Inc.  
> **username_3**: could you try `python -m pip install ont_albacore-2.1.10-cp36-cp36m-macosx_10_11_x86_64.whl`  
> **username_1**: Is this a pip / conda conflict per chance?  At one time there was severe conflict between them that this procedure was unusable. Thus the suggestion by @MichaelHall would be correct. I'd maybe look at updating conda first.  

---

## 1 answers

### Answer by username_4 on 2018-02-24. Score: 3

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.


---

