Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-02-24T11:42:26.237Z
Answers.LastActivityDate: 2018-02-26T08:45:44.387Z
Answers.LastEditDate: 2018-02-26T08:45:44.387Z
Answers.UserDisplayName: Michael Hall
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-19T13:24:15.810Z
Comments.Text: 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.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-02-22T14:53:06.123Z
Comments.Text: Are you [using a 32bit kernel](https://discussions.apple.com/thread/3200553) by any chance?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-02-22T15:22:36.033Z
Comments.Text: Which python version?
  `python --version`
  
  You are using a wheel for python3.6
Comments.UserDisplayName: Wouter De Coster
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-02-22T18:06:03.113Z
Comments.Text: RELEASE_X86_64 x86_64, so 64 bit kernel
Comments.UserDisplayName: Biomagician
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-02-22T18:06:33.003Z
Comments.Text: and Python version 3.6 python --version
  Python 3.6.4 :: Anaconda, Inc.
Comments.UserDisplayName: Biomagician
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-02-23T13:21:41.230Z
Comments.Text: could you try `python -m pip install ont_albacore-2.1.10-cp36-cp36m-macosx_10_11_x86_64.whl`
Comments.UserDisplayName: Wouter De Coster
Tags: <nanopore><minion><software-installation><albacore>
Title: Albacore wheel not supported on this platform (Mac OS X El Capitan)
ThreadText: # 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](https://mirror.oxfordnanoportal.com/software/analysis/ont_albacore-2.1.10-cp36-cp36m-macosx_10_11_x86_64.whl) 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 username_3'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?
  
  **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 @username_4 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`](https://pipenv.readthedocs.io/en/latest/) 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.
  
  
  ---
  
  