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 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:
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?