Author: Mari Iura (M1), Yamazaki Lab.
This is a produre that I installed Brain Modeling Toolkit on a virtual machine of Ubuntu 24.04 LTS on VMWare Fusion Pro.
Environment
VMWare Fusion 13 Pro
Version
$ lsb_release -a
Distributor ID: Ubuntu
Description: Ubuntu 24.04 LTS
Release: 24.04
Codename: noble
$ python3 -V
Python 3.12.3
Installation
Installed necessary packages as follows:
$ sudo apt install -y make build-essential zlib1g-dev git libssl-dev pkg-config libx11-dev bison flex automake libtool libxext-dev libncurses-dev xfonts-100dpi libopenmpi-dev libffi-dev libhdf5-dev python3-pip cython3 python3-dev python3-scipy neuron neuron-dev python3.12-venv
Built a virtual environment of Python:
$ python3 -m venv ~/bmtk_env
Activated the virtual environment:
$ source ~/bmtk_env/bin/activate
Installed further necessary packages:
(bmtk_env)$ pip3 install --upgrade pip setuptools wheel cython pkgconfig
(bmtk_env)$ pip3 install neuron numpy==1.26.4 h5py
Installed BMTK:
(bmtk_env)$ git clone https://github.com/AllenInstitute/bmtk.git
(bmtk_env)$ cd bmtk
(bmtk_env)$ python3 setup.py install
Details of the installed BMTK
$ pip3 show bmtk
Name: bmtk
Version: 1.1.0
Summary: Brain Modeling Toolkit
Home-page: https://github.com/AllenInstitute/bmtk
Author: Kael Dai
Author-email: kaeld@alleninstitute.org
License:
Location: /home/hogehoge/bmtk_env/lib/python3.12/site-packages/bmtk-1.1.0-py3.12.egg
Requires: h5py, jsonschema, matplotlib, numpy, pandas, pynrrd, scikit-image, scipy, six, sympy
Required-by:
How to deactivate/reactivate the virtual environment of Python
Can deactivate the virtual environment of Python:
(bmtk_env)$ deactivate
Can reactivate the virtual environment:
$ source ~/bmtk_env/bin/activate