Installation and Upgrade
There are several ways to install the software. The application requires python3.
To avoid interference with the other packages, it is recommended to use virtual environments, as described below.
We recommend to install the software using automatic installation scripts provided for Linux/Mac and Windows.
Releases
All releases are listed at Releases. Releases are distributed as executable (for Windows) and through The Python Package Index (PyPI). Due to numerous issues encountered while distributing through Anaconda, we discontinued Anaconda support.
Linux/Mac
To use automatic installation script for Linux/Mac make first sure that you have
latest pip
installed by running:
python3 -m pip install --user --upgrade pip
Then open terminal and go to folder where you like to install the program. Then run following command:
curl https://gitlab.com/iocbio/kinetics/-/raw/master/install.sh | bash
or
wget -qO - https://gitlab.com/iocbio/kinetics/-/raw/master/install.sh | bash
and run by
iocbio-kinetics/bin/iocbio-kinetics
Windows
Note that for Windows we provide also executable, see below. However, to install IOCBIO Kinetics software using automatic installation script make sure that you have Python installed. More information about installing Python in Windows see Python for Beginners. In addition, install Microsoft Visual C++ Redistributable for Visual Studio 2015, 2017 and 2019. Respective installer can be found here.
When Python is installed open PowerShell and make first sure that
Get-ExecutionPolicy
is not Restricted. We suggest using Bypass
to bypass the policy to
get things installed or AllSigned
for quite a bit more
security. First, run Get-ExecutionPolicy
in PowerShell. In case, it
returns Restricted
, then run Set-ExecutionPolicy AllSigned
or
Set-ExecutionPolicy Bypass -Scope Process
. When this is all set you
can install the program by running following command:
Set-ExecutionPolicy Bypass -Scope Process -Force; [System.Net.ServicePointManager]::SecurityProtocol = [System.Net.ServicePointManager]::SecurityProtocol -bor 3072; iex ((New-Object System.Net.WebClient).DownloadString('https://gitlab.com/iocbio/kinetics/-/raw/master/install.ps1'))
pip
To be able to install PySide6 using pip, you have to use python3.5 or
higher. If not available in the system, you can replace pip3
command
below with python3 -m pip
.
To install published version, run
pip3 install --user iocbio.kinetics
This will install all dependencies and it is expected to add a command iocbio-kinetics
into your PATH
.
If the command is missing after installation, check whether the default location
of pip3
installation is in your path. For Linux, it should be ~/.local/bin
.
To install, use the Git repository directly, for HTTPS users:
pip3 install --user git+https://gitlab.com/iocbio/kinetics
and for SSH users:
python3 -m pip install --user git+ssh://git@gitlab.com/iocbio/kinetics.git
For development, use
pip3 install --user -e .
in the source directory. To install the current version from the source, use
pip3 install --user .
Note that --user
is recommended to avoid messing up the system
packages.
For upgrade, add --upgrade
after install keyword. For example,
pip3 install --upgrade --user git+https://gitlab.com/iocbio/kinetics
or
python3 -m pip install --upgrade --user git+ssh://git@gitlab.com/iocbio/kinetics.git
pip with virtual environment
Sometimes packages for different applications can cause incompatibilities. To avoid it, you could use virtual environment for the software installation. To create virtual python environment, run
python -m venv iocbio-kinetics
This will create folder iocbio-kinetics
and install scripts, such as
pip
, into it. To use the environment, call pip
from that folder
and install iocbio-kinetics into it
iocbio-kinetics/bin/pip install iocbio.kinetics
and run by
iocbio-kinetics/bin/iocbio-kinetics
Windows ZIP binary
Starting from 1.1.1 release, MS Windows executable is provided in the form of ZIP file. This allows to install and use the program quickly as all the required packages are included in the provided ZIP.
To install, download the ZIP package from the link provided in the
corresponding release
notes. Unpack the ZIP
file which would result in folder Kinetics
. You could place this
folder as you see fit on your PC. To start IOCBIO Kinetics, enter the
folder and start kinetics.bat
by double clicking on it.
On the first start, after connecting to the database, you would need to enter "Settings". If you use your own modules, the path to them will have to be specified as well.
Use with R
If iocbio-banova
is used, some additional packges are needed. Install R and the following packages in R:
install.packages(c("tidyverse", "BayesFactor", "formula.tools", "ggplot2"))
In addition, you will need to install rpy2
Python package by using
pip
.