Installation

 

how-to-cite-pynanolab:

The PyNanoLab License Agreement specifies that any reports or published results obtained with PyNanoLab shall acknowledge its use and credit the developers as:

"PyNanoLab was developed by the Shaochuang Liu of Yi-Tao Loong's group at Nanjing University."

If you use PyNanoLab, please cite:

S.-C. Liu, B.-K. Xie, C.-B. Zhong, J. Wang, Y.-L. Ying, and Y.-T. Long, Rev Sci Instrum 92, 121301, (2021). DOI:10.1063/5.0067185

Electronic documents shall include a direct link to the official PyNanoLab page: https://www.pynanolab.com

Release:
Latest Version:2.3.0

changelog:

• Added: Nanopore ToolBox.
• Added: 3D figure support.

Please review the changelog

---

Install tutorials:

---

Binary installation

Briefly, you could download the binary installer we have already builded for windows, Linux and Mac OS.

For Linux *.run file, using following command (Tested on Ubuntu 20.04 +)：

chmod +x pynanolab-linux64-installer-2.2.0.run
sudo ./pynanolab-linux64-installer-2.2.0.run

and then input the install path in the terminal.

This .run fill will automatically create .desktop file and copy to you applications folders. You could find PyNanoLab in your app center.
If failed, you could create the start file by your self.
Briefly, cd the [installpath]/PyNanoLab/, and run ./PyNanoLab to run this software.

For Mac OS:
Open the *.dmg file and drag the PyNanoLab.app to Apolications folder. And you will find this software in your appcenter.

Warring：The Mac version have same uncertain bugs。When first time run after installation, click the icon to start the software will crash.
Using the command

/Applications/PyNanoLab.app/Contents/MacOS/PyNanoLab_x64

to run the software for the first time. And then you could open the software by clicking the icon in app center.

---

Source installation

For some reason, PyNanoLab not provide the original source code. But the Binary source build by Cython is provided. You could create the python envs and run it.

Tips: this is only recommended Linux and Mac OS. In windows, you could download the .exe installation package we provided.

• Download the source file for you operation system from github. and unzip it to a folder. You folder tree looks like:

  --|
  --- pynanolab
  --- main.py
  --- requirements.txt
  --- run.sh

  Then entrance this folder, the main.py is the entrance file of PyNanoLab.

• Build the pynanolab runtime environment

  1. Download the miniconda and install.
     miniconda url: https://docs.conda.io/en/latest/miniconda.html
     git-bash url (winwods only): https://gitforwindows.org/

2. Create the virtualenv for PyNanoLab
   use following command in terminal:

   conda create -n pnl python=3.10.4 -c conda-forge
   source activate # only needed in windows system when you use the git-bash for windows.
   conda activate pnl

   if you want use intel-mkl based numpy to speed up the PyNanoLab, using

   conda install numpy --yes

   to install the numpy-mkl.
   And then:

   pip install -r requirements.txt

   tips: for some requirement,you should have compiler in your system to build the package. in windows: Visual Studio; Linux: GCC ; Mac OS X： Xcode.

3. Run the PyNanoLab:
   Using following command in terminal in the same folder of main.py:

   conda activate pnl
   python main.py

   or just double click the file run.sh if you have install the git-bash on windows.