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Interactive browser for AtlasXomics Data
This software is designed as an interactive browser for processing AtlasXomics image Data. To learn more about AtlasXbrowser please visit the documentation, https://docs.atlasxomics.com/projects/AtlasXbrowser/en/latest/.
git clone https://github.com/atlasxomics/AtlasXBrowser.git
cd AtlasXBrowser
Due to the numerous dependencies as well as the requirement of running Python 3.7, we reccomend the usage of Anaconda. If Anaconda is not currently installed on your system see the following https://docs.anaconda.com/anaconda/install/index.html.
To ensure conda is installed run:
conda --version
Upon running the command with no errors, ensure conda is running the latest distribution by running:
conda update conda
To create an enviroment running Python 3.7, run:
conda create --name py37 python=3.7
Where "py37" is any desired name of the enviroment.
To activate the enviroment:
conda deactivate
conda activate py37
To ensure the proper version of python is being run enter:
python --version
This should return Python 3.7.xx. If If this is not the case, deactivate the conda enviroment using "conda deactivate'. Repeat this command until there is no conda enviorment listed at the left side of the terminal and then reactivate the enviroment.
Once the conda enviroment is setup and running, run the following commands to install the required packages.
conda install -c conda-forge scipy
conda install -c conda-forge seaborn
conda install -c conda-forge tifffile
conda install -c conda-forge jsbeautifier
conda install -c conda-forge pandas
conda install -c conda-forge pillow
conda install -c conda-forge matplotlib
conda install -c fastai opencv-python-headless
Update to the latest version before running
cd AtlasXBrowser
git pull https://github.com/atlasxomics/AtlasXBrowser.git
Run the program with following command:
python ABrowser.py
See the documentation for more details about using AtlasXbrowser, https://docs.atlasxomics.com/projects/AtlasXbrowser/en/latest/.