- A python package manager such as conda or mamba. Installing mamba is recommended as it is lightweight and fast. More information can be found here and here. Verify by typing
condaormambain the terminal. Help messages should appear.
a. On a remote server: Connect to the server (e.g. through SSH)
b. On a local machine (MacOS): Open a terminal (e.g by typing "terminal" in SpotlightSearch)
c. On a local machine (Windows): Press Windows key + X, select Windows Terminal
Navigate to a suitable location (a directory called amex_merfish_spaceolotl will be placed in there) and run the following commands:
# Create a new conda environment:
mamba create -n spaceolotl python=3.12
# Activate the environment:
mamba activate spaceolotl
# Fetch the code from github. This will create a directory called 'amex_merfish_spaceolotl'
git clone --branch main https://github.com/quadbio/amex_merfish_spaceolotl.git
# Switch to that directory
cd amex_merfish_spaceolotl
# Install (in editable mode, package will incorporate changes if code is modified)
pip install -e .
The following step is only necessary if you are working on a remote server:
# Make a directory for the data
mkdir data
In order to fetch the data (provided as a tarball ending with tar.gz), download it to you local machine from Polybox via the link shared on Slack. Then proceed with either of the following options:
a. On a remote server: The data downloaded to your local machine needs to be transferred to the remote. Use your favourite File Transfer Protocol client program (e.g. FileZilla) or simply run the following command from your terminal on your local machine:
# This command transfers the tarball to the data directory. You might be asked to authenicate yourself
scp /path/to/tarball/on/local/machine username@domain:/path/to/amex_merfish_spaceolotl/data
Note: the path to the data directory on the server should be provided as an absolute link (starting with a /). If you don't know the path, enter the data directory you created during the installation process and and type in echo $PWD.\
Upon login to the server, you should find the tarball in amex_merfish_spaceolotl/data. We can now remove unpack the data into the data directory and remove the tarball as it is no longer needed
# Unpack the data and clean up
tar -xzvf data.tar.gz && rm data.tar.gz
b. On a local machine (MacOS):
Drag and drop the tarball you downloaded from Polybox to the amex_merfish_spaceolotl directory. Double click on the tarball to decompress the object, this will create an ordinary folder called "data". After this process has finished, you can delete the data.tar.gz.
c. On a local machine (Windows): Will be added soon
a. On a remote server:
Connect to the remote server while forwarding a port:
# Make sure the ports are not already in use
ssh -L 12345:localhost:7600 username@domain
Launch the app like so:
# Change to the amex_merfish_spaceolotl directory
cd path/to/amex_merfish_spaceolotl
# Activate the conda environment
conda activate spaceolotl
# Run the app
shiny run --port 7600 src/spaceolotl/app.py
You can now access the app in your local browser by typing in localhost:12345 in the search bar.
b. On a local machine (MacOS): Open a terminal like before and execute the following commands
# Move to the amex_merfish_spaceolotl directory
cd path/to/amex_merfish_spaceolotl
# Activate the Python environment
mamba activate spaceolotl
# Run the app
shiny run src/spaceolotl/app.py
You can now access the app through the search bar in your local browser by typing localhost:8000.
Note: There might be cases where the standard port is blocked and Shiny selects a different one. In this case you won't be able to access the app as described above. Check the commandline upon startup and search for a message like
INFO: Uvicorn running on http://127.0.0.1:8000 (Press CTRL+C to quit)
Copy the part http://127.0.0.1:8000 into the search bar or your browser. This should lead you to the app.
c. On a local machine (Windows): Will be added soon