diff --git a/samui/1.0.0-next.49/.gitignore b/samui/1.0.0-next.49/.gitignore new file mode 100755 index 0000000..581237b --- /dev/null +++ b/samui/1.0.0-next.49/.gitignore @@ -0,0 +1 @@ +samui* diff --git a/samui/1.0.0-next.49/README.md b/samui/1.0.0-next.49/README.md new file mode 100755 index 0000000..a893bf7 --- /dev/null +++ b/samui/1.0.0-next.49/README.md @@ -0,0 +1,66 @@ +# Installation + +```bash +## Commands used for installing the software + +# Make sure not to rely on user packages +export PYTHONNOUSERSITE="some_value" + +# Pull Samui v1.0.0-next.49 +wget https://github.com/chaichontat/samui/archive/refs/tags/v1.0.0-next.49.tar.gz +tar -xzf v1.0.0-next.49.tar.gz +rm v1.0.0-next.49.tar.gz +mv samui-1.0.0-next.49 samui + +# Use mamba, which will be faster +module load conda/3-23.3.1 +conda create -n mamba_env -c conda-forge mamba +conda activate mamba_env + +# Create a conda environment with the recommended dependencies +mamba env create -p samui_env -f samui/environment.yml + +# Add a couple python packages +conda activate ./samui_env +pip install pyhere session_info openpyxl lxml pypng +conda deactivate + +## Ignore all downloaded/installed files +echo "samui*" > .gitignore + +# Set open permissions, except don't allow writing that could corrupt the +# conda environment for everyone +chmod 775 -R samui README.md .gitignore . +chmod 555 -R samui_env + +## Version control files +git add .gitignore +git add README.md +``` + +# Reproducibility + +```bash +## Evaluate the following commands +module list +date +echo "User: ${USER}" +echo "Hostname: ${HOSTNAME}" +``` + +```bash +## copy paste the output from the previous commands +$ module list + +Currently Loaded Modules: + 1) JHPCE_ROCKY9_DEFAULT_ENV 2) JHPCE_tools/3.0 3) conda/3-23.3.1 + + + +$ date +Wed Mar 20 10:44:53 AM EDT 2024 +$ echo "User: ${USER}" +User: neagles +$ echo "Hostname: ${HOSTNAME}" +Hostname: compute-105.cm.cluster +```