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If using macos and coreutils is installed into conda base environment (e.g. ./setup.sh --conda-env), ls uses different color schemes depending on whether conda is initialized, or whether conda base environment or other environment is activated.

Attempted fix with PR in #35

In the setup.sh script, when conda channels are setup they are also st up to require strict channel order, and this restricts conda environments from being set up properly.

Under some conditions (seems to be if conda has not been activated) running setup.sh results in the while-loop of the conda_deactivate_all function to not terminate.

On line, https://github.com/daler/dotfiles/blob/095fc12649d4434cbcb71d3219cfd05eb42a58f6/docs/starthere.rst?plain=1#L266C9-L266C9, the new command for installing mambaforge is ./setup.sh --install-conda

The setup.sh script identifies if a user is on the NIH's Biowulf or Helix clusters to determine the conda installation directory. Suggesting similar environment checks for the .path dotfile to ensure appropriate path settings.

This line needs to be configured based on cluster usage detection:

Potential location for the configuration to occur:

Furthermore, in the docs after these lines,

• or if you're on NIH's Biowulf cluster:
  adds the line export PATH="$PATH:~/data/$USER/mambaforge/condabin" to the :file:~/.path

Add feature here:

that asks if the user is in BSPC and if so appends the NICDH-core1 tools to users path via export PATH in .path:

if [[ $HOSTNAME == "helix.nih.gov" || $HOSTNAME == "biowulf.nih.gov" ]]; then
MAMBAFORGE_DIR=/data/$USER/mambaforge

 while true; do
 # Ask the user if they are in BSPC
 read -p "Are you in BSPC? (y/n): " response

 # Check the user's response
 if [[ "$response" == "y" || "$response" == "Y" ]]; then
     echo "Adding BSPC tools to .path."
     echo "export PATH=$PATH:/data/NICHD-core1/bin" >> $HOME/.path
     break
 elif [[ "$response" == "n" || "$response" == "N" ]]; then
     break
 else
     echo "Invalid response. Please answer with y or n."
 fi
done