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Home Page: https://daler.github.io/dotfiles/
dotfiles, batteries included
Home Page: https://daler.github.io/dotfiles/
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:
Line 2 in 095fc12
Potential location for the configuration to occur:
Line 450 in 095fc12
Furthermore, in the docs after these lines,
Line 259 in 095fc12
export PATH="$PATH:~/data/$USER/mambaforge/condabin"
to the :file:~/.path
Add feature here:
Line 449 in 095fc12
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
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