diff --git a/env.yml b/env.yml index 81b6747..444862a 100644 --- a/env.yml +++ b/env.yml @@ -5,11 +5,8 @@ channels: - nodefaults dependencies: # general use - - conda-forge::gh - conda-forge::awscli - - conda-forge::wget - conda-forge::nbconvert - - conda-forge::tree # Command Line - bioconda::samtools>=1.15 - bioconda::bcftools>=1.15 diff --git a/setup_env.sh b/setup_env.sh index d0113ee..ce9f5d3 100644 --- a/setup_env.sh +++ b/setup_env.sh @@ -3,19 +3,17 @@ set -eu if [ ! -d "$HOME/.oh-my-bash" ]; then - bash -c "$(curl -fsSL https://raw.githubusercontent.com/ohmybash/oh-my-bash/master/tools/install.sh)" + bash -c "$(curl -fsSL https://raw.githubusercontent.com/ohmybash/oh-my-bash/master/tools/install.sh)" --unattended fi if [ ! -f "$HOME/.pixi/bin/pixi" ]; then curl -fsSL https://pixi.sh/install.sh | bash touch ~/.bashrc echo 'eval "$(pixi completion --shell bash)"' >> ~/.bashrc + export PATH=$HOME/.pixi/bin:$PATH + pixi g i git gh zellij ripgrep dust bat sd tree fi -source ~/.bashrc - -pixi g i git gh zellij ripgrep dust bat sd - sd 'OSH_THEME="font"' 'OSH_THEME="axin"' ~/.bashrc if [ ! -f "$HOME/Miniforge3-Linux-x86_64.sh" ]; then @@ -25,10 +23,11 @@ fi if [ ! -d "$HOME/miniforge3" ]; then bash $HOME/Miniforge3-Linux-x86_64.sh -b + export PATH="$HOME/miniforge3/bin:$PATH" + mamba init + source ~/.bashrc fi -export PATH="$HOME/miniforge3/bin:$PATH" - if [ ! -d "$HOME/miniforge3/envs/bootcamp" ]; then echo Installing bootcamp environment script_dir=$(realpath "$0" | xargs dirname) @@ -37,9 +36,6 @@ if [ ! -d "$HOME/miniforge3/envs/bootcamp" ]; then mamba run -n bootcamp Rscript -e 'IRkernel::installspec(name="R_bootcamp", displayname="R (bootcamp)")' fi -mamba init -source ~/.bashrc - touch ~/.bash_profile cat >> ~/.bash_profile << EOF if [ -f ~/.bashrc ]; then @@ -48,3 +44,5 @@ fi EOF rm ~/Miniforge3-Linux-x86_64.sh + +echo Done! \ No newline at end of file