Merge branch 'main' of github.com:bioinfo-ucsd/BISB-Bootcamp-2024

merge_new_changes

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

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!