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

…2024

.gitattributes

@@ -0,0 +1,2 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

.gitignore

@@ -3,3 +3,6 @@ modules/02-sequencing/ref
 modules/02-sequencing/tmp
 **/*.h5ad
 **/*.ipynb_checkpoints
+# pixi environments
+.pixi
+*.egg-info

env.yml

@@ -15,9 +15,9 @@ dependencies:
   - bioconda::bcftools>=1.15
   - bioconda::bedtools>=2.30.0
   - bioconda::picard>=2.27.4
-  - bioconda::gatk4
+#   - bioconda::gatk4
   - bioconda::fastqc
-  - bioconda::multiqc
+#   - bioconda::multiqc
   # Python
   - conda-forge::python>=3.7
   - conda-forge::pip

setup_env.sh

@@ -2,20 +2,40 @@
 
 set -eu
 
-if [ ! -e "$HOME/Miniforge3-Linux-x86_64.sh" ]; then
-    wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh -P $HOME
+if [ ! -d "$HOME/.oh-my-bash" ]; then
+    bash -c "$(curl -fsSL https://raw.githubusercontent.com/ohmybash/oh-my-bash/master/tools/install.sh)"
 fi
 
-if [ ! -e "$HOME/miniforge3" ]; then
+if [ ! -f "$HOME/.pixi/bin/pixi" ]; then
+    curl -fsSL https://pixi.sh/install.sh | bash
+    touch ~/.bashrc
+    echo 'eval "$(pixi completion --shell bash)"' >> ~/.bashrc
+fi
+
+source ~/.bashrc
+
+pixi g i git gh zellij ripgrep dust bat sd
+
+sd 'OSH_THEME="font"' 'OSH_THEME="axin"' ~/.bashrc
+
+if [ ! -f "$HOME/Miniforge3-Linux-x86_64.sh" ]; then
+    wget --timeout=5 -t 5 -P $HOME \
+        https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
+fi
+
+if [ ! -d "$HOME/miniforge3" ]; then
     bash $HOME/Miniforge3-Linux-x86_64.sh -b
 fi
 
 export PATH="$HOME/miniforge3/bin:$PATH"
 
-script_dir=$(realpath "$0") && dirname "$script_dir"
-mamba env create -f $script_dir/env.yml -y
-mamba run -n bootcamp ipython kernel install --user --name=python_bootcamp --display-name="Python 3 (bootcamp)"
-mamba run -n bootcamp Rscript -e 'IRkernel::installspec(name="R_bootcamp", displayname="R (bootcamp)")'
+if [ ! -d "$HOME/miniforge3/envs/bootcamp" ]; then
+    echo Installing bootcamp environment
+    script_dir=$(realpath "$0" | xargs dirname)
+    mamba env create -f $script_dir/env.yml -y
+    mamba run -n bootcamp ipython kernel install --user --name=python_bootcamp --display-name="Python 3 (bootcamp)"
+    mamba run -n bootcamp Rscript -e 'IRkernel::installspec(name="R_bootcamp", displayname="R (bootcamp)")'
+fi
 
 mamba init
 source ~/.bashrc