From fc610a6c90f13c755d5e5ae6dff09f29cdeedad6 Mon Sep 17 00:00:00 2001
From: RuiDongDR <rui.dong.dr@gmail.com>
Date: Wed, 25 Feb 2026 21:46:14 -0500
Subject: [PATCH 01/12] add minimal and pop-up for installation path

---
 envs/minimal_packages.txt |  74 +++++++++++++++++++++++
 init.sh                   |  25 ++++----
 pixi-install.sh           |   7 ++-
 pixi-setup.sh             | 122 +++++++++++++++++++++++++++-----------
 4 files changed, 180 insertions(+), 48 deletions(-)
 create mode 100644 envs/minimal_packages.txt

diff --git a/envs/minimal_packages.txt b/envs/minimal_packages.txt
new file mode 100644
index 0000000..def5f96
--- /dev/null
+++ b/envs/minimal_packages.txt
@@ -0,0 +1,74 @@
+# Minimal package list - general purpose only, no bioinformatics tools
+# Sections: [global], [python], [r]
+
+# [global]
+curl
+diffutils
+findutils
+gawk
+git
+grep
+less
+parallel
+pandoc
+perl
+python=3.12
+r-base=4.4
+ripgrep
+ruby
+sed
+tree
+unzip
+vim
+wget
+
+# [python]
+cython
+dill
+ipykernel
+ipywidgets
+ipympl
+ipyparallel
+ipython
+jedi-language-server
+jupyterlab
+jupyter_client
+jupyter_console
+jupyter_core
+jupyter_server
+jupyter-lsp
+jupyterlab-lsp
+matplotlib-base
+nb_conda_kernels
+nbconvert-core
+nbdime
+nbformat
+notebook
+numba
+numexpr
+numpy
+openpyxl
+pandas
+pillow
+ptpython
+pyarrow
+python-lsp-server
+scikit-learn
+scipy
+seaborn
+statsmodels
+sympy
+tqdm
+widgetsnbextension
+
+# [r]
+r-biocmanager
+r-corrplot
+r-devtools
+r-glmnet
+r-httpgd
+r-igraph
+r-irkernel
+r-languageserver
+r-pacman
+r-tidyverse
diff --git a/init.sh b/init.sh
index 596ce60..792ce98 100755
--- a/init.sh
+++ b/init.sh
@@ -2,9 +2,12 @@
 
 set -o errexit -o nounset -o xtrace -o pipefail
 
+# Use PIXI_HOME if set (e.g. custom HPC path), otherwise fall back to default
+PIXI_HOME="${PIXI_HOME:-${HOME}/.pixi}"
+
 # Use Rprofile.site so that only pixi-installed R can see r-base packages
-mkdir -p ${HOME}/.pixi/envs/python/lib/R/etc
-echo ".libPaths('${HOME}/.pixi/envs/r-base/lib/R/library')" > ${HOME}/.pixi/envs/python/lib/R/etc/Rprofile.site
+mkdir -p ${PIXI_HOME}/envs/python/lib/R/etc
+echo ".libPaths('${PIXI_HOME}/envs/r-base/lib/R/library')" > ${PIXI_HOME}/envs/python/lib/R/etc/Rprofile.site
 
 # Create config files for rstudio
 mkdir -p ${HOME}/.config/rstudio
@@ -13,7 +16,7 @@ directory=${HOME}/.local/var/lib/rstudio-server
 EOF
 
 tee ${HOME}/.config/rstudio/rserver.conf << EOF
-rsession-which-r=${HOME}/.pixi/envs/r-base/bin/R
+rsession-which-r=${PIXI_HOME}/envs/r-base/bin/R
 auth-none=1
 database-config-file=${HOME}/.config/rstudio/database.conf
 server-daemonize=0
@@ -21,10 +24,10 @@ server-data-dir=${HOME}/.local/var/run/rstudio-server
 server-user=${USER}
 EOF
 
-# Register Juypter kernels
-find ${HOME}/.pixi/envs/python/share/jupyter/kernels/ -maxdepth 1 -mindepth 1 -type d | \
+# Register Jupyter kernels
+find ${PIXI_HOME}/envs/python/share/jupyter/kernels/ -maxdepth 1 -mindepth 1 -type d | \
     xargs -I % jupyter-kernelspec install --log-level=50 --user %
-find ${HOME}/.pixi/envs/r-base/share/jupyter/kernels/ -maxdepth 1 -mindepth 1 -type d | \
+find ${PIXI_HOME}/envs/r-base/share/jupyter/kernels/ -maxdepth 1 -mindepth 1 -type d | \
     xargs -I % jupyter-kernelspec install --log-level=50 --user %
 # ark --install
 
@@ -49,7 +52,9 @@ else
    code-server --install-extension usernamehw.errorlens
 fi
 
-# Temporary fix to run post-link scripts
-bash -c "PREFIX=${HOME}/.pixi/envs/r-base PATH=${HOME}/.pixi/envs/r-base/bin:${PATH} .bioconductor-genomeinfodbdata-post-link.sh"
-find ${HOME}/.pixi/envs/r-base/bin -name '*bioconductor-*-post-link.sh' | \
-xargs -I % bash -c "PREFIX=${HOME}/.pixi/envs/r-base PATH=${HOME}/.pixi/envs/r-base/bin:${PATH} %"
+# Temporary fix to run post-link scripts (only present in full install with bioconductor packages)
+if [ -f "${PIXI_HOME}/envs/r-base/bin/.bioconductor-genomeinfodbdata-post-link.sh" ]; then
+    bash -c "PREFIX=${PIXI_HOME}/envs/r-base PATH=${PIXI_HOME}/envs/r-base/bin:${PATH} .bioconductor-genomeinfodbdata-post-link.sh"
+fi
+find ${PIXI_HOME}/envs/r-base/bin -name '*bioconductor-*-post-link.sh' | \
+xargs -I % bash -c "PREFIX=${PIXI_HOME}/envs/r-base PATH=${PIXI_HOME}/envs/r-base/bin:${PATH} %"
diff --git a/pixi-install.sh b/pixi-install.sh
index aa9db9e..d30d3a2 100755
--- a/pixi-install.sh
+++ b/pixi-install.sh
@@ -27,8 +27,9 @@ else
 fi
 
 # Configure shell
-if ! grep -q 'export PATH=${HOME}/.pixi/bin:${PATH}' "${CONFIG_FILE}"; then
-    echo 'export PATH=${HOME}/.pixi/bin:${PATH}' >> "${CONFIG_FILE}"
+_pixi_bin="${PIXI_HOME:-${HOME}/.pixi}/bin"
+if ! grep -q "${_pixi_bin}" "${CONFIG_FILE}"; then
+    echo "export PATH=${_pixi_bin}:\${PATH}" >> "${CONFIG_FILE}"
 fi
 if ! grep -q 'unset PYTHONPATH' "${CONFIG_FILE}"; then
   echo "unset PYTHONPATH" >> "${CONFIG_FILE}"
@@ -38,4 +39,4 @@ if ! grep -q 'export PYDEVD_DISABLE_FILE_VALIDATION=1' "${CONFIG_FILE}"; then
 fi
 
 # set default channels
-mkdir -p ${HOME}/.pixi && echo 'default_channels = ["dnachun", "conda-forge", "bioconda"]' > ${HOME}/.pixi/config.toml
+mkdir -p "${PIXI_HOME:-${HOME}/.pixi}" && echo 'default_channels = ["dnachun", "conda-forge", "bioconda"]' > "${PIXI_HOME:-${HOME}/.pixi}/config.toml"
diff --git a/pixi-setup.sh b/pixi-setup.sh
index a1837a2..b8b42d2 100755
--- a/pixi-setup.sh
+++ b/pixi-setup.sh
@@ -5,7 +5,7 @@ set -o nounset -o errexit -o pipefail
 safe_expose_remove() {
     environment=$1
     executable=$2
-    if [ -d ${HOME}/.pixi/envs/${environment} ]; then
+    if [ -d ${PIXI_HOME}/envs/${environment} ]; then
         exposed_exes=$(pixi global list --environment ${environment} | tail -n 3 | head -n 1 | tr ',' '\n')
         if [[ " ${exposed_exes[*]} " =~ [[:space:]]${executable}[[:space:]] ]]; then
             pixi global expose remove ${executable}
@@ -17,18 +17,18 @@ export -f safe_expose_remove
 
 install_global_packages() {
     package_list=$1
-    
+
     # Check if the directory exists, if not, create an empty list of packages
-    if [ ! -d ${HOME}/.pixi/envs ]; then
-        mkdir -p ${HOME}/.pixi/envs
+    if [ ! -d ${PIXI_HOME}/envs ]; then
+        mkdir -p ${PIXI_HOME}/envs
         existing_pkgs=""
     else
-        existing_pkgs=$(ls ${HOME}/.pixi/envs 2>/dev/null | sort -u || echo "")
+        existing_pkgs=$(ls ${PIXI_HOME}/envs 2>/dev/null | sort -u || echo "")
     fi
-    
+
     # Use the existing packages or empty string to compare with desired packages
     missing_pkgs=$(comm -13 <(echo "$existing_pkgs" | sort -u) <(sort -u ${package_list}))
-    
+
     if (($(echo ${missing_pkgs} | wc -w) > 0 )); then
         pixi global install $(echo ${missing_pkgs} | tr '\n' ' ')
     fi
@@ -39,14 +39,14 @@ export -f install_global_packages
 inject_packages() {
     environment=$1
     package_list=$2
-    
+
     # Check if the environment exists before trying to list packages
-    if [ ! -d ${HOME}/.pixi/envs/${environment} ]; then
+    if [ ! -d ${PIXI_HOME}/envs/${environment} ]; then
         missing_pkgs=$(cat ${package_list})
     else
         missing_pkgs=$(comm -13 <(pixi global list --environment ${environment} | cut -f 1 -d ' ' | head -n -6 | tail -n +3 | sort -u) <(sort -u ${package_list}))
     fi
-    
+
     if (( $(echo ${missing_pkgs} | wc -w) > 0 )); then
         pixi global install --environment ${environment} $(echo ${missing_pkgs} | tr '\n' ' ')
     fi
@@ -54,47 +54,99 @@ inject_packages() {
 
 export -f inject_packages
 
-# If PIXI_HOME is not set already, set it to ${HOME}/.pixi
-if [[ -z ${PIXI_HOME:-} ]]; then
-    export PIXI_HOME="${HOME}/.pixi"
-fi
+extract_section() {
+    local file=$1 section=$2
+    awk "/^# \[${section}\]/{found=1; next} /^# \[/{found=0} found && !/^#/ && NF" "$file"
+}
+
+export -f extract_section
+
+# --- Prompt: installation path ---
+_default_pixi_home="${HOME}/.pixi"
+echo ""
+echo "Where should pixi store its environments and packages?"
+echo "  Default: ${_default_pixi_home}"
+echo "  NOTE: Home directories often have storage quotas on HPC systems."
+echo "  Consider a path on a larger filesystem, e.g.:"
+echo "    /scratch/${USER}/.pixi   or   /lab/yourlab/.pixi"
+echo ""
+read -r -p "Installation path [${_default_pixi_home}]: " _user_pixi_home
+export PIXI_HOME="${_user_pixi_home:-${_default_pixi_home}}"
+echo "Using PIXI_HOME=${PIXI_HOME}"
+
+# --- Prompt: install type ---
+echo ""
+echo "Choose installation type:"
+echo "  1) minimal - Essential CLI tools + Python data science + base R (fast)"
+echo "  2) full    - Complete bioinformatics environment (samtools, GATK, plink,"
+echo "               STAR, Seurat, bioconductor packages, etc.)"
+echo ""
+read -r -p "Install type [1=minimal, 2=full, default=1]: " _install_type_input
+case "${_install_type_input:-1}" in
+    2|full)    INSTALL_TYPE="full" ;;
+    *)         INSTALL_TYPE="minimal" ;;
+esac
+echo "Installation type: ${INSTALL_TYPE}"
 
 # Ensure PIXI_HOME exists
-mkdir -p ${PIXI_HOME}
+mkdir -p "${PIXI_HOME}"
 
 # Install pixi and source it right after installation to move forward
 curl -fsSL https://raw.githubusercontent.com/StatFunGen/pixi-setup/main/pixi-install.sh | bash
-export PATH="${HOME}/.pixi/bin:${PATH}"
+export PATH="${PIXI_HOME}/bin:${PATH}"
 
-# Install global packages
-install_global_packages <(curl -fsSL https://raw.githubusercontent.com/StatFunGen/pixi-setup/main/envs/global_packages.txt | grep -v "#")
+if [[ "${INSTALL_TYPE}" == "minimal" ]]; then
+    # --- Minimal install ---
+    _minimal_url="https://raw.githubusercontent.com/StatFunGen/pixi-setup/main/envs/minimal_packages.txt"
+    _minimal_file=$(mktemp)
+    curl -fsSL "${_minimal_url}" -o "${_minimal_file}"
 
-if [[ "$OSTYPE" == "linux-gnu"* ]]; then
-    safe_expose_remove util-linux kill
-fi
+    install_global_packages <(extract_section "${_minimal_file}" "global")
+    install_global_packages <(echo "coreutils")
 
-install_global_packages <(echo "coreutils")
+    echo "Installing minimal R packages ..."
+    inject_packages r-base <(extract_section "${_minimal_file}" "r")
 
-if [[ "$OSTYPE" == "linux-gnu"* ]]; then
-    safe_expose_remove coreutils kill
-    safe_expose_remove coreutils uptime
-    install_global_packages <(curl -fsSL https://raw.githubusercontent.com/StatFunGen/pixi-setup/main/envs/global_packages_linux.txt | grep -v "#")
-fi
+    echo "Installing minimal Python packages ..."
+    inject_packages python <(extract_section "${_minimal_file}" "python")
 
-echo "Installing recommended R libraries ..."
-inject_packages r-base <(curl -fsSL https://raw.githubusercontent.com/StatFunGen/pixi-setup/main/envs/r_packages.txt | grep -v "#")
+    rm -f "${_minimal_file}"
+    pixi clean cache -y
 
-echo "Installing recommended Python packages ..."
-inject_packages python <(curl -fsSL https://raw.githubusercontent.com/StatFunGen/pixi-setup/main/envs/python_packages.txt | grep -v "#")
+    # Install config files (init.sh handles missing bioconductor packages gracefully)
+    curl -fsSL https://raw.githubusercontent.com/StatFunGen/pixi-setup/main/init.sh | bash
 
-pixi clean cache -y
+else
+    # --- Full install ---
+    install_global_packages <(curl -fsSL https://raw.githubusercontent.com/StatFunGen/pixi-setup/main/envs/global_packages.txt | grep -v "#")
 
-# Install config files
-curl -fsSL https://raw.githubusercontent.com/StatFunGen/pixi-setup/main/init.sh | bash
+    if [[ "$OSTYPE" == "linux-gnu"* ]]; then
+        safe_expose_remove util-linux kill
+    fi
+
+    install_global_packages <(echo "coreutils")
+
+    if [[ "$OSTYPE" == "linux-gnu"* ]]; then
+        safe_expose_remove coreutils kill
+        safe_expose_remove coreutils uptime
+        install_global_packages <(curl -fsSL https://raw.githubusercontent.com/StatFunGen/pixi-setup/main/envs/global_packages_linux.txt | grep -v "#")
+    fi
+
+    echo "Installing recommended R libraries ..."
+    inject_packages r-base <(curl -fsSL https://raw.githubusercontent.com/StatFunGen/pixi-setup/main/envs/r_packages.txt | grep -v "#")
+
+    echo "Installing recommended Python packages ..."
+    inject_packages python <(curl -fsSL https://raw.githubusercontent.com/StatFunGen/pixi-setup/main/envs/python_packages.txt | grep -v "#")
+
+    pixi clean cache -y
+
+    # Install config files
+    curl -fsSL https://raw.githubusercontent.com/StatFunGen/pixi-setup/main/init.sh | bash
+fi
 
 # print messages
 BB='\033[1;34m'
 NC='\033[0m'
-echo -e "${BB}Installation completed.${NC}"
+echo -e "${BB}Installation completed. Pixi is installed at: ${PIXI_HOME}${NC}"
 echo -e "${BB}Note: From now on you can install other R packages as needed with 'pixi global install --environment r-base ...'${NC}"
 echo -e "${BB}and Python with 'pixi global install --environment python ...'${NC}"

From 12ea4d777bd3e4b51eabdc618d4a3d96674c54d3 Mon Sep 17 00:00:00 2001
From: RuiDongDR <rui.dong.dr@gmail.com>
Date: Wed, 25 Feb 2026 21:58:29 -0500
Subject: [PATCH 02/12] remove my name

---
 pixi-setup.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pixi-setup.sh b/pixi-setup.sh
index b8b42d2..5d0f491 100755
--- a/pixi-setup.sh
+++ b/pixi-setup.sh
@@ -68,7 +68,7 @@ echo "Where should pixi store its environments and packages?"
 echo "  Default: ${_default_pixi_home}"
 echo "  NOTE: Home directories often have storage quotas on HPC systems."
 echo "  Consider a path on a larger filesystem, e.g.:"
-echo "    /scratch/${USER}/.pixi   or   /lab/yourlab/.pixi"
+echo "    /lab/yourlab/.pixi"
 echo ""
 read -r -p "Installation path [${_default_pixi_home}]: " _user_pixi_home
 export PIXI_HOME="${_user_pixi_home:-${_default_pixi_home}}"

From 3c20733dac585af5be114b2d57868f7017263ae8 Mon Sep 17 00:00:00 2001
From: RuiDongDR <rui.dong.dr@gmail.com>
Date: Wed, 25 Feb 2026 22:04:07 -0500
Subject: [PATCH 03/12] add file count

---
 pixi-setup.sh | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/pixi-setup.sh b/pixi-setup.sh
index 5d0f491..63f4cb2 100755
--- a/pixi-setup.sh
+++ b/pixi-setup.sh
@@ -67,8 +67,7 @@ echo ""
 echo "Where should pixi store its environments and packages?"
 echo "  Default: ${_default_pixi_home}"
 echo "  NOTE: Home directories often have storage quotas on HPC systems."
-echo "  Consider a path on a larger filesystem, e.g.:"
-echo "    /lab/yourlab/.pixi"
+echo "  Consider a path on a larger filesystem, e.g. /lab/yourlab/.pixi"
 echo ""
 read -r -p "Installation path [${_default_pixi_home}]: " _user_pixi_home
 export PIXI_HOME="${_user_pixi_home:-${_default_pixi_home}}"
@@ -77,9 +76,11 @@ echo "Using PIXI_HOME=${PIXI_HOME}"
 # --- Prompt: install type ---
 echo ""
 echo "Choose installation type:"
-echo "  1) minimal - Essential CLI tools + Python data science + base R (fast)"
+echo "  1) minimal - Essential CLI tools + Python data science + base R"
+echo "               ~7 GB, ~100k files"
 echo "  2) full    - Complete bioinformatics environment (samtools, GATK, plink,"
 echo "               STAR, Seurat, bioconductor packages, etc.)"
+echo "               ~35 GB, ~350k files"
 echo ""
 read -r -p "Install type [1=minimal, 2=full, default=1]: " _install_type_input
 case "${_install_type_input:-1}" in

From 799da4e372e7b1e77a40078f806fe61dbed3e861 Mon Sep 17 00:00:00 2001
From: RuiDongDR <rui.dong.dr@gmail.com>
Date: Wed, 25 Feb 2026 22:25:50 -0500
Subject: [PATCH 04/12] improve on interface to users

---
 init.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/init.sh b/init.sh
index 792ce98..be91659 100755
--- a/init.sh
+++ b/init.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-set -o errexit -o nounset -o xtrace -o pipefail
+set -o errexit -o nounset -o pipefail
 
 # Use PIXI_HOME if set (e.g. custom HPC path), otherwise fall back to default
 PIXI_HOME="${PIXI_HOME:-${HOME}/.pixi}"

From 405781ad97bf2c7ab64b4f1457f54fd22d05a488 Mon Sep 17 00:00:00 2001
From: RuiDongDR <rui.dong.dr@gmail.com>
Date: Wed, 25 Feb 2026 23:01:36 -0500
Subject: [PATCH 05/12] move cache folder to user-assigned path too

---
 pixi-install.sh | 9 +++++++--
 pixi-setup.sh   | 2 +-
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/pixi-install.sh b/pixi-install.sh
index d30d3a2..37c83a7 100755
--- a/pixi-install.sh
+++ b/pixi-install.sh
@@ -38,5 +38,10 @@ if ! grep -q 'export PYDEVD_DISABLE_FILE_VALIDATION=1' "${CONFIG_FILE}"; then
   echo "export PYDEVD_DISABLE_FILE_VALIDATION=1" >> "${CONFIG_FILE}"
 fi
 
-# set default channels
-mkdir -p "${PIXI_HOME:-${HOME}/.pixi}" && echo 'default_channels = ["dnachun", "conda-forge", "bioconda"]' > "${PIXI_HOME:-${HOME}/.pixi}/config.toml"
+# set default channels and redirect cache into PIXI_HOME
+_pixi_dir="${PIXI_HOME:-${HOME}/.pixi}"
+mkdir -p "${_pixi_dir}"
+cat > "${_pixi_dir}/config.toml" << EOF
+default_channels = ["dnachun", "conda-forge", "bioconda"]
+cache_dir = "${_pixi_dir}/cache"
+EOF
diff --git a/pixi-setup.sh b/pixi-setup.sh
index 63f4cb2..a4881f7 100755
--- a/pixi-setup.sh
+++ b/pixi-setup.sh
@@ -77,7 +77,7 @@ echo "Using PIXI_HOME=${PIXI_HOME}"
 echo ""
 echo "Choose installation type:"
 echo "  1) minimal - Essential CLI tools + Python data science + base R"
-echo "               ~7 GB, ~100k files"
+echo "               ~5 GB, ~120k files"
 echo "  2) full    - Complete bioinformatics environment (samtools, GATK, plink,"
 echo "               STAR, Seurat, bioconductor packages, etc.)"
 echo "               ~35 GB, ~350k files"

From d05a08eb522e162fbe87078be30e168fb1fade71 Mon Sep 17 00:00:00 2001
From: RuiDongDR <rui.dong.dr@gmail.com>
Date: Wed, 25 Feb 2026 23:15:12 -0500
Subject: [PATCH 06/12] set cache folder in bashrc

---
 pixi-setup.sh | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/pixi-setup.sh b/pixi-setup.sh
index a4881f7..6af374b 100755
--- a/pixi-setup.sh
+++ b/pixi-setup.sh
@@ -66,11 +66,12 @@ _default_pixi_home="${HOME}/.pixi"
 echo ""
 echo "Where should pixi store its environments and packages?"
 echo "  Default: ${_default_pixi_home}"
-echo "  NOTE: Home directories often have storage quotas on HPC systems."
-echo "  Consider a path on a larger filesystem, e.g. /lab/yourlab/.pixi"
+echo "  NOTE: Home directories have storage quotas. On HPC, prefer VAST over"
+echo "  GPFS/Lustre for better small-file I/O. e.g. /lab/yourlab/.pixi"
 echo ""
 read -r -p "Installation path [${_default_pixi_home}]: " _user_pixi_home
 export PIXI_HOME="${_user_pixi_home:-${_default_pixi_home}}"
+export RATTLER_CACHE_DIR="${PIXI_HOME}/cache"
 echo "Using PIXI_HOME=${PIXI_HOME}"
 
 # --- Prompt: install type ---
@@ -148,6 +149,14 @@ fi
 # print messages
 BB='\033[1;34m'
 NC='\033[0m'
+if [[ "$OSTYPE" == "darwin"* ]]; then
+    _shell_config="${HOME}/.zshrc"
+else
+    _shell_config="${HOME}/.bashrc"
+fi
 echo -e "${BB}Installation completed. Pixi is installed at: ${PIXI_HOME}${NC}"
 echo -e "${BB}Note: From now on you can install other R packages as needed with 'pixi global install --environment r-base ...'${NC}"
 echo -e "${BB}and Python with 'pixi global install --environment python ...'${NC}"
+echo -e "${BB}To keep the package cache in ${PIXI_HOME}/cache across all future sessions,${NC}"
+echo -e "${BB}add this line to ${_shell_config}:${NC}"
+echo -e "${BB}  export RATTLER_CACHE_DIR=\"${PIXI_HOME}/cache\"${NC}"

From e57b52fedbd514b0f4344a7f695a3c161583cfcc Mon Sep 17 00:00:00 2001
From: RuiDongDR <rui.dong.dr@gmail.com>
Date: Wed, 25 Feb 2026 23:44:43 -0500
Subject: [PATCH 07/12] update cache folder again

---
 pixi-install.sh | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/pixi-install.sh b/pixi-install.sh
index 37c83a7..8a87e16 100755
--- a/pixi-install.sh
+++ b/pixi-install.sh
@@ -38,10 +38,7 @@ if ! grep -q 'export PYDEVD_DISABLE_FILE_VALIDATION=1' "${CONFIG_FILE}"; then
   echo "export PYDEVD_DISABLE_FILE_VALIDATION=1" >> "${CONFIG_FILE}"
 fi
 
-# set default channels and redirect cache into PIXI_HOME
+# set default channels
 _pixi_dir="${PIXI_HOME:-${HOME}/.pixi}"
 mkdir -p "${_pixi_dir}"
-cat > "${_pixi_dir}/config.toml" << EOF
-default_channels = ["dnachun", "conda-forge", "bioconda"]
-cache_dir = "${_pixi_dir}/cache"
-EOF
+echo 'default_channels = ["dnachun", "conda-forge", "bioconda"]' > "${_pixi_dir}/config.toml"

From b7b0e74b74478446a4c9d8a372427d0eac0cba64 Mon Sep 17 00:00:00 2001
From: RuiDongDR <rui.dong.dr@gmail.com>
Date: Thu, 26 Feb 2026 00:19:58 -0500
Subject: [PATCH 08/12] update number of files

---
 pixi-setup.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pixi-setup.sh b/pixi-setup.sh
index 6af374b..d6d3646 100755
--- a/pixi-setup.sh
+++ b/pixi-setup.sh
@@ -78,7 +78,7 @@ echo "Using PIXI_HOME=${PIXI_HOME}"
 echo ""
 echo "Choose installation type:"
 echo "  1) minimal - Essential CLI tools + Python data science + base R"
-echo "               ~5 GB, ~120k files"
+echo "               ~5 GB, ~100k files"
 echo "  2) full    - Complete bioinformatics environment (samtools, GATK, plink,"
 echo "               STAR, Seurat, bioconductor packages, etc.)"
 echo "               ~35 GB, ~350k files"

From dde7a8e004bc3ac561464da66efdd9ff0e3ed646 Mon Sep 17 00:00:00 2001
From: RuiDongDR <rui.dong.dr@gmail.com>
Date: Thu, 26 Feb 2026 11:35:52 -0500
Subject: [PATCH 09/12] update

---
 .github/workflows/ci.yml          |   6 +-
 .github/workflows/dispatch_ci.yml |   6 +-
 envs/full_packages.txt            | 191 ++++++++++++++++++++++++++++++
 pixi-setup.sh                     |  15 ++-
 4 files changed, 207 insertions(+), 11 deletions(-)
 create mode 100644 envs/full_packages.txt

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 726df50..6329d88 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -25,7 +25,7 @@ jobs:
         run: |
           sed -i "s?main?${{ github.event.pull_request.head.ref }}?g" pixi-setup.sh
           sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.event.pull_request.head.ref }},g' | bash?" pixi-setup.sh
-          ./pixi-setup.sh
+          printf '\n\n' | ./pixi-setup.sh
 
   osx-64:
     runs-on: macos-13
@@ -48,7 +48,7 @@ jobs:
         run: |
           sed -i "s?main?${{ github.event.pull_request.head.ref }}?g" pixi-setup.sh
           sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.event.pull_request.head.ref }},g' | bash?" pixi-setup.sh
-          ./pixi-setup.sh
+          printf '\n\n' | ./pixi-setup.sh
 
   osx-arm64:
     runs-on: macos-14
@@ -71,4 +71,4 @@ jobs:
         run: |
           sed -i "s?main?${{ github.event.pull_request.head.ref }}?g" pixi-setup.sh
           sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.event.pull_request.head.ref }},g' | bash?" pixi-setup.sh
-          ./pixi-setup.sh
+          printf '\n\n' | ./pixi-setup.sh
diff --git a/.github/workflows/dispatch_ci.yml b/.github/workflows/dispatch_ci.yml
index 6f8db5a..9082c87 100644
--- a/.github/workflows/dispatch_ci.yml
+++ b/.github/workflows/dispatch_ci.yml
@@ -25,7 +25,7 @@ jobs:
         run: |
           sed -i "s?main?${{ github.event.pull_request.head.ref }}?g" pixi-setup.sh
           sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.event.pull_request.head.ref }},g' | bash?" pixi-setup.sh
-          ./pixi-setup.sh
+          printf '\n\n' | ./pixi-setup.sh
 
   osx-64_pixi:
     runs-on: macos-latest
@@ -48,7 +48,7 @@ jobs:
         run: |
           sed -i "s?main?${{ github.event.pull_request.head.ref }}?g" pixi-setup.sh
           sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.event.pull_request.head.ref }},g' | bash?" pixi-setup.sh
-          ./pixi-setup.sh
+          printf '\n\n' | ./pixi-setup.sh
 
   osx-arm64_pixi:
     runs-on: macos-14
@@ -71,4 +71,4 @@ jobs:
         run: |
           sed -i "s?main?${{ github.event.pull_request.head.ref }}?g" pixi-setup.sh
           sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.event.pull_request.head.ref }},g' | bash?" pixi-setup.sh
-          ./pixi-setup.sh
+          printf '\n\n' | ./pixi-setup.sh
diff --git a/envs/full_packages.txt b/envs/full_packages.txt
new file mode 100644
index 0000000..5f91dec
--- /dev/null
+++ b/envs/full_packages.txt
@@ -0,0 +1,191 @@
+# Full package list - complete bioinformatics environment
+# Sections: [global], [global_linux], [python], [r]
+
+# [global]
+ark
+awscli
+bamtools
+bcftools
+bedtools
+curl
+deeptools
+diffutils
+ensembl-vep
+fastqc
+fastp
+findutils
+gatk4
+gawk
+gffread
+git
+go-ghq
+grep
+gtex-pipeline-gene_model
+gtex-pipeline-qtl
+gtex-pipeline-rnaseq
+htslib
+king
+kent-tools
+less
+metal
+multiqc
+pandoc
+parallel
+perl
+picard
+plink
+plink2
+python=3.12
+quantas
+r-base=4.4
+regtools
+ripgrep
+rnaseqc
+rsem
+ruby
+samtools
+sed
+snpeff
+snpsift
+star
+tree
+trimmomatic
+unzip
+util-linux
+vim
+wget
+
+# [global_linux]
+code-server
+fastlmmc
+gcta
+ldstore
+procps-ng
+regenie
+
+# [python]
+altair
+bash_kernel
+bitarray
+cython
+dill
+feather-format
+imageio
+ipykernel
+ipywidgets
+ipympl
+ipyparallel
+ipython
+jedi-language-server
+jupyterlab
+jupyter_client
+jupyter_console
+jupyter_core
+jupyter_server
+jupyter-lsp
+jupyterlab-lsp
+jupyterlab-sos
+jupyterhub
+markdown
+markdown-kernel
+matplotlib-base
+mofapy2
+multipy
+nb_conda_kernels
+nbconvert-core
+nbdime
+nbformat
+notebook
+numba
+numexpr
+numpy
+openpyxl
+pandas
+pgenlib
+pillow
+ptpython
+pyarrow
+pybigwig
+python-ldstore
+python-lsp-server
+qvalue
+scikit-learn
+scipy
+seaborn
+statsmodels
+sympy
+tqdm
+tensorqtl
+wand
+widgetsnbextension
+sos
+sos-bash
+sos-notebook
+sos-python
+sos-r
+
+# [r]
+bioconductor-annotationdbi
+bioconductor-clusterprofiler
+bioconductor-edger
+bioconductor-illuminahumanmethylation450kmanifest
+bioconductor-illuminahumanmethylationepicmanifest
+bioconductor-impute
+bioconductor-limma
+bioconductor-minfi
+bioconductor-mofa2
+bioconductor-org.hs.eg.db
+bioconductor-pcatools
+bioconductor-preprocesscore
+bioconductor-psichomics
+bioconductor-qvalue
+bioconductor-sesame
+bioconductor-sesamedata
+bioconductor-variantannotation
+r-abind
+r-arrow
+r-ape
+r-bedtoolsr
+r-bigsnpr
+r-biocmanager
+r-bitops
+r-catools
+r-colocboost
+r-complexupset
+r-corrplot
+r-devtools
+r-flashpcar
+r-fsusier
+r-gbj
+r-genio
+r-glmnet
+r-gplots
+r-gtools
+r-gwasrapidd
+r-harmonicmeanp
+r-httpgd
+r-hudson
+r-igraph
+r-irkernel
+r-languageserver
+r-mediation
+r-missforest
+r-mr.ash.alpha
+r-mr.mash.alpha
+r-mvsusier
+r-pacman
+r-pecotmr
+r-pgenlibr
+r-plinkqc
+r-profvis
+r-qgg
+r-qqman
+r-qrank
+r-quadprog
+r-quantreg
+r-rfast
+r-rgl
+r-rmtstat
+r-seurat
+r-tidyverse
+r-watershedr
diff --git a/pixi-setup.sh b/pixi-setup.sh
index d6d3646..76a2cc2 100755
--- a/pixi-setup.sh
+++ b/pixi-setup.sh
@@ -67,7 +67,7 @@ echo ""
 echo "Where should pixi store its environments and packages?"
 echo "  Default: ${_default_pixi_home}"
 echo "  NOTE: Home directories have storage quotas. On HPC, prefer VAST over"
-echo "  GPFS/Lustre for better small-file I/O. e.g. /lab/yourlab/.pixi"
+echo "  GPFS/Lustre for better small-file I/O. e.g. /lab/$USER/.pixi"
 echo ""
 read -r -p "Installation path [${_default_pixi_home}]: " _user_pixi_home
 export PIXI_HOME="${_user_pixi_home:-${_default_pixi_home}}"
@@ -120,7 +120,11 @@ if [[ "${INSTALL_TYPE}" == "minimal" ]]; then
 
 else
     # --- Full install ---
-    install_global_packages <(curl -fsSL https://raw.githubusercontent.com/StatFunGen/pixi-setup/main/envs/global_packages.txt | grep -v "#")
+    _full_url="https://raw.githubusercontent.com/StatFunGen/pixi-setup/main/envs/full_packages.txt"
+    _full_file=$(mktemp)
+    curl -fsSL "${_full_url}" -o "${_full_file}"
+
+    install_global_packages <(extract_section "${_full_file}" "global")
 
     if [[ "$OSTYPE" == "linux-gnu"* ]]; then
         safe_expose_remove util-linux kill
@@ -131,15 +135,16 @@ else
     if [[ "$OSTYPE" == "linux-gnu"* ]]; then
         safe_expose_remove coreutils kill
         safe_expose_remove coreutils uptime
-        install_global_packages <(curl -fsSL https://raw.githubusercontent.com/StatFunGen/pixi-setup/main/envs/global_packages_linux.txt | grep -v "#")
+        install_global_packages <(extract_section "${_full_file}" "global_linux")
     fi
 
     echo "Installing recommended R libraries ..."
-    inject_packages r-base <(curl -fsSL https://raw.githubusercontent.com/StatFunGen/pixi-setup/main/envs/r_packages.txt | grep -v "#")
+    inject_packages r-base <(extract_section "${_full_file}" "r")
 
     echo "Installing recommended Python packages ..."
-    inject_packages python <(curl -fsSL https://raw.githubusercontent.com/StatFunGen/pixi-setup/main/envs/python_packages.txt | grep -v "#")
+    inject_packages python <(extract_section "${_full_file}" "python")
 
+    rm -f "${_full_file}"
     pixi clean cache -y
 
     # Install config files

From 553d89d79ac700f8eb91ef1dff14495adfd822ec Mon Sep 17 00:00:00 2001
From: RuiDongDR <rui.dong.dr@gmail.com>
Date: Thu, 26 Feb 2026 11:41:48 -0500
Subject: [PATCH 10/12] fix

---
 .github/workflows/dispatch_ci.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/dispatch_ci.yml b/.github/workflows/dispatch_ci.yml
index 9082c87..5e620e3 100644
--- a/.github/workflows/dispatch_ci.yml
+++ b/.github/workflows/dispatch_ci.yml
@@ -23,8 +23,8 @@ jobs:
       - name: Run setup script
         shell: pixi exec --spec sed -- bash -e {0}
         run: |
-          sed -i "s?main?${{ github.event.pull_request.head.ref }}?g" pixi-setup.sh
-          sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.event.pull_request.head.ref }},g' | bash?" pixi-setup.sh
+          sed -i "s?main?${{ github.ref_name }}?g" pixi-setup.sh
+          sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.ref_name }},g' | bash?" pixi-setup.sh
           printf '\n\n' | ./pixi-setup.sh
 
   osx-64_pixi:
@@ -46,8 +46,8 @@ jobs:
       - name: Run setup script
         shell: pixi exec --spec sed -- bash -e {0}
         run: |
-          sed -i "s?main?${{ github.event.pull_request.head.ref }}?g" pixi-setup.sh
-          sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.event.pull_request.head.ref }},g' | bash?" pixi-setup.sh
+          sed -i "s?main?${{ github.ref_name }}?g" pixi-setup.sh
+          sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.ref_name }},g' | bash?" pixi-setup.sh
           printf '\n\n' | ./pixi-setup.sh
 
   osx-arm64_pixi:
@@ -69,6 +69,6 @@ jobs:
       - name: Run setup script
         shell: pixi exec --spec sed -- bash -e {0}
         run: |
-          sed -i "s?main?${{ github.event.pull_request.head.ref }}?g" pixi-setup.sh
-          sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.event.pull_request.head.ref }},g' | bash?" pixi-setup.sh
+          sed -i "s?main?${{ github.ref_name }}?g" pixi-setup.sh
+          sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.ref_name }},g' | bash?" pixi-setup.sh
           printf '\n\n' | ./pixi-setup.sh

From 74cf3e54fdfdd99d520e69a89465c15d6c32f812 Mon Sep 17 00:00:00 2001
From: RuiDongDR <rui.dong.dr@gmail.com>
Date: Thu, 26 Feb 2026 12:06:15 -0500
Subject: [PATCH 11/12] try again..

---
 .github/workflows/ci.yml          | 6 +++---
 .github/workflows/dispatch_ci.yml | 6 +++---
 pixi-setup.sh                     | 2 +-
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6329d88..4440d00 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -25,7 +25,7 @@ jobs:
         run: |
           sed -i "s?main?${{ github.event.pull_request.head.ref }}?g" pixi-setup.sh
           sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.event.pull_request.head.ref }},g' | bash?" pixi-setup.sh
-          printf '\n\n' | ./pixi-setup.sh
+          printf "\n1\n" | ./pixi-setup.sh
 
   osx-64:
     runs-on: macos-13
@@ -48,7 +48,7 @@ jobs:
         run: |
           sed -i "s?main?${{ github.event.pull_request.head.ref }}?g" pixi-setup.sh
           sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.event.pull_request.head.ref }},g' | bash?" pixi-setup.sh
-          printf '\n\n' | ./pixi-setup.sh
+          printf "\n1\n" | ./pixi-setup.sh
 
   osx-arm64:
     runs-on: macos-14
@@ -71,4 +71,4 @@ jobs:
         run: |
           sed -i "s?main?${{ github.event.pull_request.head.ref }}?g" pixi-setup.sh
           sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.event.pull_request.head.ref }},g' | bash?" pixi-setup.sh
-          printf '\n\n' | ./pixi-setup.sh
+          printf "\n1\n" | ./pixi-setup.sh
\ No newline at end of file
diff --git a/.github/workflows/dispatch_ci.yml b/.github/workflows/dispatch_ci.yml
index 5e620e3..5dea958 100644
--- a/.github/workflows/dispatch_ci.yml
+++ b/.github/workflows/dispatch_ci.yml
@@ -25,7 +25,7 @@ jobs:
         run: |
           sed -i "s?main?${{ github.ref_name }}?g" pixi-setup.sh
           sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.ref_name }},g' | bash?" pixi-setup.sh
-          printf '\n\n' | ./pixi-setup.sh
+          printf "\n1\n" | ./pixi-setup.sh
 
   osx-64_pixi:
     runs-on: macos-latest
@@ -48,7 +48,7 @@ jobs:
         run: |
           sed -i "s?main?${{ github.ref_name }}?g" pixi-setup.sh
           sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.ref_name }},g' | bash?" pixi-setup.sh
-          printf '\n\n' | ./pixi-setup.sh
+          printf "\n1\n" | ./pixi-setup.sh
 
   osx-arm64_pixi:
     runs-on: macos-14
@@ -71,4 +71,4 @@ jobs:
         run: |
           sed -i "s?main?${{ github.ref_name }}?g" pixi-setup.sh
           sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.ref_name }},g' | bash?" pixi-setup.sh
-          printf '\n\n' | ./pixi-setup.sh
+          printf "\n1\n" | ./pixi-setup.sh
\ No newline at end of file
diff --git a/pixi-setup.sh b/pixi-setup.sh
index 76a2cc2..68d7c9c 100755
--- a/pixi-setup.sh
+++ b/pixi-setup.sh
@@ -67,7 +67,7 @@ echo ""
 echo "Where should pixi store its environments and packages?"
 echo "  Default: ${_default_pixi_home}"
 echo "  NOTE: Home directories have storage quotas. On HPC, prefer VAST over"
-echo "  GPFS/Lustre for better small-file I/O. e.g. /lab/$USER/.pixi"
+echo "  GPFS/Lustre for better small-file I/O. e.g. /lab/\$USER/.pixi"
 echo ""
 read -r -p "Installation path [${_default_pixi_home}]: " _user_pixi_home
 export PIXI_HOME="${_user_pixi_home:-${_default_pixi_home}}"

From ded4a77714523e4adc71d649a643e43a05d58731 Mon Sep 17 00:00:00 2001
From: RuiDongDR <rui.dong.dr@gmail.com>
Date: Thu, 26 Feb 2026 12:16:24 -0500
Subject: [PATCH 12/12] fix the hardcoded repo owner name

---
 .github/workflows/dispatch_ci.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/dispatch_ci.yml b/.github/workflows/dispatch_ci.yml
index 5dea958..eeb3d6e 100644
--- a/.github/workflows/dispatch_ci.yml
+++ b/.github/workflows/dispatch_ci.yml
@@ -23,8 +23,8 @@ jobs:
       - name: Run setup script
         shell: pixi exec --spec sed -- bash -e {0}
         run: |
-          sed -i "s?main?${{ github.ref_name }}?g" pixi-setup.sh
-          sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.ref_name }},g' | bash?" pixi-setup.sh
+          sed -i "s?StatFunGen/pixi-setup/main?${{ github.repository }}/${{ github.ref_name }}?g" pixi-setup.sh
+          sed -i "s?init.sh | bash?init.sh | sed 's,StatFunGen/pixi-setup/main,${{ github.repository }}/${{ github.ref_name }},g' | bash?" pixi-setup.sh
           printf "\n1\n" | ./pixi-setup.sh
 
   osx-64_pixi:
@@ -46,8 +46,8 @@ jobs:
       - name: Run setup script
         shell: pixi exec --spec sed -- bash -e {0}
         run: |
-          sed -i "s?main?${{ github.ref_name }}?g" pixi-setup.sh
-          sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.ref_name }},g' | bash?" pixi-setup.sh
+          sed -i "s?StatFunGen/pixi-setup/main?${{ github.repository }}/${{ github.ref_name }}?g" pixi-setup.sh
+          sed -i "s?init.sh | bash?init.sh | sed 's,StatFunGen/pixi-setup/main,${{ github.repository }}/${{ github.ref_name }},g' | bash?" pixi-setup.sh
           printf "\n1\n" | ./pixi-setup.sh
 
   osx-arm64_pixi:
@@ -69,6 +69,6 @@ jobs:
       - name: Run setup script
         shell: pixi exec --spec sed -- bash -e {0}
         run: |
-          sed -i "s?main?${{ github.ref_name }}?g" pixi-setup.sh
-          sed -i "s?init.sh | bash?init.sh | sed 's,main,${{ github.ref_name }},g' | bash?" pixi-setup.sh
+          sed -i "s?StatFunGen/pixi-setup/main?${{ github.repository }}/${{ github.ref_name }}?g" pixi-setup.sh
+          sed -i "s?init.sh | bash?init.sh | sed 's,StatFunGen/pixi-setup/main,${{ github.repository }}/${{ github.ref_name }},g' | bash?" pixi-setup.sh
           printf "\n1\n" | ./pixi-setup.sh
\ No newline at end of file