Install devcontainer tools natively instead of using conda (#609)

* install nextflow and nf-test with bash instead of conda

* devcontainer: install needed cli tools using uv

Author: kenibrewer

.devcontainer/codespaces-dev/devcontainer.json

@@ -16,9 +16,12 @@
         "ghcr.io/rocker-org/devcontainer-features/miniforge:2": {
             "version": "latest"
         },
+        "ghcr.io/va-h/devcontainers-features/uv": {},
         "../local-features/apptainer": {},
         "../local-features/tower-agent": {},
-        "../local-features/conda-packages": {}
+        "../local-features/nextflow": {},
+        "../local-features/conda-channels": {},
+        "../local-features/uv-tools": {}
     },
     "workspaceFolder": "/workspaces/training",
     "remoteUser": "root",

.devcontainer/local-dev/devcontainer.json

@@ -16,9 +16,12 @@
         "ghcr.io/rocker-org/devcontainer-features/miniforge:2": {
             "version": "latest"
         },
+        "ghcr.io/va-h/devcontainers-features/uv": {},
         "../local-features/apptainer": {},
         "../local-features/tower-agent": {},
-        "../local-features/conda-packages": {}
+        "../local-features/nextflow": {},
+        "../local-features/conda-channels": {},
+        "../local-features/uv-tools": {}
     },
     "workspaceFolder": "${localWorkspaceFolder}",
     "workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind",

.devcontainer/local-features/conda-channels/devcontainer-feature.json

@@ -0,0 +1,6 @@
+{
+    "id": "conda-channels",
+    "name": "Nextflow Training Conda Channels",
+    "description": "Sets default conda channels for Nextflow Training",
+    "installsAfter": ["ghcr.io/rocker-org/devcontainer-features/miniforge"]
+}

.devcontainer/local-features/conda-channels/install.sh

@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+
+# Install conda packages needed for Nextflow Training
+
+conda config --add channels bioconda
+conda config --add channels conda-forge
+conda config --set channel_priority strict

.devcontainer/local-features/conda-packages/devcontainer-feature.json

@@ -0,0 +1,14 @@
+{
+    "id": "nextflow",
+    "name": "Nextflow Installation",
+    "description": "Install Nextflow and nf-test",
+    "options": {
+        "version": {
+            "type": "string",
+            "proposals": ["latest"],
+            "default": "latest",
+            "description": "Select or enter a version."
+        }
+    },
+    "installsAfter": ["ghcr.io/devcontainers/features/java:1"]
+}

.devcontainer/local-features/conda-packages/install.sh

@@ -0,0 +1,53 @@
+#!/usr/bin/env bash
+
+set -eux
+USERNAME="${USERNAME:-"${_REMOTE_USER:-"automatic"}"}"
+NEXTFLOW_INSTALL_DIR=/usr/local/bin
+
+if [ "$(id -u)" -ne 0 ]; then
+    echo -e 'Script must be run as root. Use sudo, su, or add "USER root" to your Dockerfile before running this script.'
+    exit 1
+fi
+
+# Determine the appropriate non-root user
+if [ "${USERNAME}" = "auto" ] || [ "${USERNAME}" = "automatic" ]; then
+    USERNAME=""
+    POSSIBLE_USERS=("vscode" "node" "codespace" "$(awk -v val=1000 -F ":" '$3==val{print $1}' /etc/passwd)")
+    for CURRENT_USER in "${POSSIBLE_USERS[@]}"; do
+        if id -u ${CURRENT_USER} > /dev/null 2>&1; then
+            USERNAME=${CURRENT_USER}
+            break
+        fi
+    done
+    if [ "${USERNAME}" = "" ]; then
+        USERNAME=root
+    fi
+elif [ "${USERNAME}" = "none" ] || ! id -u ${USERNAME} > /dev/null 2>&1; then
+    USERNAME=root
+fi
+
+# Add the nextflow group if it doesn't exist
+if ! cat /etc/group | grep -e "^nextflow:" > /dev/null 2>&1; then
+    groupadd -r nextflow
+fi
+# Add the user to the nextflow group
+usermod -a -G nextflow "${USERNAME}"
+
+# Install Nextflow
+echo "Installing Nextflow..."
+cd $NEXTFLOW_INSTALL_DIR
+curl -s https://get.nextflow.io | bash
+
+# Install nf-test
+echo "Installing nf-test..."
+cd $NEXTFLOW_INSTALL_DIR
+curl -fsSL https://get.nf-test.com | bash
+
+# Set ownership and permissions on the nextflow and nf-test executables
+chown "${USERNAME}:nextflow" "${NEXTFLOW_INSTALL_DIR}"/nextflow
+chown "${USERNAME}:nextflow" "${NEXTFLOW_INSTALL_DIR}"/nf-test
+chmod g+r+w "${NEXTFLOW_INSTALL_DIR}"/nextflow
+chmod g+r+w "${NEXTFLOW_INSTALL_DIR}"/nf-test
+#find "${NEXTFLOW_INSTALL_DIR}" -type d -print0 | xargs -n 1 -0 chmod g+s
+
+echo "Done!"

.devcontainer/local-features/nextflow/devcontainer-feature.json

@@ -0,0 +1,6 @@
+{
+    "id": "uv-tools",
+    "name": "uv tools",
+    "description": "Install required python cli tools using uv",
+    "installsAfter": ["ghcr.io/va-h/devcontainers-features/uv"]
+}

.devcontainer/local-features/nextflow/install.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+
+# Install python cli tools using uv
+
+uv tool install pre-commit
+uv tool install nf-core