Enhance OBITools4 installation script with version control and documentation

Update installation script to support specific version installation, list available versions, and improve documentation.

- Add support for installing specific versions with -v/--version flag
- Add -l/--list flag to list all available versions
- Improve help message with examples
- Update README.md to reflect new installation options and examples
- Add note on version compatibility between OBITools2 and OBITools4
- Remove ecoprimers directory
- Improve error handling and user feedback during installation
- Add version detection and download logic from GitHub releases
- Update installation process to use tagged releases instead of master branch

.github/workflows/release.yml

@@ -32,12 +32,11 @@ jobs:
             goos: linux
             goarch: amd64
             output_name: linux_amd64
-          - os: ubuntu-latest
+          - os: ubuntu-24.04-arm
             goos: linux
             goarch: arm64
             output_name: linux_arm64
-            cross_compile: true
+          - os: macos-15-intel
-          - os: macos-latest
             goos: darwin
             goarch: amd64
             output_name: darwin_amd64
@@ -63,25 +62,23 @@ jobs:
           TAG=${GITHUB_REF#refs/tags/Release_}
           echo "version=$TAG" >> $GITHUB_OUTPUT
 
-      - name: Install cross-compilation tools (Linux ARM64 only)
+      - name: Install build tools (macOS)
-        if: matrix.cross_compile
+        if: runner.os == 'macOS'
         run: |
-          sudo apt-get update
+          # Ensure Xcode Command Line Tools are installed
-          sudo apt-get install -y gcc-aarch64-linux-gnu
+          xcode-select --install 2>/dev/null || true
+          xcode-select -p
 
       - name: Build binaries
         env:
           GOOS: ${{ matrix.goos }}
           GOARCH: ${{ matrix.goarch }}
-          CC: ${{ matrix.cross_compile && 'aarch64-linux-gnu-gcc' || '' }}
           VERSION: ${{ steps.get_version.outputs.version }}
         run: |
           make obitools
           mkdir -p artifacts
-          cd build
+          # Create a single tar.gz with all binaries for this platform
-          for binary in *; do
+          tar -czf artifacts/obitools4_${VERSION}_${{ matrix.output_name }}.tar.gz -C build .
-            tar -czf ../artifacts/${binary}_${VERSION}_${{ matrix.output_name }}.tar.gz ${binary}
-          done
 
       - name: Upload artifacts
         uses: actions/upload-artifact@v4
@@ -139,29 +136,29 @@ jobs:
           echo "" >> release_notes.md
           echo "## Installation" >> release_notes.md
           echo "" >> release_notes.md
-          echo "Download the appropriate binary for your system and extract it:" >> release_notes.md
+          echo "Download the appropriate archive for your system and extract it:" >> release_notes.md
           echo "" >> release_notes.md
           echo "### Linux (AMD64)" >> release_notes.md
           echo '```bash' >> release_notes.md
-          echo "tar -xzf <tool>_${VERSION}_linux_amd64.tar.gz" >> release_notes.md
+          echo "tar -xzf obitools4_${VERSION}_linux_amd64.tar.gz" >> release_notes.md
           echo '```' >> release_notes.md
           echo "" >> release_notes.md
           echo "### Linux (ARM64)" >> release_notes.md
           echo '```bash' >> release_notes.md
-          echo "tar -xzf <tool>_${VERSION}_linux_arm64.tar.gz" >> release_notes.md
+          echo "tar -xzf obitools4_${VERSION}_linux_arm64.tar.gz" >> release_notes.md
           echo '```' >> release_notes.md
           echo "" >> release_notes.md
           echo "### macOS (Intel)" >> release_notes.md
           echo '```bash' >> release_notes.md
-          echo "tar -xzf <tool>_${VERSION}_darwin_amd64.tar.gz" >> release_notes.md
+          echo "tar -xzf obitools4_${VERSION}_darwin_amd64.tar.gz" >> release_notes.md
           echo '```' >> release_notes.md
           echo "" >> release_notes.md
           echo "### macOS (Apple Silicon)" >> release_notes.md
           echo '```bash' >> release_notes.md
-          echo "tar -xzf <tool>_${VERSION}_darwin_arm64.tar.gz" >> release_notes.md
+          echo "tar -xzf obitools4_${VERSION}_darwin_arm64.tar.gz" >> release_notes.md
           echo '```' >> release_notes.md
           echo "" >> release_notes.md
-          echo "Available tools: Replace \`<tool>\` with one of the obitools commands." >> release_notes.md
+          echo "All OBITools4 binaries are included in each archive." >> release_notes.md
 
       - name: Create GitHub Release
         uses: softprops/action-gh-release@v1

README.md

@@ -16,12 +16,17 @@ The easiest way to run it is to copy and paste the following command into your t
 curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash
 ```
 
-By default, the script installs the *OBITools* commands and other associated files into the `/usr/local` directory.
+By default, the script installs the latest version of *OBITools* commands and other associated files into the `/usr/local` directory.
-The names of the commands in the new *OBITools4* are mostly identical to those in *OBITools2*.
-Therefore, installing the new *OBITools* may hide or delete the old ones. If you want both versions to be 
-available on your system, the installation script offers two options:
 
+### Installation Options
 
+The installation script offers several options:
+
+>  -l, --list              List all available versions and exit.
+> 
+>  -v, --version           Install a specific version (e.g., `-v 4.4.3`).
+>                          By default, the latest version is installed.
+> 
 >  -i, --install-dir       Directory where obitools are installed 
 >                          (as example use `/usr/local` not `/usr/local/bin`).
 > 
@@ -30,14 +35,31 @@ available on your system, the installation script offers two options:
 >                          same time on your system (as example `-p g` will produce 
 >                          `gobigrep` command instead of `obigrep`).
 
-You can use these options by following the installation command:
+### Examples
 
+List all available versions:
+```{bash}
+curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash -s -- --list
+```
+
+Install a specific version:
+```{bash}
+curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash -s -- --version 4.4.3
+```
+
+Install in a custom directory with command prefix:
 ```{bash}
 curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | \
       bash -s -- --install-dir test_install --obitools-prefix k
 ```
 
-In this case, the binaries will be installed in the `test_install` directory and all command names will be prefixed with the letter `k`. Thus, `obigrep` will be named `kobigrep`.
+In this last example, the binaries will be installed in the `test_install` directory and all command names will be prefixed with the letter `k`. Thus, `obigrep` will be named `kobigrep`.
+
+### Note on Version Compatibility
+
+The names of the commands in the new *OBITools4* are mostly identical to those in *OBITools2*.
+Therefore, installing the new *OBITools* may hide or delete the old ones. If you want both versions to be 
+available on your system, use the `--install-dir` and `--obitools-prefix` options as shown above.
 
 ## Continuing the analysis...
 

install_obitools.sh

@@ -1,27 +1,56 @@
 #!/bin/bash
 
-INSTALL_DIR="/usr/local"
+# Default values
-OBITOOLS_PREFIX=""
-# default values
 URL="https://go.dev/dl/"
-OBIURL4="https://github.com/metabarcoding/obitools4/archive/refs/heads/master.zip"
+GITHUB_REPO="https://github.com/metabarcoding/obitools4"
 INSTALL_DIR="/usr/local"
 OBITOOLS_PREFIX=""
+VERSION=""
+LIST_VERSIONS=false
 
-# help message
+# Help message
 function display_help {
   echo "Usage: $0 [OPTIONS]"
   echo ""
   echo "Options:"
   echo "  -i, --install-dir       Directory where obitools are installed "
-  echo "                          (as example use /usr/local not /usr/local/bin)."
+  echo "                          (e.g., use /usr/local not /usr/local/bin)."
   echo "  -p, --obitools-prefix   Prefix added to the obitools command names if you"
   echo "                          want to have several versions of obitools at the"
-  echo "                          same time on your system (as example -p g will produce "
+  echo "                          same time on your system (e.g., -p g will produce "
   echo "                          gobigrep command instead of obigrep)."
+  echo "  -v, --version           Install a specific version (e.g., 4.4.8)."
+  echo "                          If not specified, installs the latest version."
+  echo "  -l, --list              List all available versions and exit."
   echo "  -h, --help              Display this help message."
+  echo ""
+  echo "Examples:"
+  echo "  $0                      # Install latest version"
+  echo "  $0 -l                   # List available versions"
+  echo "  $0 -v 4.4.8             # Install specific version"
+  echo "  $0 -i /opt/local        # Install to custom directory"
 }
 
+# List available versions from GitHub releases
+function list_versions {
+  echo "Fetching available versions..." 1>&2
+  echo ""
+  curl -s "https://api.github.com/repos/metabarcoding/obitools4/releases" \
+    | grep '"tag_name":' \
+    | sed -E 's/.*"tag_name": "Release_([0-9.]+)".*/\1/' \
+    | sort -V -r
+}
+
+# Get latest version from GitHub releases
+function get_latest_version {
+  curl -s "https://api.github.com/repos/metabarcoding/obitools4/releases" \
+    | grep '"tag_name":' \
+    | sed -E 's/.*"tag_name": "Release_([0-9.]+)".*/\1/' \
+    | sort -V -r \
+    | head -1
+}
+
+# Parse command line arguments
 while [ "$#" -gt 0 ]; do
   case "$1" in
     -i|--install-dir)
@@ -32,28 +61,57 @@ while [ "$#" -gt 0 ]; do
       OBITOOLS_PREFIX="$2"
       shift 2
       ;;
+    -v|--version)
+      VERSION="$2"
+      shift 2
+      ;;
+    -l|--list)
+      LIST_VERSIONS=true
+      shift
+      ;;
     -h|--help)
-      display_help  1>&2 
+      display_help
       exit 0
       ;;
     *)
       echo "Error: Unsupported option $1" 1>&2
+      display_help 1>&2
       exit 1
       ;;
   esac
 done
 
-# the directory from where the script is run
+# List versions and exit if requested
+if [ "$LIST_VERSIONS" = true ]; then
+  echo "Available OBITools4 versions:"
+  echo "=============================="
+  list_versions
+  exit 0
+fi
+
+# Determine version to install
+if [ -z "$VERSION" ]; then
+  echo "Fetching latest version..." 1>&2
+  VERSION=$(get_latest_version)
+  if [ -z "$VERSION" ]; then
+    echo "Error: Could not determine latest version" 1>&2
+    exit 1
+  fi
+  echo "Latest version: $VERSION" 1>&2
+else
+  echo "Installing version: $VERSION" 1>&2
+fi
+
+# Construct source URL for the specified version
+OBIURL4="${GITHUB_REPO}/archive/refs/tags/Release_${VERSION}.zip"
+
+# The directory from where the script is run
 DIR="$(pwd)"
 
-# the temp directory used, within $DIR
+# Create temporary directory
-# omit the -p parameter to create a temporal directory in the default location
-# WORK_DIR=$(mktemp -d -p "$DIR"  "obitools4.XXXXXX" 2> /dev/null || \
-#            mktemp -d -t "$DIR"  "obitools4.XXXXXX")
-
 WORK_DIR=$(mktemp -d "obitools4.XXXXXX")
 
-# check if tmp dir was created
+# Check if tmp dir was created
 if [[ ! "$WORK_DIR" || ! -d "$WORK_DIR" ]]; then
   echo "Could not create temp dir" 1>&2
   exit 1
@@ -63,7 +121,7 @@ mkdir -p "${WORK_DIR}/cache" \
   || (echo "Cannot create ${WORK_DIR}/cache directory" 1>&2
       exit 1)
 
-
+# Create installation directory
 mkdir -p "${INSTALL_DIR}/bin" 2> /dev/null \
   || (echo "Please enter your password for installing obitools in ${INSTALL_DIR}" 1>&2
       sudo mkdir -p "${INSTALL_DIR}/bin")
@@ -75,12 +133,18 @@ fi
 
 INSTALL_DIR="$(cd ${INSTALL_DIR} && pwd)"
 
+echo "================================" 1>&2
+echo "OBITools4 Installation" 1>&2
+echo "================================" 1>&2
+echo "VERSION=$VERSION" 1>&2
 echo "WORK_DIR=$WORK_DIR" 1>&2
 echo "INSTALL_DIR=$INSTALL_DIR" 1>&2
 echo "OBITOOLS_PREFIX=$OBITOOLS_PREFIX" 1>&2
+echo "================================" 1>&2
 
-pushd "$WORK_DIR"|| exit
+pushd "$WORK_DIR" > /dev/null || exit
 
+# Detect OS and architecture
 OS=$(uname -a | awk '{print $1}')
 ARCH=$(uname -m)
 
@@ -92,7 +156,9 @@ if [[ "$ARCH" == "aarch64" ]] ; then
     ARCH="arm64"
 fi
 
-GOFILE=$(curl "$URL" \
+# Download and install Go
+echo "Downloading Go..." 1>&2
+GOFILE=$(curl -s "$URL" \
             | grep 'class="download"' \
             | grep "\.tar\.gz" \
             | sed -E 's@^.*/dl/(go[1-9].+\.tar\.gz)".*$@\1@' \
@@ -100,44 +166,71 @@ GOFILE=$(curl "$URL" \
             | grep -i "$ARCH" \
             | head -1)
 
-GOURL=$(curl "${URL}${GOFILE}" \
+GOURL=$(curl -s "${URL}${GOFILE}" \
         | sed -E 's@^.*href="(.*\.tar\.gz)".*$@\1@')
 
-echo "Install GO from : $GOURL" 1>&2
+echo "Installing Go from: $GOURL" 1>&2
 
-curl "$GOURL" \
+curl -s "$GOURL" | tar zxf -
-    | tar zxf -
 
 PATH="$(pwd)/go/bin:$PATH"
 export PATH
 GOPATH="$(pwd)/go"
 export GOPATH
-
 export GOCACHE="$(pwd)/cache"
-echo "GOCACHE=$GOCACHE" 1>&2@
+
+echo "GOCACHE=$GOCACHE" 1>&2
 mkdir -p "$GOCACHE"
 
+# Download OBITools4 source
+echo "Downloading OBITools4 v${VERSION}..." 1>&2
+echo "Source URL: $OBIURL4" 1>&2
 
-curl -L "$OBIURL4" > master.zip
+if ! curl -sL "$OBIURL4" > obitools4.zip; then
-unzip master.zip
+  echo "Error: Could not download OBITools4 version ${VERSION}" 1>&2
+  echo "Please check that this version exists with: $0 --list" 1>&2
+  exit 1
+fi
 
-echo "Install OBITOOLS from : $OBIURL4"
+unzip -q obitools4.zip
 
-cd obitools4-master || exit
+# Find the extracted directory
-mkdir vendor
+OBITOOLS_DIR=$(ls -d obitools4-* 2>/dev/null | head -1)
 
+if [ -z "$OBITOOLS_DIR" ] || [ ! -d "$OBITOOLS_DIR" ]; then
+  echo "Error: Could not find extracted OBITools4 directory" 1>&2
+  exit 1
+fi
+
+echo "Building OBITools4..." 1>&2
+cd "$OBITOOLS_DIR" || exit
+mkdir -p vendor
+
+# Build with or without prefix
 if [[ -z "$OBITOOLS_PREFIX" ]] ; then
   make GOFLAGS="-buildvcs=false"
 else
   make GOFLAGS="-buildvcs=false" OBITOOLS_PREFIX="${OBITOOLS_PREFIX}"
 fi
 
+# Install binaries
+echo "Installing binaries to ${INSTALL_DIR}/bin..." 1>&2
 (cp build/* "${INSTALL_DIR}/bin" 2> /dev/null) \
-   || (echo "Please enter your password for installing obitools in ${INSTALL_DIR}" 
+   || (echo "Please enter your password for installing obitools in ${INSTALL_DIR}" 1>&2
        sudo cp build/* "${INSTALL_DIR}/bin")
 
-popd || exit
+popd > /dev/null || exit
 
+# Cleanup
+echo "Cleaning up..." 1>&2
 chmod -R +w "$WORK_DIR"
 rm -rf "$WORK_DIR"
 
+echo "" 1>&2
+echo "================================" 1>&2
+echo "OBITools4 v${VERSION} installed successfully!" 1>&2
+echo "Binaries location: ${INSTALL_DIR}/bin" 1>&2
+if [[ -n "$OBITOOLS_PREFIX" ]] ; then
+  echo "Command prefix: ${OBITOOLS_PREFIX}" 1>&2
+fi
+echo "================================" 1>&2

pkg/obioptions/version.go

@@ -3,7 +3,7 @@ package obioptions
 // Version is automatically updated by the Makefile from version.txt
 // The patch number (third digit) is incremented on each push to the repository
 
-var _Version = "Release 4.4.7"
+var _Version = "Release 4.4.10"
 
 // Version returns the version of the obitools package.
 //

version.txt

@@ -1 +1 @@
-4.4.7
+4.4.10