Merge pull request #81 from metabarcoding/push-nrylumyxtxnr

Push nrylumyxtxnr
2026-03-25 13:30:52 +00:00 · 2026-02-06 10:10:22 +01:00
parent da8d851d4d f79b018430
commit cd5562fb30
4 changed files with 168 additions and 53 deletions
--- a/README.md
+++ b/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.
-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:
+By default, the script installs the latest version of *OBITools* commands and other associated files into the `/usr/local` directory.

+### 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...

--- a/install_obitools.sh
+++ b/install_obitools.sh
@@ -1,27 +1,56 @@
 #!/bin/bash

-INSTALL_DIR="/usr/local"
-OBITOOLS_PREFIX=""
-# default values
+# 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 $DIR
-# omit the -p parameter to create a temporal directory in the default location
-# WORK_DIR=$(mktemp -d -p "$DIR"  "obitools4.XXXXXX" 2> /dev/null || \
-#            mktemp -d -t "$DIR"  "obitools4.XXXXXX")
-
+# Create temporary directory
 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 "$GOURL" \
-    | tar zxf -
+curl -s "$GOURL" | 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 "$OBIURL4" > master.zip
-unzip master.zip
+if ! curl -sL "$OBIURL4" > obitools4.zip; then
+  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
-mkdir vendor
+# Find the extracted directory
+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
--- a/pkg/obioptions/version.go
+++ b/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 4.4.10"
+var _Version = "Release 4.4.11"

 // Version returns the version of the obitools package.
 //
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-4.4.10
+4.4.11
@@ -1 +1 @@
 .4.10
 .4.11