mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
121 lines
3.0 KiB
Bash
Executable File
121 lines
3.0 KiB
Bash
Executable File
#!/bin/bash
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INSTALL_DIR="/usr/local"
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OBITOOLS_PREFIX=""
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# default values
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URL="https://go.dev/dl/"
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OBIURL4="https://git.metabarcoding.org/obitools/obitools4/obitools4/-/archive/master/obitools4-master.tar.gz"
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INSTALL_DIR="/usr/local"
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OBITOOLS_PREFIX=""
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# help message
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function display_help {
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echo "Usage: $0 [OPTIONS]"
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echo ""
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echo "Options:"
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echo " -i, --install-dir Directory where obitools are installed "
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echo " (as example use /usr/local not /usr/local/bin)."
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echo " -p, --obitools-prefix Prefix added to the obitools command names if you"
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echo " want to have several versions of obitools at the"
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echo " same time on your system (as example -p g will produce "
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echo " gobigrep command instead of obigrep)."
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echo " -h, --help Display this help message."
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}
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while [ "$#" -gt 0 ]; do
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case "$1" in
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-i|--install-dir)
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INSTALL_DIR="$2"
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shift 2
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;;
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-p|--obitools-prefix)
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OBITOOLS_PREFIX="$2"
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shift 2
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;;
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-h|--help)
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display_help
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exit 0
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;;
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*)
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echo "Error: Unsupported option $1"
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exit 1
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;;
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esac
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done
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# the directory from where the script is run
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DIR="$(pwd)"
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# the temp directory used, within $DIR
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# omit the -p parameter to create a temporal directory in the default location
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# WORK_DIR=$(mktemp -d -p "$DIR" "obitools4.XXXXXX" 2> /dev/null || \
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# mktemp -d -t "$DIR" "obitools4.XXXXXX")
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WORK_DIR=$(mktemp -d "obitools4.XXXXXX")
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# check if tmp dir was created
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if [[ ! "$WORK_DIR" || ! -d "$WORK_DIR" ]]; then
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echo "Could not create temp dir"
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exit 1
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fi
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mkdir -p "${INSTALL_DIR}/bin" 2> /dev/null \
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|| (echo "Please enter your password for installing obitools in ${INSTALL_DIR}"
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sudo mkdir -p "${INSTALL_DIR}/bin")
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if [[ ! "${INSTALL_DIR}/bin" || ! -d "${INSTALL_DIR}/bin" ]]; then
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echo "Could not create ${INSTALL_DIR}/bin directory for installing obitools"
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exit 1
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fi
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INSTALL_DIR="$(cd $INSTALL_DIR && pwd)"
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echo WORK_DIR=$WORK_DIR
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echo INSTALL_DIR=$INSTALL_DIR
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echo OBITOOLS_PREFIX=$OBITOOLS_PREFIX
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pushd $WORK_DIR
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OS=$(uname -a | awk '{print $1}')
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ARCH=$(uname -m)
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if [[ "$ARCH" == "x86_64" ]] ; then
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ARCH="amd64"
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fi
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GOFILE=$(curl "$URL" \
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| grep 'class="download"' \
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| grep "\.tar\.gz" \
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| sed -E 's@^.*/dl/(go[1-9].+\.tar\.gz)".*$@\1@' \
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| grep -i "$OS" \
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| grep -i "$ARCH" \
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| head -1)
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GOURL=$(curl "${URL}${GOFILE}" \
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| sed -E 's@^.*href="(.*\.tar\.gz)".*$@\1@')
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curl "$GOURL" \
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| tar zxf -
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export PATH="$(pwd)/go/bin:$PATH"
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curl "$OBIURL4" \
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| tar zxf -
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cd obitools4-master
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if [[ -z "$OBITOOLS_PREFIX" ]] ; then
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make
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else
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make OBITOOLS_PREFIX="${OBITOOLS_PREFIX}"
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fi
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(cp build/* "${INSTALL_DIR}/bin" 2> /dev/null) \
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|| (echo "Please enter your password for installing obitools in ${INSTALL_DIR}"
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sudo cp build/* "${INSTALL_DIR}/bin")
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popd
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rm -rf "$WORK_DIR"
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