Hammock_v_1.0.5_install

#!/usr/bin/env bash

###############################################
# User install script for Hammock, also runnable by do-hammock-install alias in hammock module.
#
# by Heather Kelly, 2016
#

NAME=${NAME:-Hammock}
VERSION=${VERSION:-1.0.5}
INSTALL_PREFIX=${INSTALL_PREFIX:-$HOME}
SRC_ARCHIVE=${SRC_ARCHIVE:-https://github.com/hammock-dev/hammock/releases/download/v${VERSION}/${NAME}_v_${VERSION}.7z}
MD5=${MD5:-fd8ad5f2c7f0e5da4fc287883a3c6ad7}

set -e

# module prereqs for installing
dirname=$(dirname $0 2>/dev/null)
INCLUDES_DIR=${INCLUDES_DIR:-${dirname}/includes}
source ${INCLUDES_DIR}/require_inc.sh
require gcc-libs/4.9.2
require p7zip/15.09/gnu-4.9.2

cd $INSTALL_PREFIX

wget $SRC_ARCHIVE
archive=$(basename "${SRC_ARCHIVE}")

CHECKSUM=`md5sum $archive| awk '{print $1}'`

if [ "$MD5" == "$CHECKSUM" ]
then

  7z x $archive

  echo "------------------------------"
  echo "Backing up settings.prop to settings.prop.orig, modifying to use clustal-omega and hmmer from modules."

  # Back up original settings
  settings=${INSTALL_PREFIX}/${NAME}_v_${VERSION}/settings/settings.prop
  cp $settings ${INSTALL_PREFIX}/${NAME}_v_${VERSION}/settings/settings.prop.orig 

  # Modify settings.prop to use our modules for clustal-omega and hmmer: pick the executables that are in your PATH.
  sed -i -e "s|#clustalOmegaCommand=|clustalOmegaCommand=clustalo|" $settings
  sed -i -e "s|#hmmbuildCommand=|hmmbuildCommand=hmmbuild|" $settings
  sed -i -e "s|#hmmsearchCommand=|hmmsearchCommand=hmmsearch|" $settings

  # Set temporary directory to your Scratch - can't use environment variables like $TMPDIR inside settings.prop.
  sed -i -e "s|#tempDirectory=|tempDirectory=${HOME}/Scratch|" $settings

  echo "Using Scratch for temporary files, written as directories called Hammock_temp_time."
  echo "You will want to clear these up at intervals."

else
  echo "Hash mismatch."
  echo "Expected: $MD5"
  echo "Got: $CHECKSUM"
fi