HISAT2-2.2.1_install

#!/usr/bin/env bash

###############################################
# Installing HISAT2 2.2.1
#

# by Brian Alston June 2023

set -e
export PATH=$INSTALL_PREFIX/bin:$PATH

dirname=$(dirname $0 2>/dev/null || pwd)
# dirname=/shared/ucl/apps/build_scripts
INCLUDES_DIR=${INCLUDES_DIR:-${dirname}/includes}
source ${INCLUDES_DIR}/module_maker_inc.sh
source ${INCLUDES_DIR}/require_inc.sh


require gcc-libs
require compilers/gnu/4.9.2
require python3/recommended

APPNAME=${APPNAME:-hisat2}
VERSION=${VERSION:-2.2.1}
COMPILER_TAG=${COMPILER_TAG:-gnu-4.9.2}
INSTALL_PREFIX=${INSTALL_PREFIX:-/shared/ucl/apps/$APPNAME/$VERSION/$COMPILER_TAG}
MD5=${MD5:-7acec4dfd5844c4ce3e9ccd3e364a8b2}
# No version number on the download site!
SRC_ARCHIVE=${SRC_ARCHIVE:-https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi/download}

mkdir -p /dev/shm/$APPNAME
temp_dir=`mktemp -d -p /dev/shm/$APPNAME`

cd $temp_dir

archive=${APPNAME}-${VERSION}-source.zip
wget $SRC_ARCHIVE -O $archive

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

if [ "$MD5" == "$CHECKSUM" ]
then
  unzip -x $archive

  cd ${APPNAME}-${VERSION}

  # update Makefile to use UCL gcc location
  sed -i 's|^GCC_PREFIX.*$|GCC_PREFIX = /shared/ucl/apps/gcc/4.9.2/bin|' Makefile

  make

  # no make install so:

  mkdir -p $INSTALL_PREFIX
  cp hisat2 hisat2-align-s hisat2-align-l hisat2-build hisat2-build-s hisat2-build-l hisat2-inspect hisat2-inspect-s hisat2-inspect-l ${INSTALL_PREFIX}/
 
else
  echo "Hash mismatch."
  echo "Expected: $MD5"
  echo "Got: $CHECKSUM"
fi