kallisto-0.42.5

#!/usr/bin/env bash

###############################################
# Installing OMA standalone
#
# by Javier Herrero, 2016 
#
# Will need modules: compilers/gnu/4.9.2 and hdf/5-1.8.15/gnu-4.9.2 

APPNAME=${APPNAME:-kallisto}
VERSION=${VERSION:-0.42.5}
INSTALL_PREFIX=${INSTALL_PREFIX:-/shared/ucl/depts/cancer/apps/$APPNAME/$VERSION}
MD5=${MD5:-11947b7411fca3a25b14d38827b8f93b}
SHA1=${SHA1:-REPLACE}
SRC_ARCHIVE=${SRC_ARCHIVE:-https://github.com/pachterlab/kallisto/archive/v${VERSION}.tar.gz}

# Use Intel defate library
NATIVE_LIB=${NATIVE_LIB:-NO}

set -e

export PATH=$INSTALL_PREFIX/bin:$PATH

mkdir -p $INSTALL_PREFIX

cd $INSTALL_PREFIX

wget $SRC_ARCHIVE 

CHECKSUM=`md5sum v${VERSION}.tar.gz | awk '{print $1}'`

if [ "$MD5" == "$CHECKSUM" ]
then
  tar xvzf v${VERSION}.tar.gz
  cd ${APPNAME}-${VERSION}
  mkdir build
  cd build
  cmake .. -DCMAKE_INSTALL_PREFIX:PATH=$INSTALL_PREFIX
  make
  make install
else
  echo "Hash mismatch."
  echo "Expected: $MD5"
  echo "Got: $CHECKSUM"
fi