#
# Installs the latest SRA tools
#
set -ue

# Select the download based on the platform.
if [ "$(uname)" == "Darwin" ]; then
  SRA_NAME=sratoolkit.3.0.0-mac64
else
  SRA_NAME=sratoolkit.3.0.0-ubuntu64
fi

# The SRA libraries.
SRA_TAR=${SRA_NAME}.tar.gz

# The SRA urls.
SRA_URL=https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/3.0.0/${SRA_TAR}

# The location of the binaries
BIN=~/bin

# Create the bin directory
mkdir -p ${BIN}

# Download the library
(cd ${BIN} && (curl ${SRA_URL} > ${SRA_TAR}))

# Unpack the software.
(cd ${BIN} && tar zxf ${SRA_TAR})

# The bash profile
PROFILE=~/.bash_profile

# Alter the PATH if necessary.
grep -qF ${SRA_NAME} ${PROFILE} || echo "export PATH=~/bin/${SRA_NAME}/bin:\$PATH" >> ${PROFILE}

echo "#"
echo "# Installation complete "
echo "#"
echo "# Close and reopen the terminal."
echo "#"
echo "# In the new terminal activate the bioinfo environment."
echo "#"