installbiobash

#!/usr/bin/env bash
#
# Performs the installation of BIOBASH.
#

#Common libraries
source lib/shml/shml.sh
source lib/bb_utility/check.sh
source lib/bb_utility/file.sh


#----------------------------------------------------------------------------
#
#  FUNCTIONS
#
#----------------------------------------------------------------------------

# Reads user input to define installation directory. Returns real path to dir.
function define_install_dir() {
    read -p " Install in (/usr/local): " dir

    #If user hitted ENTER, $dir comes empty, so use default install dir.
    #Otherwise use user provided path.
    if [ -z "$dir" ]; then
        dir=$default
    else
        dir=$dir
    fi
    #realpath for installDir. No relative paths allowed.
    #There is a bug with paths like "~/path/to/dir". For some reason "realpath" do not
    #resolve this type of path in the script, but it does in the shell!!??
    #return=$(realpath "${dir}")
    return=$(file::full_path "${dir}")
    
    #Return value
    echo -n "$return"
}




# Some propaganda/user feedback.
v=$(cat version)
echo "
$(fgcolor gray '...............................................................') $(fgcolor end) 
$(a bold)$(fgcolor lightblue '                   BIOBASH INSTALLER') $(fgcolor end)  $(a end)
$(fgcolor lightblue '      Bioinformatics and Systems Biology Laboratory') $(fgcolor end)
$(fgcolor lightblue '  Institute for Genetics - National University of Colombia') $(fgcolor end)
$(fgcolor lightblue '                 https://gibbs.unal.edu.co') $(fgcolor end)
"



#----------------------------------------------------------------------------
#
#  BEFORE ATTEMPTING ANYTHING... check pre-requisites.
#
#----------------------------------------------------------------------------
./check_dependencies.sh

#If check dependencies was succesful it creates a "flag" file: depend_ok
#otherwise (file doesn`t exist) there are dependencies to be met. Stop installation.
if [[ ! -e depend_ok ]];then
	
	echo "$(fgcolor yellow)  Quitting installation of BioBash.$(fgcolor end)
	"
	exit 1
fi

# If we reached this point it means dependencies check was succesful and therefore
# it is safe to erase depend_ok file. It is not needed from now on.
rm depend_ok




#----------------------------------------------------------------------------
#
#          START ACTUAL INSTALLATION
#
#-----------------------------------------------------------------------------

# We are assuming a standard installation on a Linux Machine (at least
# for now). This is the default directory for installation.
default="/usr/local"


echo " $(fgcolor lightblue) $(a bold)SELECT THE INSTALLATION DIRECTORY$(a end).$(fgcolor end)"
echo "$(hr)"

echo  "$(fgcolor gray)
 The installation directory is the place where all BioBash related 
 files will be stored, including libraries and binaries. By default 
 BioBash will be installed in '$default' directory, nevertheless you 
 need write permissions on that folder. Alternatively you can define a
 path to another installation directory.$(fgcolor end)
 
 Hit ENTER to use the default installation directory ($default) or 
 provide a valid installation path:
"

installDir="$(define_install_dir)"


# Wether install will be performed on user defined or default install dir, it is
# important to make sure that it exists and that we can write on it.
# Does it exist?
if [ ! -d "${installDir}" ];then
    
 
	echo "$(fgcolor red)$installDir does not exist. Please make sure it is a valid directory.$(fgcolor end)
	"
	exit 1

fi

# If we reached this point it means directoy exists. Check if it is writable.
if [ ! -w "$installDir" ];then
	echo "I can not write to: $installDir. Please make sure you have the right permissions on that folder."
	exit 1

fi



#If we reached this point, it means we can proceed with installation. 
#----------------------------------------------------------------------
#
#                          MAIN INSTALLATION
#
#-----------------------------------------------------------------------
# "version" is a file in main install dir
BBVERSION=$(cat version)
BIOBASH_HOME=$(echo "$installDir/biobash-$BBVERSION")

#User feedback

echo "
$(fgcolor green)I am ready to install BioBash version $BBVERSION in $BIOBASH_HOME.$(fgcolor end)
"
echo "
$(fgcolor lightblue) $(a bold)INSTALL BIOBASH IN ${BIOBASH_HOME} $(a end)$(fgcolor end)
$(hr)
$(fgcolor gray)
 We have now all necessary information to install BioBASH in this machine.
 The ${BIOBASH_HOME} folder will be the root of this 
 installation and all necessary scripts, dependencies 
 and executables will be installed there.
$(fgcolor end)
"

#Flow control. Answer should be "y" or "n"
continue=0
until [ $continue  == "y" ] || [ $continue == "n" ]
do
    read -p 'Proceed? [y/n]: ' continue
done

if [[ $continue == "n" ]]; then
    
    echo "$(fgcolor green)
    Leaving BioBash Installation. Nothing done. 
    
    Bye!
    $(fgcolor end)
    "
    exit 0
    
elif [[ $continue == "y" ]];then

    echo "
    $(fgcolor lightblue)$(a bold) STARTING BioBASH INSTALLATION $(a end) $(fgcolor end)
    $(hr)"
    
else
    echo "$(fgcolor red)
    ERROR: Installation can not proceed. Unknown reason.
    $(fgcolor end)"
    exit 1
fi



#Create BIOBASH directory. The "-p" option is useful when re-trying the installation multiple times,
#so if the directory was created before it won't complain because directory already exists.
echo "$(fgcolor green) Creating BioBASH home in: ${BIOBASH_HOME}$(fgcolor end)"

mkdir -p "$BIOBASH_HOME"


#----------------------------------------------------------------------------
#
#                            SETUP ENVIRONMENT
#
# This routine puts all needed  environmental variables into bashrc
# 
#----------------------------------------------------------------------------
#Note that we are sending the $BIOBASH_HOME variable to the script!!!
echo "$(fgcolor green) Setting up the environment$(fgcolor end)"
./setup_environment.sh "$BIOBASH_HOME"

#If environment setup was succesful it creates a "flag" file: environ_ok
#otherwise (file doesn`t exist) there were errors. Stop installation.
if [[ ! -e environ_ok ]];then
	
	echo "$(fgcolor red) [ERROR] UNABLE TO PERFORM INSTALLATION. 
    Please check previous messages for possible reasons.
    Quitting installation of BioBash.$(fgcolor end)
	"
	exit 1
fi

# If we reached this point it means environment set up was succesful and therefore
# it is safe to erase depend_ok file. It is not needed from now on.
rm environ_ok



#----------------------------------------------------------------------------
#
#                            Copy libraries
#
#            This routine copies libraries and stuff in BIOBASH_HOME
# 
#----------------------------------------------------------------------------
echo "$(fgcolor green) Copying binaries and executables in $BIOBASH_HOME $(fgcolor end)
"

# Future version needs a better selection of what to install.
cp -r ./lib "$BIOBASH_HOME"
cp -r ./bin "$BIOBASH_HOME"
cp -r ./unitesting "$BIOBASH_HOME"
cp -r ./testdata "$BIOBASH_HOME"
cp ./version "$BIOBASH_HOME"
cp exec/bb_* "$BIOBASH_HOME" #These are all the actual BB scripts.


#----------------------------------------------------------------------------
#
#               Source enviroment
# 
#----------------------------------------------------------------------------
source ~/.bashrc

echo "
$(fgcolor lightblue)
$(emoji thumbsup) [BIOBASH WAS INSTALLED SUCCESFULLY!]
$(fgcolor end)

$(attribute bold) You can start using BioBash right now! $(attribute end)
 Nevertheless it is possible that you will need to inform your shell  that BioBASH was installed.
 So, please  update your environment with the following command:

   > source ~/.bashrc
   
 Alternatively you can open a new terminal or logout and login from your account.

$(attribute bold) Thank you for installing BIOBASH $(attribute end)

$(fgcolor lightblue)
           Bioinformatics and Systems Biology Laboratory
    Institute for Genetics - National University of Colombia
                    Bogota - Colombia
$(fgcolor end)
"

exit 0