#########################################################################
# File Name:configure.sh
# Author:Cheng Yang
# Description: configure LncADeep
#########################################################################

#!/bin/bash
#set -x


# 1. Pre-requisite for LncADeep: lncRNA identification:
# ---------------------------

echo "Pre-requisite for lncRNA identification:"
echo "1. Python, version >= 2.7.6"
echo "2. numpy, version >= 1.8.2"
echo "3. HMMER package: can be downloaded from http://hmmer.org/download.html"
echo "-------------------------------------------"


# 2. Pre-requisite for LncADeep: predict lncRNA-protein interactions and conduct function annotations:
# ---------------------------

echo "Pre-requisite for lncRNA functional annotations:"
echo "1. Python 2, version >= 2.7.6"
echo "2. numpy, version >= 1.8.2"
echo "3. theano, version >= 0.8.2"
echo "4. pandas, version >= 0.18.0"
echo "5. Keras, version 1.2.2 (https://github.com/fchollet/keras). Please install Keras according to the online installation manual."
echo "6. MCL package: https://micans.org/mcl/"
echo "7. iGraph R package (optional): http://igraph.org/r/"
echo "-------------------------------------------"


# 3. pre-defined variables
# ------------------------

workdir=`pwd`
readonly workdir
echo "The working directory is $workdir"


# 4. Install HMMER 3.1b2
# ----------------------

echo "Check HMMER"

HMMERdir=$workdir/LncADeep_lncRNA/src
HMMERexe=$workdir/LncADeep_lncRNA/src/hmmsearch
chmod +x $HMMERexe

echo "export PATH=\$PATH:$HMMERdir" >> $HOME/.bash_profile

if [ ! -f "$HMMERexe" ]; then
    cd $HMMERdir
    wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz
    hmm_target_file="hmmer-3.1b2-linux-intel-x86_64.tar.gz"
    hmm_target_dir="hmmer-3.1b2-linux-intel-x86_64"

    tar xzvf $hmm_target_file -C $HMMERdir
    hmm_bin_dir=$HMMERdir/$hmm_target_dir/binaries
    echo $hmm_bin_dir
    echo "export PATH=\$PATH:$hmm_bin_dir" >> $HOME/.bash_profile
fi



# 5. Check Pfam database
# -------------------------

echo "Check Pfam 29.0 database"

pfam_dir=$workdir/LncADeep_lncRNA/src
cd $pfam_dir

pfam_file="Pfam-A.hmm.gz"
pfam_target="$pfam_dir"/"Pfam-A.hmm"

if [ ! -f "$pfam_target" ]; then
    cd $pfam_dir
    wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam29.0/Pfam-A.hmm.gz
    gzip -d $pfam_file
fi


# 6. Add directory to environment path 
# -------------------------

LncADeep_src_dir=$workdir/LncADeep_anno/src
chmod +x -R $LncADeep_src_dir 
echo "export PATH=\$PATH:$LncADeep_src_dir" >> $HOME/.bash_profile


# 7. Add LncADeep to environment path
# ------------------------------------------

cd $workdir
echo "export PATH=\$PATH:$workdir" >> $HOME/.bash_profile

echo "Please run the following command to complete installation:"
echo "source \$HOME/.bash_profile"