install_UBUNTU_safe.sh

#!/bin/sh

set -eu
# WARNING: you need to adapt the dependency list first
# 
# shell script allowing to install all CRISPRCasFinder.pl-v4.2's dependencies
#
# same version than CRISPRCasFinder.pl, here 4.2.17
# authors: David Couvin, Fabrice Leclerc, Claire Toffano-Nioche
# adapted to non sudo install by M. Dondrup

packageManagmentInstall='conda install '
distribution='Linux_x86_64'


#------------------------
function launchInstall {
# $1 $packageManagmentInstall
# $2 package name
# $3 $LOGFILE
    echo "Installation of $2" >> $3
    $1 $2 | tee -a $3
}
#------------------------

#save the current directory:
CURDIR=`pwd` 

#create log file:
LOGFILE=$CURDIR/crisprcasfinder-install.log

#create src & bin folders:
echo "create $CURDIR/src and $CURDIR/bin folders" >> $LOGFILE
mkdir -p src;
mkdir -p bin; 

#geting OS info: 
ostype=`echo $OSTYPE`
echo "$ostype" >> $LOGFILE

CONDA=`which conda`

if [  "$CONDAxxx" = "xxx" ]; then
    echo 'Sorry, you need conda and activate bioconda'
    exit 1
else
      
    #important packages
    # not sure these need to be installed in conda:
    launchInstall "$packageManagmentInstall" "wget" "$LOGFILE"
    # don't see any use of curl
    launchInstall "$packageManagmentInstall" "curl" "$LOGFILE"
    # don't see any use of git
    launchInstall "$packageManagmentInstall" "git" "$LOGFILE"
    # which version is default in Ubuntu (which version) and is it used?
    launchInstall "$packageManagmentInstall" "default-jre" "$LOGFILE"
    # I guess it is python2? Need to specify version
    launchInstall "$packageManagmentInstall" "python" "$LOGFILE"
    launchInstall "$packageManagmentInstall" "parallel" "$LOGFILE"
    # might pull a complete perl install, any version requrirements?
    launchInstall "$packageManagmentInstall" "cpanminus" "$LOGFILE"

    #"bioinfo" packages, most likely the package names don't match
    # the conda package name, you need to check all the packages exist in bioconda
    launchInstall "$packageManagmentInstall" "hmmer" "$LOGFILE" # checked for conda
    launchInstall "$packageManagmentInstall" "emboss" "$LOGFILE" # checked for conda
    # launchInstall "$packageManagmentInstall" "emboss-lib" "$LOGFILE" # not found, might be included in emboss
    launchInstall "$packageManagmentInstall" "blast" "$LOGFILE" # checked for conda
    launchInstall "$packageManagmentInstall" "perl-bioperl" "$LOGFILE" # checked
    launchInstall "$packageManagmentInstall" "perl-bioperl-run" "$LOGFILE" # checked
    launchInstall "$packageManagmentInstall" "perl-datetime" "$LOGFILE" # checked
    launchInstall "$packageManagmentInstall" "perl-xml-simple" "$LOGFILE" # checked
    launchInstall "$packageManagmentInstall" "perl-digest-md5" "$LOGFILE" # checked
    launchInstall "$packageManagmentInstall" "clustalw" "$LOGFILE" # checked
    #install muscle
    launchInstall "$packageManagmentInstall" "muscle" "$LOGFILE" # checked
 
    #install prodigal
    launchInstall "$packageManagmentInstall" "prodigal" "$LOGFILE" # checked


    

    # echo "copy /usr/bin/clustalw to $CURDIR/bin/clustalw2" >> $LOGFILE
    # sudo cp /usr/bin/clustalw $CURDIR/bin/clustalw2
    cpanm Try::Tiny >> $LOGFILE
    cpanm Test::Most >> $LOGFILE
    cpanm JSON::Parse >> $LOGFILE
    cpanm Class::Struct >> $LOGFILE
    cpanm Bio::DB::Fasta >> $LOGFILE
    cpanm File::Copy  >> $LOGFILE
    cpanm Bio::Seq Bio::SeqIO >> $LOGFILE
    cpanm Bio::Tools::Run::Alignment::Clustalw >> $LOGFILE 
    cpanm Bio::Tools::Run::Alignment::Muscle >> $LOGFILE

    #install vmatch # no conda package for vmatch
    
    echo "Installation of Vmatch" >> $LOGFILE
    echo "change directory to $CURDIR/src" >> $LOGFILE
    cd $CURDIR/src
    wget http://vmatch.de/distributions/vmatch-2.3.0-${distribution}-64bit.tar.gz >> $LOGFILE
    tar -zxf vmatch-2.3.0-${distribution}-64bit.tar.gz >> $LOGFILE
    gcc -Wall -Werror -fPIC -O3 -shared vmatch-2.3.0-${distribution}-64bit/SELECT/sel392.c -o $CURDIR/sel392v2.so >> $LOGFILE
    echo "copy $CURDIR/src/vmatch-2.3.0-${distribution}-64bit/vmatch, mkvtree and vsubseqselect to $CURDIR/bin/" >> $LOGFILE
    cp $CURDIR/src/vmatch-2.3.0-${distribution}-64bit/vmatch $CURDIR/bin/vmatch2
    cp $CURDIR/src/vmatch-2.3.0-${distribution}-64bit/mkvtree $CURDIR/bin/mkvtree2
    cp $CURDIR/src/vmatch-2.3.0-${distribution}-64bit/vsubseqselect $CURDIR/bin/vsubseqselect2
    echo "change directory to $CURDIR" >> $LOGFILE
    cd $CURDIR

   
    #install macsyfinder
    echo "Installation of MacSyFinder" >> $LOGFILE
    cd ${CURDIR}
    wget https://dl.bintray.com/gem-pasteur/MacSyFinder/macsyfinder-1.0.5.tar.gz >> $LOGFILE
    tar -xzf macsyfinder-1.0.5.tar.gz
    mkdir -p bin
    cd bin
    ln -s ../macsyfinder-1.0.5/bin/macsyfinder
    cd ${CURDIR}
    echo "add definition of MACSY_HOME (${CURDIR}/macsyfinder-1.0.5/) in .profile" >> $LOGFILE
    echo "export MACSY_HOME=${CURDIR}/macsyfinder-1.0.5/" >> $HOME/.profile

    echo "add bin folder ($CURDIR/bin) to the definition of PATH in $HOME/.profile" >> $LOGFILE
    echo "export PATH=${CURDIR}/bin:${PATH}" >> $HOME/.profile
    
    #set environment variables
    source $HOME/.profile

# if CONDA
fi