installation of CRISPRCasFinder

install.sh

wget https://crisprcas.i2bc.paris-saclay.fr/Home/DownloadFile?filename=CRISPRCasFinder.zip
unzip DownloadFile?filename=CRISPRCasFinder.zip
cd CRISPRCasFinder

# install perl modules
curl -L http://cpanmin.us | perl - App::cpanminus
cpanm --local-lib=~/perl5 local::lib && eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)
cpanm JSON::Parse

# install prodigal
mkdir prodigal
cd prodigal
wget https://github.com/hyattpd/Prodigal/releases/download/v2.6.3/prodigal.linux
chmod a+x prodigal.linux
echo "export PATH=/net/metagenomics/projects/pmuench_oligomm_ab/tools/CRISPRCasFinder/prodigal:$PATH" >> ~/.bashrc
cd ..

#install hmmer on a custom folder using --prefix argument
wget http://eddylab.org/software/hmmer/hmmer-3.2.1.tar.gz
tar xvzf hmmer-3.2.1.tar.gz
cd hmmer-3.2.1
mkdir bin
./configure --prefix=/net/metagenomics/projects/pmuench_oligomm_ab/tools/CRISPRCasFinder/hmmer-3.2.1/bin
make
make install
# try out if this works
/net/metagenomics/projects/pmuench_oligomm_ab/tools/CRISPRCasFinder/hmmer-3.2.1/bin/bin/hmmsearch
# if so, put it in your ~/.bashrc
echo "export PATH=/net/metagenomics/projects/pmuench_oligomm_ab/tools/CRISPRCasFinder/hmmer-3.2.1/bin/bin:$PATH" >> ~/.bashrc
cd ..

# MacSyFinder
wget https://dl.bintray.com/gem-pasteur/MacSyFinder/macsyfinder-1.0.5.tar.gz 
tar -xzf macsyfinder-1.0.5.tar.gz
export MACSY_HOME=/net/metagenomics/projects/pmuench_oligomm_ab/tools/CRISPRCasFinder/macsyfinder-1.0.5/ # you can use 'pwd' to print your position in the file system
# I got error message when running macsyfinder till I activates a new virtual env environment, not really sure why
virtualenv env
source env/bin/activate

# try if its working
perl CRISPRCasFinder.pl -v

> Possible precedence issue with control flow operator at /usr/local/share/perl/5.24.1/Bio/DB/IndexedBase.pm line 845.
>This is CRISPRCasFinder.pl, version 4.2.19,
> a perl script to identify CRISPR arrays and associated Cas genes from DNA sequences