Setting up Ensembl-VEP (avoid system Perl!)

#DO NOT use cpan to install Bio::Perl !!!
#You will be irritated by the conflicts of different perl dependency in different modules!
#We can use apt-get/aptitude to install Perlbrew
sudo aptitude install perlbrew

#init the perlbrew
perlbrew init

#Add the perlbrew setting into bash environment
source ~/perl5/perlbrew/etc/bashrc
#Logout and re-login to bash is needed to let the environments setting to take effect

#List the available perl version to install in perlbrew
perlbrew available

#I choose version perl-5.27.5 to install
perlbrew install 5.27.5
#It will take about 20~40mins
#Fail on install 5.18.4

#Switch to perl-5.27.5 from system perl
perlbrew use perl-5.27.5

#Make sure perl has been switched from system Perl to perl-5.27.5 in perlbrew environment
perlbrew info

#Install cpanm, a installer of perl modules
perlbrew install-cpanm

#Use cpanm to install DBI, DBD::mysql, Bio::Perl, the "-v" option is to make sure is there anything goes wrong during install process
cpanm -v DBI
cpanm -v DBD::mysql
cpanm -v Bio::Perl

#Check if all the modules which Ensembl-VEP needed are installed
perlbrew list-modules

#Install Ensembl-VEP form conda if you haven't install
conda install ensembl-vep

#Set-up Ensembl-VEP
vep_install -a cf -s oreochromis_niloticus  -c /data/vep --CONVERT

#We have to install Bio::DB::HTS modules =__=", and I've figure out the install way

#First, point out the HTSLib path
export HTSLIB_DIR=/data/jhangyu/anaconda/pkgs/htslib-1.6-0/lib/

#And install the zlib
sudo apt-get install zlib1g-dev

#Finally we can install the Bio::DB::HTS
cpanm -v Bio::DB::HTS

#We are great to GO!!


#####Ensembl-VEP Setting#####

#Install the VEP, Set-up the cache for oreochromis_niloticus
vep_install -a cf -s oreochromis_niloticus  -c /data/vep --CONVERT


#Parepare the GFF file
#Pack the GFF
grep -v "#" tilapia_20171005_with_yp_genes.gff3 | sort -k1,1 -k4,4n -k5,5n -t$'\t' | bgzip -c > rtilapia_20171005_with_yp_genes.gff.gz
#Index the GFF
tabix -p gff tilapia_20171005_with_yp_genes.gff.gz

#Prepare the Chromosome file
bgzip /data/tilapia_source_file/tilapia.fa

#Run!!
vep --species "oreochromis_niloticus" -i /data/fastq/Gong/NT1_HISAT2_output.vcf -gff /data/tilapia_source_file/tilapia_20171005_with_yp_genes.gff.gz -fasta /data/tilapia_source_file/tilapia.fa.gz --offline --dir "/data/vep/" --dir_cache "/data/vep/"