#How to setup Fast-Plast on Metacentrum

#Start interactive job
qsub -I -l walltime=4:0:0 -q default@meta-pbs.metacentrum.cz -l select=1:ncpus=8:mem=8gb:scratch_local=8gb
cd /storage/brno2/home/$LOGNAME/
mkdir FASTPLAST
cd FASTPLAST


#First enable necessary software
#module add perl/perl-5.30.3-gcc-4.8.5-giw6nuv #necessary for multi-threading with SSPACE
module add gcc-4.9.2 #necessary for compilation of 'afin'
module add jdk-7
#module add bioperl-1.6.9-gcc
module add bowtie2-2.2.9
module add bowtie-1.0.0
module add trimmomatic-0.39
module add spades-3.15.4
module add blast-plus/2.12.0-gcc-8.3.0-ohlv7t4
module add R-3.6.2-gcc
module add jellyfish-2.3.0

#Clone Fast-Plast from GitHub and run interactive installer
#git clone https://github.com/mrmckain/Fast-Plast
#cd Fast-Plast
#Get older release 1.2.8. (works actually until completion for our data!)
wget https://github.com/mrmckain/Fast-Plast/archive/refs/tags/v.1.2.8.tar.gz
tar -xvf v.1.2.8.tar.gz
cd Fast-Plast-v.1.2.8
perl INSTALL.pl
#During the installation:
#Do you have all dependencies installed : No
#Do you want me to try to install them : All
#check whether 'afin' is working
./afin/afin
#you should get two error messages about files to be provided

#Modify 'fast-plast.pl' - modify path to system versions of tools
cp fast-plast.pl fast-plast.pl.bak #backup the file
grep -v "^my \$SPADES" fast-plast.pl > modif.pl
sed -i '27imy \$SPADES=\"/software/spades/3.15.4/bin/spades.py\";' modif.pl
grep -v "^my \$BOWTIE1" modif.pl > tmp && mv tmp modif.pl
sed -i '30imy \$BOWTIE1=\"/software/bowtie-1.0.0/bin\";' modif.pl
grep -v "^my \$JELLYFISH" modif.pl > tmp && mv tmp modif.pl
sed -i '31imy \$JELLYFISH=\"/software/jellyfish/2.2.4/bin/jellyfish\";' modif.pl
mv modif.pl fast-plast.pl

#modify dirs
mv bin/bowtie2-2.3.5.1-linux-x86_64 bin/bowtie2-2.3.5.1
#Get the test data
cp /storage/projects/ginger/ZingiberalesCourse/10rawreads/Ensete-superbum_S375/Ensete-superbum_S375_L001_R{1,2}_001.fastq.gz .

#Run the analysis
perl fast-plast.pl -1 Ensete-superbum_S375_L001_R1_001.fastq.gz -2 Ensete-superbum_S375_L001_R2_001.fastq.gz --name Ensete-superbum_S375 --bowtie_index Zingiberales --coverage_analysis