#!/bin/bash
# RNA-Seq Pipeline
# 2022 March


# =============================================================================================================================================================
# ==                                                          Settings for SLURM                                                                             ==
# =============================================================================================================================================================

#SBATCH --nodes=1			
#SBATCH --ntasks-per-node=1
#SBATCH --mem=32GB
#SBATCH --job-name=Bowtie2
#SBATCH --time=24:00:00

# Personal stuff; Change this to your personal settings 

#SBATCH --mail-type=END
#SBATCH --mail-user=youremail@student.rug.nl
#SBATCH --output=slurm-Bowtie2-%j.log




# this is a short script to format the genome for Bowtie2 
# This script can be run on peregrine-interactive command line, so no need to use 'sbatch'

# setting global parameters
SOFTWAREDIR=/data/pg-molgen/software
# Make chromsizes file for BEDtools
export PERL5LIB=$SOFTWAREDIR/molgentools_mirror/lib
module load BioPerl/1.7.7-GCCcore-9.3.0

# Make index for Bowtie2
module load Bowtie2/2.4.4-GCC-9.3.0


# genome=/data/pg-molgen/rnaseq/genomes/Escherichia_coli_BL21DE3_ASM956v1_genomic
# genome=/data/pg-molgen/EVBiotech/EV/20211217_Gloom_bl21de3_Myrthe.annotation/20211217_Gloom_bl21de3_Myrthe
# genome=/data/pg-molgen/rnaseq/genomes/Trypanosoma_brucei_TREU927_ASM244v1/GCF_000002445.2_ASM244v1_genomic
# genome=/data/pg-molgen/rnaseq/genomes/Bacillus_subtilis_subsp_subtilis_str_168_ASM904v1_pLS20

#genome=/data/pg-molgen/rnaseq/genomes/Synechococcus_RS9916
#genome=/data/pg-molgen/rnaseq/genomes/Marinobacter_MC3
#genome=/data/pg-molgen/rnaseq/GRCh38.p14/GCF_000001405.40.rna
#genome=/data/pg-molgen/rnaseq/genomes/Acinetobacter_baumanni_K09-14


genome=Bamyloliquefasciens_B1895_genome-plus-pBamB1895_startRapat75
bowtie2-build $genome.fna $genome
$SOFTWAREDIR/molgentools_mirror/rnaseq/make_chromsizes.pl -i $genome.fna -o $genome.chromsizes

genome=Batrophaeus_NRS213_genomic-plus-pBatNRS213_startRapAt75
bowtie2-build $genome.fna $genome
$SOFTWAREDIR/molgentools_mirror/rnaseq/make_chromsizes.pl -i $genome.fna -o $genome.chromsizes

genome=Blicheniformis_B4092_genomic-plus-pBli4092_reconstructed_startRapAt75
bowtie2-build $genome.fna $genome
$SOFTWAREDIR/molgentools_mirror/rnaseq/make_chromsizes.pl -i $genome.fna -o $genome.chromsizes

genome=Bpumilus_NRS576_genome-plus-p576_startRapAt75
bowtie2-build $genome.fna $genome
$SOFTWAREDIR/molgentools_mirror/rnaseq/make_chromsizes.pl -i $genome.fna -o $genome.chromsizes

genome=Bsp_NMCC4_genome-plus-pBspNMCC4_startRapAt75
bowtie2-build $genome.fna $genome
$SOFTWAREDIR/molgentools_mirror/rnaseq/make_chromsizes.pl -i $genome.fna -o $genome.chromsizes

genome=Bthuringiensis_kurstaki_HD73_chromosome-plus-pAW63_startRapAt75
bowtie2-build $genome.fna $genome
$SOFTWAREDIR/molgentools_mirror/rnaseq/make_chromsizes.pl -i $genome.fna -o $genome.chromsizes