bash bin/Anaconda3-2018.12-Linux-x86_64.sh # do not install VS (needs root privileges)
mamba install -c anaconda perl
mamba install -c anaconda biopython
mamba conda install -c bioconda perl-app-cpanminus
mamba install -c bioconda perl-file-spec
mamba install -c bioconda perl-hash-merge
mamba install -c bioconda perl-list-util
mamba install -c bioconda perl-module-load-conditional
mamba install -c bioconda perl-posix
mamba install -c bioconda perl-file-homedir
mamba install -c bioconda perl-parallel-forkmanager
mamba install -c bioconda perl-scalar-util-numeric
mamba install -c bioconda perl-yaml
mamba install -c bioconda perl-class-data-inheritable
mamba install -c bioconda perl-exception-class
mamba install -c bioconda perl-test-pod
mamba install -c bioconda perl-file-which # skip if you are not comparing to reference annotation
mamba install -c bioconda perl-mce
mamba install -c bioconda perl-threaded
mamba install -c bioconda perl-list-util
mamba install -c bioconda perl-math-utils
mamba install -c bioconda cdbtools
mamba install -c eumetsat perl-yaml-xs
mamba install -c bioconda perl-data-dumper
#Change perl paths to work with conda
perl change_path_in_perl_scripts.pl "/home/chase/miniforge3/envs/braker3env/bin perl"
braker.pl --genome=<genome.fasta> --prot_seq=<proteins.fa> --bam=genome.bam --threads=<n>--busco_lineage=<fabales_odb10>
/Path_to_ausgustus/agat_sp_statistics.pl -gff braker.gtf -g Lotus_use.fasta