follow instructions on the metago repo
OR
if logged into flux, source pre-installed metago dependencies
$source /nfs/turbo/lsa-duhaimem/devel/gumm/workflows/metaGO/dependencies/miniconda/bin/activate
$git clone https://github.com/jordangumm/metago_demo.git
$cd metago_demo && ./build.sh
$metago -o \<path_to_metago_demo\>/output/01_QC qc --sample \<path_to_metago_demo\>/genomes/final
$metago -o \<path_to_metago_demo\>/output/02_ASSEMBLY assembly --sample \<path_to_metago_demo\>/output/01_QC/final
$metago -o \<path_to_metago_demo\>/output/03_BINNING binning -c \<path_to_metago_demo\>/output/02_ASSEMBLY/final/assembly/final.contigs.fa -r \<path_to_metago_demo\>/output/01_QC/final/final.fastq
$metago -o \<path_to_metago_demo\>/output/05_MAPPING/phiX174 mapping --sample \<path_to_metago_demo\>/output/02_ASSEMBLY/final/assembly/final.contigs.fa --paired --visualize -r \<path_to_metago_demo\>/genomes/original/phiX174_whole_genome_sequence.fasta
$metago -o \<path_to_metago_demo\>/output/05_MAPPING/marinobacter mapping --sample \<path_to_metago_demo\>/output/02_ASSEMBLY/final/assembly/final.contigs.fa --paired --visualize -r \<path_to_metago_demo\>/genomes/original/Marinobacter_aquaeolei_GenBank_CP000514.1.fasta
$metago -o \<path_to_metago_demo\>/output/05_MAPPING/LEM01 mapping --sample \<path_to_metago_demo\>/output/02_ASSEMBLY/final/assembly/final.contigs.fa --paired --visualize -r \<path_to_metago_demo\>/genomes/original/LakeErie_Microcystis_virus_nucleotide_sequence.fasta
metago -o \<path_to_metago_demo\>/output/04_VIRSORTER virsorter --fasta \<path_to_metago_demo\>/output/02_ASSEMBLY/final/assembly/final.contigs.fa
$metago -o \<path_to_metago_demo\>/output/05_MAPPING/LEM01_VIRSORTER mapping --sample \<path_to_metago_demo\>/output/04_VIRSORTER/virsorter_output/Predicted_viral_sequences/VIRSorter_cat-2.fasta --visualize -r \<path_to_metago_demo\>/genomes/original/LakeErie_Microcystis_virus_nucleotide_sequence.fasta
$metago -o \<path_to_metago_demo\>/output/05_MAPPING/phiX174_VIRSORTER mapping --sample \<path_to_metago_demo\>/output/04_VIRSORTER/virsorter_output/Predicted_viral_sequences/VIRSorter_cat-2.fasta --visualize -r \<path_to_metago_demo\>/genomes/original/phiX174_whole_genome_sequence.fasta