Example run:
cd dir_to_this_repo_folder
. /pipeline_beta_ultron.sh -d /mnt/files/syy/adipose/rna/cr_rna_results -s 'AB_GEX_FL_TAM_OM AB_GEX_FL_TAM_SQ AB_GEX_001_OM AB_GEX_001_SQ AB_GEX_002_OM AB_GEX_002_SQ AB_GEX_003_OM AB_GEX_003_SQ AB_GEX_004_OM AB_GEX_004_SQ' -a "aws_url" -g ./data/marker_list/Arionas_marker_gene_list_noquotes.csv -n /mnt/files/syy/adipose/rna/cr_rna_results/sample_cell_num.tsv -c 2000 -m 1
or
cd dir_to_this_repo_folder
bash pipeline_beta_ultron.sh -d /mnt/files/syy/adipose/rna/cr_rna_results -s 'AB_GEX_FL_TAM_OM AB_GEX_FL_TAM_SQ AB_GEX_001_OM AB_GEX_001_SQ AB_GEX_002_OM AB_GEX_002_SQ AB_GEX_003_OM AB_GEX_003_SQ AB_GEX_004_OM AB_GEX_004_SQ' -a "aws_url" -g ./data/marker_list/Arionas_marker_gene_list_noquotes.csv -n /mnt/files/syy/adipose/rna/cr_rna_results/sample_cell_num.tsv -c 2000 -m 1