Broad_GSEA_CLI.sh

/usr/bin/java --module-path=./modules -Xmx16g -Djava.awt.headless=true @./gsea.args --patch-module=jide.common=./lib/jide-components-3.7.4.jar:./lib/jide-dock-3.7.4.jar:./lib/jide-grids-3.7.4.jar --module=org.gsea_msigdb.gsea/xapps.gsea.CLI GSEA -res /Volumes/ncatssctl/NGS_related/Chromium/IS021/GSEA/IS021_raw_counts.gct -cls /Volumes/ncatssctl/NGS_related/Chromium/IS021/GSEA/IS021_phenotypes.cls#Day -gmx ftp.broadinstitute.org://pub/gsea/gene_sets/c5.bp.v7.1.symbols.gmt -collapse No_Collapse -mode Max_probe -norm meandiv -nperm 1000 -permute phenotype -rnd_type no_balance -scoring_scheme weighted -rpt_label IS021_TE_GSEA -metric Pearson -sort real -order descending -chip ftp.broadinstitute.org://pub/gsea/annotations_versioned/Human_RefSeq_ID_MSigDB.v7.0.chip -create_gcts false -create_svgs true -include_only_symbols true -make_sets true -median false -num 100 -plot_top_x 50 -rnd_seed timestamp -save_rnd_lists false -set_max 500 -set_min 15 -zip_report true -out /Volumes/ncatssctl/NGS_related/Chromium/IS021/GSEA