sudo apt update # Install Java sudo apt install default\-jre # When prompted, enter Y # Install Nextflow curl -s https://get.nextflow.io | bash # Set Java memory limit # Add to .bashrc directly echo 'NXF_OPTS="-Xms1g -Xmx4g"' >> ~/.bashrc # Source .bashrc to apply changes source ~/.bashrc ./nextflow run nf-core/differentialabundance --input ~/Assignment_2/data/samplesheet.csv --contrasts ~/Assignment_2/data/contrasts.csv --matrix ~Assignment_2/reference_genome/GSE180869_norm_counts_TPM_GRCh38.p13_NCBI.tsv --transcript_length_matrix Assignment_2/reference_genome/GSE180869_raw_counts_GRCh38.p13_NCBI.tsv --gtf ~/Assignment_2/reference_genome/GCF_000001405.40_GRCh38.p14_genomic.gtf.gz --filtering_min_proportion 0.3 --filtering_grouping_var condition --deseq2_cores 4 --gsea_run true --gsea_permute ~/Assignment_2/reference_genome/GO_All_Homo_sapiens_GeneSymbol.gmt \ --gprofiler2_run true --gprofiler2_organism hsapiens --gprofiler2_sources "GO,GO:MF,GO:BP,GO:CC" --gprofiler2_correction_method gSCS --shinyngs_build_app true \ --max_cpus 8 --max_memory 8.GB --outdir ~/Assignment_2/scratch/homo_analysis_filtered -w ~/Assignment_2/scratch/work/homo_analysis -profile rnaseq,docker ./nextflow run nf-core/differentialabundance --input ~/Assignment_2/data/samplesheet.csv --contrasts ~/Assignment_2/data/contrasts.csv --matrix ~Assignment_2/reference_genome/GSE180869_norm_counts_TPM_GRCh38.p13_NCBI.tsv --transcript_length_matrix Assignment_2/reference_genome/GSE180869_raw_counts_GRCh38.p13_NCBI.tsv --gtf ~/Assignment_2/reference_genome/GCF_000001405.40_GRCh38.p14_genomic.gtf.gz --filtering_min_proportion 0.3 --filtering_grouping_var condition --deseq2_cores 4 --gsea_run true --gsea_permute ~/Assignment_2/reference_genome/GO_All_Homo_sapiens_GeneSymbol.gmt --gprofiler2_run true --gprofiler2_organism hsapiens --gprofiler2_sources "GO,GO:MF,GO:BP,GO:CC" --gprofiler2_correction_method gSCS --shinyngs_build_app true --max_cpus 8 --max_memory 8.GB --outdir ~/Assignment_2/scratch/homo_analysis_filtered -w ~/Assignment_2/scratch/work/homo_analysis -profile rnaseq,docker ./nextflow run nf-core/differentialabundance --input /home/user/Assignment_2/data/samplesheet.csv --contrasts /home/user/Assignment_2/data/contrasts.csv --matrix /home/userAssignment_2/reference_genome/GSE180869_norm_counts_TPM_GRCh38.p13_NCBI.tsv --transcript_length_matrix Assignment_2/reference_genome/GSE180869_raw_counts_GRCh38.p13_NCBI.tsv --gtf /home/user/Assignment_2/reference_genome/GCF_000001405.40_GRCh38.p14_genomic.gtf.gz --filtering_min_proportion 0.3 --filtering_grouping_var condition --deseq2_cores 4 --gsea_run true --gsea_permute /home/user/Assignment_2/reference_genome/GO_All_Homo_sapiens_GeneSymbol.gmt --gprofiler2_run true --gprofiler2_organism hsapiens --gprofiler2_sources "GO,GO:MF,GO:BP,GO:CC" --gprofiler2_correction_method gSCS --shinyngs_build_app true --max_cpus 8 --max_memory 8.GB --outdir /home/user/Assignment_2/scratch/homo_analysis_filtered -w /home/user/Assignment_2/scratch/work/homo_analysis -profile rnaseq,docker ./nextflow run nf-core/differentialabundance --input /home/user/Assignment_2/data/samplesheet.csv --contrasts /home/user/Assignment_2/data/contrasts.csv --matrix /home/user/Assignment_2/reference_genome/GSE180869_norm_counts_TPM_GRCh38.p13_NCBI.tsv --transcript_length_matrix Assignment_2/reference_genome/GSE180869_raw_counts_GRCh38.p13_NCBI.tsv --gtf /home/user/Assignment_2/reference_genome/GCF_000001405.40_GRCh38.p14_genomic.gtf.gz --filtering_min_proportion 0.3 --filtering_grouping_var condition --deseq2_cores 4 --gsea_run true --gsea_permute /home/user/Assignment_2/reference_genome/GO_All_Homo_sapiens_GeneSymbol.gmt --gprofiler2_run true --gprofiler2_organism hsapiens --gprofiler2_sources "GO,GO:MF,GO:BP,GO:CC" --gprofiler2_correction_method gSCS --shinyngs_build_app true --max_cpus 8 --max_memory 8.GB --outdir /home/user/Assignment_2/scratch/homo_analysis_filtered -w /home/user/Assignment_2/scratch/work/homo_analysis -profile rnaseq,docker ./nextflow run nf-core/differentialabundance --input /home/user/Assignment_2/data/samplesheet.csv --contrasts /home/user/Assignment_2/data/contrasts.csv --matrix /home/user/Assignment_2/reference_genome/GSE180869_norm_counts_TPM_GRCh38.p13_NCBI.tsv --transcript_length_matrix /home/user/Assignment_2/reference_genome/GSE180869_raw_counts_GRCh38.p13_NCBI.tsv --gtf /home/user/Assignment_2/reference_genome/GCF_000001405.40_GRCh38.p14_genomic.gtf.gz --filtering_min_proportion 0.3 --filtering_grouping_var condition --deseq2_cores 4 --gsea_run true --gsea_permute /home/user/Assignment_2/reference_genome/GO_All_Homo_sapiens_GeneSymbol.gmt --gprofiler2_run true --gprofiler2_organism hsapiens --gprofiler2_sources "GO,GO:MF,GO:BP,GO:CC" --gprofiler2_correction_method gSCS --shinyngs_build_app true --max_cpus 8 --max_memory 8.GB --outdir /home/user/Assignment_2/scratch/homo_analysis_filtered -w /home/user/Assignment_2/scratch/work/homo_analysis -profile rnaseq,docker ./nextflow run nf-core/differentialabundance --input /home/user/Assignment_2/data/samplesheet.csv --contrasts /home/user/Assignment_2/data/contrasts.csv --matrix /home/user/Assignment_2/reference_genome/GSE180869_norm_counts_TPM_GRCh38.p13_NCBI.tsv --transcript_length_matrix /home/user/Assignment_2/reference_genome/GSE180869_raw_counts_GRCh38.p13_NCBI.tsv --gtf /home/user/Assignment_2/reference_genome/GCF_000001405.40_GRCh38.p14_genomic.gtf.gz --filtering_min_proportion 0.3 --filtering_grouping_var condition --deseq2_cores 4 --gsea_run true --gene_sets_files /home/user/Assignment_2/reference_genome/GO_All_Homo_sapiens_GeneSymbol.gmt --gsea_permute gene_set --gprofiler2_run true --gprofiler2_organism hsapiens --gprofiler2_sources "GO,GO:MF,GO:BP,GO:CC"--gprofiler2_correction_method gSCS --shinyngs_build_app true --max_cpus 8 --max_memory 8.GB --outdir /home/user/Assignment_2/scratch/homo_analysis_filtered -w /home/user/Assignment_2/scratch/work/homo_analysis -profile rnaseq,docker ./nextflow run nf-core/differentialabundance --input /home/user/Assignment_2/data/samplesheet.csv --contrasts /home/user/Assignment_2/data/contrasts.csv --matrix /home/user/Assignment_2/reference_genome/GSE180869_norm_counts_TPM_GRCh38.p13_NCBI.tsv --transcript_length_matrix /home/user/Assignment_2/reference_genome/GSE180869_raw_counts_GRCh38.p13_NCBI.tsv --gtf /home/user/Assignment_2/reference_genome/GCF_000001405.40_GRCh38.p14_genomic.gtf --filtering_min_proportion 0.3 --filtering_grouping_var condition --deseq2_cores 4 --gsea_run true --gene_sets_files /home/user/Assignment_2/reference_genome/GO_All_Homo_sapiens_GeneSymbol.gmt --gsea_permute gene_set --gprofiler2_run true --gprofiler2_organism hsapiens --gprofiler2_sources "GO,GO:MF,GO:BP,GO:CC"--gprofiler2_correction_method gSCS --shinyngs_build_app true --max_cpus 8 --max_memory 8.GB --outdir /home/user/Assignment_2/scratch/homo_analysis_filtered -w /home/user/Assignment_2/scratch/work/homo_analysis -profile rnaseq,docker ./nextflow run nf-core/differentialabundance --input /home/user/Assignment_2/data/samplesheet.csv --contrasts /home/user/Assignment_2/data/contrasts.csv --matrix /home/user/Assignment_2/reference_genome/GSE180869_norm_counts_TPM_GRCh38.p13_NCBI.tsv --transcript_length_matrix /home/user/Assignment_2/reference_genome/GSE180869_raw_counts_GRCh38.p13_NCBI.tsv --gtf /home/user/Assignment_2/reference_genome/GCF_000001405.40_GRCh38.p14_genomic.gtf --filtering_min_proportion 0.3 --filtering_grouping_var condition --deseq2_cores 4 --gsea_run true --gene_sets_files /home/user/Assignment_2/reference_genome/GO_All_Homo_sapiens_GeneSymbol.gmt --gsea_permute gene_set --gprofiler2_run true --gprofiler2_organism hsapiens --gprofiler2_sources "GO,GO:MF,GO:BP,GO:CC"--gprofiler2_correction_method gSCS --shinyngs_build_app true --max_cpus 8 --max_memory 8.GB --outdir /home/user/Assignment_2/scratch/homo_analysis_filtered -w /home/user/Assignment_2/scratch/work/homo_analysis -profile rnaseq,docker ./nextflow run nf-core/differentialabundance --input /home/user/Assignment_2/data/samplesheet.csv --contrasts /home/user/Assignment_2/data/contrasts.csv --matrix /home/user/Assignment_2/reference_genome/GSE180869_norm_counts_TPM_GRCh38.p13_NCBI.tsv --transcript_length_matrix /home/user/Assignment_2/reference_genome/GSE180869_raw_counts_GRCh38.p13_NCBI.tsv --gtf /home/user/Assignment_2/reference_genome/GCF_000001405.40_GRCh38.p14_genomic.gtf --filtering_min_proportion 0.3 --filtering_grouping_var condition --deseq2_cores 4 --gsea_run true --gene_sets_files /home/user/Assignment_2/reference_genome/GO_All_Homo_sapiens_GeneSymbol.gmt --gsea_permute gene_set --gprofiler2_run true --gprofiler2_organism hsapiens --gprofiler2_sources "GO,GO:MF,GO:BP,GO:CC"--gprofiler2_correction_method gSCS --shinyngs_build_app true --max_cpus 8 --max_memory 8.GB --outdir /home/user/Assignment_2/scratch/homo_analysis_filtered -w /home/user/Assignment_2/scratch/work/homo_analysis -profile rnaseq,docker ./nextflow run nf-core/differentialabundance --input /home/user/Assignment_2/data/samplesheet.csv --contrasts /home/user/Assignment_2/data/contrasts.csv --matrix /home/user/Assignment_2/reference_genome/GSE180869_norm_counts_TPM_GRCh38.p13_NCBI.tsv --transcript_length_matrix /home/user/Assignment_2/reference_genome/GSE180869_raw_counts_GRCh38.p13_NCBI.tsv --gtf /home/user/Assignment_2/reference_genome/GCF_000001405.40_GRCh38.p14_genomic.gtf --filtering_min_proportion 0.3 --filtering_grouping_var condition --deseq2_cores 4 --gsea_run true --gene_sets_files /home/user/Assignment_2/reference_genome/GO_All_Homo_sapiens_GeneSymbol.gmt --gsea_permute gene_set --gprofiler2_run true --gprofiler2_organism hsapiens --gprofiler2_sources "GO,GO:MF,GO:BP,GO:CC"--gprofiler2_correction_method gSCS --shinyngs_build_app true --max_cpus 8 --max_memory 8.GB --outdir /home/user/Assignment_2/scratch/homo_analysis_filtered -w /home/user/Assignment_2/scratch/work/homo_analysis -profile rnaseq,docker ./nextflow run nf-core/differentialabundance --input /home/user/labs/data/case_study/GSE180869/samplesheet_with_condition.csv --contrasts /home/user/Assignment_2/data/contrasts.csv --matrix /home/user/labs/data/case_study/GSE180869/salmon.merged.gene_counts.tsv --transcript_length_matrix /home/user/labs/data/case_study/GSE180869/salmon.merged.gene_lengths.tsv --genome GRCh38 --filtering_min_proportion 0.3 --filtering_grouping_var condition --deseq2_cores 4 --gsea_run true --gsea_permute gene_set --gsea_make_sets true --gsea_permute_n 1000 --gene_sets_files /home/user/Assignment_2/reference_genome/GO_All_Homo_sapiens_GeneSymbol.gmt --max_cpus 8 --max_memory 8.GB --outdir /home/user/Assignment_2/scratch/homo_analysis_filtered -w /home/user/Assignment_2/scratch/work/homo_analysis -profile docker ./nextflow run nf-core/differentialabundance --input /home/user/labs/data/case_study/GSE180869/samplesheet_with_condition.csv --contrasts /home/user/Assignment_2/data/contrasts.csv --matrix /home/user/labs/data/case_study/GSE180869/salmon.merged.gene_counts.tsv --transcript_length_matrix /home/user/labs/data/case_study/GSE180869/salmon.merged.gene_lengths.tsv --genome GRCh38 --filtering_min_proportion 0.3 --filtering_grouping_var condition --deseq2_cores 4 --gsea_run true --gsea_permute /home/user/Assignment_2/reference_genome/GO_All_Homo_sapiens_GeneSymbol.gmt --gprofiler2_run true --gprofiler2_organism hsapiens --gprofiler2_sources "GO,GO:MF,GO:BP,GO:CC"--gprofiler2_correction_method gSCS --shinyngs_build_app true --max_cpus 8 --max_memory 8.GB --outdir /home/user/Assignment_2/scratch/homo_analysis_filtered -w /home/user/Assignment_2/scratch/work/homo_analysis -profile rnaseq,docker ./nextflow run nf-core/differentialabundance --input /home/user/labs/data/case_study/GSE180869/samplesheet_with_condition.csv --contrasts /home/user/Assignment_2/data/contrasts.csv --matrix /home/user/labs/data/case_study/GSE180869/salmon.merged.gene_counts.tsv --transcript_length_matrix /home/user/labs/data/case_study/GSE180869/salmon.merged.gene_lengths.tsv --genome GRCh38 --filtering_min_proportion 0.3 --filtering_grouping_var condition --deseq2_cores 4 --gsea_run true --gene_sets_files /home/user/Assignment_2/reference_genome/GO_All_Homo_sapiens_GeneSymbol.gmt --gsea_permute gene_set --gprofiler2_run true --gprofiler2_organism hsapiens --gprofiler2_sources "GO,GO:MF,GO:BP,GO:CC"--gprofiler2_correction_method gSCS --shinyngs_build_app true --max_cpus 8 --max_memory 8.GB --outdir /home/user/Assignment_2/scratch/homo_analysis_filtered -w /home/user/Assignment_2/scratch/work/homo_analysis -profile rnaseq,docker ./nextflow run nf-core/differentialabundance --input /home/user/labs/data/case_study/GSE180869/samplesheet_with_condition.csv --contrasts /home/user/Assignment_2/data/contrasts.csv --matrix /home/user/labs/data/case_study/GSE180869/salmon.merged.gene_counts.tsv --transcript_length_matrix /home/user/labs/data/case_study/GSE180869/salmon.merged.gene_lengths.tsv --genome GRCh38 --filtering_min_proportion 0.3 --filtering_grouping_var condition --deseq2_cores 4 --gsea_run true --gsea_permute gene_set --gsea_make_sets true --gsea_permute_n 1000 --gsea_metric Diff_of_Classes --gene_sets_files /home/user/Assignment_2/reference_genome/GO_All_Homo_sapiens_GeneSymbol.gmt --max_cpus 8 --max_memory 8.GB --outdir /home/user/Assignment_2/scratch/homo_analysis_filtered -w /home/user/Assignment_2/scratch/work/homo_analysis -profile docker ./nextflow run nf-core/differentialabundance --input /home/user/labs/data/case_study/GSE180869/samplesheet_with_condition.csv --contrasts /home/user/Assignment_2/data/contrasts.csv --matrix /home/user/labs/data/case_study/GSE180869/salmon.merged.gene_counts.tsv --transcript_length_matrix /home/user/labs/data/case_study/GSE180869/salmon.merged.gene_lengths.tsv --genome GRCh38 --filtering_min_proportion 0.3 --filtering_grouping_var condition --deseq2_cores 4 --gsea_run true --gsea_permute gene_set --gsea_make_sets true --gsea_permute_n 1000 --gsea_metric Diff_of_Classes --gene_sets_files /home/user/Assignment_2/reference_genome/GO_All_Homo_sapiens_GeneSymbol.gmt --gprofiler2_run true --gprofiler2_organism hsapiens --gprofiler2_sources "GO,GO:MF,GO:BP,GO:CC" --gprofiler2_max_qval 0.05 --gprofiler2_correction_method gSCS --shinyngs_build_app true --max_cpus 8 --max_memory 8.GB --outdir /home/user/Assignment_2/scratch/homo_analysis_filtered -w /home/user/Assignment_2/scratch/work/homo_analysis -profile docker ls -l /home/user/Assignment_2/scratch/work/homo_analysis/0d/a33bd8ac4ff9ec7f48b60ea39c5556/ tail -n 50 .nextflow.log nextflow run nf-core/differentialabundance -resume -process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GSEA_GSEA
