sudo apt update sudo apt install default\-jre # When prompted, enter Y curl -s https://get.nextflow.io | bash echo 'NXF_OPTS="-Xms1g -Xmx4g"' >> ~/.bashrc source ~/.bashrc ./nextflow run nf-core/fetchngs --input ~labs/data/case_study/GSE180869/ids.csv --outdir ~/Assignment_2/scratch/fetchngs --max_cpus 32 --max_memory 128.GB --download_method sratools --nf_core_pipeline rnaseq -w ~/Assignment_2/scratch/work/fetchngs -profile docker ./nextflow run nf-core/fetchngs --input home/user/labs/data/case_study/GSE180869/ids.csv --outdir home/user/Assignment_2/scratch/fetchngs --max_cpus 32 --max_memory 128.GB --download_method sratools --nf_core_pipeline rnaseq -w home/user/Assignment_2/scratch/work/fetchngs -profile docker ./nextflow run nf-core/differentialabundance --input ~labs/data/case_study/GSE180869/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 gene_set \ --gsea_make_sets true --gene_sets_files ~/Assignment_2/reference_genome/GO_All_Homo_sapiens_GeneSymbol.gmt --gprofiler2_run true \ ./nextflow run nf-core/differentialabundance --input ~labs/data/case_study/GSE180869/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 gene_set \ --gsea_make_sets true --gene_sets_files ~/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,KEGG,REAC" --gprofiler2_max_qval 0.05 --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 docker ./nextflow run nf-core/differentialabundance --input ~labs/data/case_study/GSE180869/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 gene_set \ --gsea_make_sets true --gene_sets_files ~/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,KEGG,REAC" --gprofiler2_max_qval 0.05 --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 docker
