Add shell script to generate analysis files that are included in data releases

scripts/generate-analysis-files-for-release.sh

@@ -0,0 +1,123 @@
+#!/bin/sh
+
+set -e
+set -o pipefail
+
+# Set the working directory to the directory of this file
+cd "$(dirname "${BASH_SOURCE[0]}")"
+
+# If RUN_LOCAL is used, the time-intensive steps are skipped because they cannot
+# be run on a local computer -- the idea is that setting RUN_LOCAL=1 will allow for
+# local testing running/testing of all other steps
+RUN_LOCAL=${RUN_LOCAL:-0}
+
+# Get base directory of project
+cd ..
+BASEDIR="$(pwd)"
+cd -
+
+analyses_dir="$BASEDIR/analyses"
+data_dir="$BASEDIR/data"
+scratch_dir="$BASEDIR/scratch"
+
+# Compile all the files that need to be included in the release in one place
+# in the scratch directory
+compiled_dir=${scratch_dir}/analysis_files_for_release
+mkdir -p ${compiled_dir}
+
+# Collapsed RNA-seq files
+echo "Create collapse RSEM files"
+bash ${analyses_dir}/collapse-rnaseq/run-collapse-rnaseq.sh
+
+# Create the independent sample list using the *BASE* histology file
+echo "Create independent sample list"
+OPENPBTA_BASE_RELEASE=1 bash ${analyses_dir}/independent-samples/run-independent-samples.sh
+
+# Fusion filtering
+echo "Create fusion filtered list"
+OPENPBTA_BASE_RELEASE=1 bash ${analyses_dir}/fusion_filtering/run_fusion_merged.sh
+
+# Fusion summary
+echo "Run fusion summary for subtypes"
+bash ${analyses_dir}/fusion-summary/run-new-analysis.sh
+
+# Copy over collapsed RNA-seq files
+cp ${analyses_dir}/collapse-rnaseq/results/pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds ${compiled_dir}
+cp ${analyses_dir}/collapse-rnaseq/results/pbta-gene-expression-rsem-fpkm-collapsed.polya.rds ${compiled_dir}
+
+# Copy over independent specimen lists
+cp ${analyses_dir}/independent-samples/results/independent-specimens.*  ${compiled_dir}
+
+# Copy over fusions lists
+cp ${analyses_dir}/fusion_filtering/results/pbta-fusion-putative-oncogenic.tsv ${compiled_dir}
+cp ${analyses_dir}/fusion_filtering/results/pbta-fusion-recurrently-fused-genes-* ${compiled_dir}
+
+# Copy over fusion summary
+cp ${analyses_dir}/fusion-summary/results/* ${compiled_dir}
+
+# Run modules that cannot be run locally due to memory requirements
+if [ "$RUN_LOCAL" -lt "1" ]; then
+
+  # Run SNV consensus & TMB step for PBTA data
+  echo "Run SNV callers module for PBTA data"
+  OPENPBTA_BASE_RELEASE=1 bash ${analyses_dir}/snv-callers/run_caller_consensus_analysis-pbta.sh
+
+  # Run SNV consensus & TMB step for TCGA data
+  echo "Run SNV callers module for TCGA data"
+  bash ${analyses_dir}/snv-callers/run_caller_consensus_analysis-tcga.sh
+
+  # Copy over SNV callers
+  ## PBTA
+  cp ${analyses_dir}/snv-callers/results/consensus/pbta-snv-consensus-mutation.maf.tsv.gz ${compiled_dir}
+  cp ${analyses_dir}/snv-callers/results/consensus/pbta-snv-mutation-tmb-coding.tsv ${compiled_dir}
+  cp ${analyses_dir}/snv-callers/results/consensus/pbta-snv-mutation-tmb-all.tsv ${compiled_dir}
+  ## TCGA
+  cp ${analyses_dir}/snv-callers/results/consensus/tcga-snv-consensus-snv.maf.tsv.gz ${compiled_dir}
+  cp ${analyses_dir}/snv-callers/results/consensus/tcga-snv-mutation-tmb-coding.tsv ${compiled_dir}
+  cp ${analyses_dir}/snv-callers/results/consensus/tcga-snv-mutation-tmb-all.tsv ${compiled_dir}
+
+  # Run hotspot detection
+  echo "Run hotspots detection"
+  bash ${analyses_dir}/hotspots-detection/run_overlaps_hotspots.sh
+
+  # Copy over hotspots detection
+  cp ${analyses_dir}/hotspots-detection/results/pbta-snv-scavenged-hotspots.maf.tsv.gz ${compiled_dir}
+
+  # Run consensus CN caller step
+  echo "Run CNV consensus"
+  bash ${analyses_dir}/copy_number_consensus_call/run_consensus_call.sh
+
+  # Copy over CNV consensus
+  cp ${analyses_dir}/copy_number_consensus_call/results/pbta-cnv-consensus.seg.gz ${compiled_dir}
+
+  # Run GISTIC step -- only the part that generates ZIP file
+  echo "Run GISTIC"
+  # Run a step that subs ploidy for NA to allow GISTIC to run
+  Rscript ${analyses_dir}/run-gistic/scripts/prepare_seg_for_gistic.R \
+    --in_consensus ${analyses_dir}/copy_number_consensus_call/results/pbta-cnv-consensus.seg.gz \
+    --out_consensus ${analyses_dir}/run-gistic/results/pbta-cnv-consensus-gistic-only.seg.gz \
+    --histology ${data_dir}/pbta-histologies-base.tsv
+
+  # This will use the file that just got generated above
+  bash ${analyses_dir}/run-gistic/scripts/run-gistic-openpbta.sh
+
+  # Copy over GISTIC
+  cp ${analyses_dir}/run-gistic/results/pbta-cnv-consensus-gistic.zip ${compiled_dir}
+
+  # Run step that generates "most focal CN" files (annotation) using the *BASE* histology file
+  echo "Run focal CN file preparation"
+  OPENPBTA_BASE_RELEASE=1 bash ${analyses_dir}/focal-cn-file-preparation/run-prepare-cn.sh
+
+  # Copy over focal CN
+  cp ${analyses_dir}/focal-cn-file-preparation/results/consensus_seg_annotated_cn_autosomes.tsv.gz ${compiled_dir}
+  cp ${analyses_dir}/focal-cn-file-preparation/results/consensus_seg_annotated_cn_x_and_y.tsv.gz ${compiled_dir}
+
+fi
+
+# Create an md5sum file for all the files in the directory where the analysis
+# files are compiled
+cd ${compiled_dir}
+# Remove old file if it exists
+rm -f analysis_files_md5sum.txt
+# Create a new md5sum.txt file
+md5sum * > analysis_files_md5sum.txt