Revert "Merge branch 'master' into v18-ci"

This reverts commit 27dec43.

.circleci/config.yml

@@ -68,7 +68,7 @@ jobs:
          name: Molecular Subtyping Neurocytoma
          command: ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-neurocytoma/run_subtyping.sh
 
-     # Commenting this out for now; the code is expected to change
+     # Commenting this out for now; the code is expected to change 
      # - run:
      #    name: Molecular Subtyping - Compile and incorporate pathology feedback
      #    command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-pathology/run-subtyping-aggregation.sh
@@ -132,17 +132,17 @@ jobs:
           name: Independent samples
           command: ./scripts/run_in_ci.sh bash analyses/independent-samples/run-independent-samples.sh
 
-#      - run:
-#          name: Interaction plot
-#          command: OPENPBTA_ALL=0 ./scripts/run_in_ci.sh bash analyses/interaction-plots/01-create-interaction-plots.sh
+      - run:
+          name: Interaction plot
+          command: OPENPBTA_ALL=0 ./scripts/run_in_ci.sh bash analyses/interaction-plots/01-create-interaction-plots.sh
 
       - run:
-          name: Mutational Signatures
+          name: Mutational Signatures 
           command: OPENPBTA_QUICK_MUTSIGS=1 ./scripts/run_in_ci.sh bash analyses/mutational-signatures/run_mutational_signatures.sh
 
-#      - run:
-#          name: Chromosomal instability breakpoints
-#          command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash analyses/chromosomal-instability/run_breakpoint_analysis.sh
+      - run:
+          name: Chromosomal instability breakpoints
+          command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash analyses/chromosomal-instability/run_breakpoint_analysis.sh
 
       - run:
           name: Copy number consensus
@@ -156,33 +156,33 @@ jobs:
           name: Survival analysis
           command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/survival-analysis/survival-analysis_template.Rmd', params = list(plot_ci = FALSE), clean = TRUE)"
 
-#      - run:
-#          name: Comparative RNASeq - generate correlation matrix - rsem-tpm.polya
-#          command: ./scripts/run_in_ci.sh python3 analyses/comparative-RNASeq-analysis/01-correlation-matrix.py ../../data/pbta-gene-expression-rsem-tpm.polya.rds --clinical-path ../../data/pbta-histologies.tsv --qc-manifest-path ../../data/pbta-mend-qc-manifest.tsv --qc-results-path ../../data/pbta-mend-qc-results.tar.gz --prefix rsem-tpm-polya- --verbose
+      - run:
+          name: Comparative RNASeq - generate correlation matrix - rsem-tpm.polya
+          command: ./scripts/run_in_ci.sh python3 analyses/comparative-RNASeq-analysis/01-correlation-matrix.py ../../data/pbta-gene-expression-rsem-tpm.polya.rds --clinical-path ../../data/pbta-histologies.tsv --qc-manifest-path ../../data/pbta-mend-qc-manifest.tsv --qc-results-path ../../data/pbta-mend-qc-results.tar.gz --prefix rsem-tpm-polya- --verbose
 
-#      - run:
-#          name: Comparative RNASeq - generate correlation matrix - rsem-tpm.stranded
-#          command: ./scripts/run_in_ci.sh python3 analyses/comparative-RNASeq-analysis/01-correlation-matrix.py ../../data/pbta-gene-expression-rsem-tpm.stranded.rds --clinical-path ../../data/pbta-histologies.tsv --qc-manifest-path ../../data/pbta-mend-qc-manifest.tsv --qc-results-path ../../data/pbta-mend-qc-results.tar.gz --prefix rsem-tpm-stranded- --verbose
+      - run:
+          name: Comparative RNASeq - generate correlation matrix - rsem-tpm.stranded
+          command: ./scripts/run_in_ci.sh python3 analyses/comparative-RNASeq-analysis/01-correlation-matrix.py ../../data/pbta-gene-expression-rsem-tpm.stranded.rds --clinical-path ../../data/pbta-histologies.tsv --qc-manifest-path ../../data/pbta-mend-qc-manifest.tsv --qc-results-path ../../data/pbta-mend-qc-results.tar.gz --prefix rsem-tpm-stranded- --verbose
 
-#      - run:
-#          name: Comparative RNASeq - generate thresholds and outliers - rsem-tpm.stranded
-#          command: ./scripts/run_in_ci.sh python3 analyses/comparative-RNASeq-analysis/02-thresholds-and-outliers.py --prefix rsem-tpm-stranded- --results results --verbose
+      - run:
+          name: Comparative RNASeq - generate thresholds and outliers - rsem-tpm.stranded
+          command: ./scripts/run_in_ci.sh python3 analyses/comparative-RNASeq-analysis/02-thresholds-and-outliers.py --prefix rsem-tpm-stranded- --results results --verbose
 
       - run:
           name: Process SV file
           command: ./scripts/run_in_ci.sh Rscript analyses/sv-analysis/01-process-sv-file.R
 
-#      - run:
-#          name: Oncoprint plotting
-#          command: ./scripts/run_in_ci.sh bash "analyses/oncoprint-landscape/run-oncoprint.sh"
+      - run:
+          name: Oncoprint plotting
+          command: ./scripts/run_in_ci.sh bash "analyses/oncoprint-landscape/run-oncoprint.sh"
 
       - run:
           name: GISTIC Plots
           command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/cnv-chrom-plot/gistic_plot.Rmd', clean = TRUE)"
 
-#      - run:
-#          name: CN Status Heatmap
-#          command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/cnv-chrom-plot/cn_status_heatmap.Rmd', clean = TRUE)"
+      - run:
+          name: CN Status Heatmap
+          command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/cnv-chrom-plot/cn_status_heatmap.Rmd', clean = TRUE)"
 
       - run:
           name: Gene set enrichment analysis to generate GSVA scores
@@ -205,9 +205,9 @@ jobs:
          #### Add your analysis here ####
          ################################
 
-#      - run:
-#          name: RNA-Seq composition
-#          command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/rna-seq-composition/rna-seq-composition.Rmd', clean = TRUE)"
+      - run:
+          name: RNA-Seq composition
+          command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/rna-seq-composition/rna-seq-composition.Rmd', clean = TRUE)"
 
       - run:
           name: TCGA SNV Caller Analysis
@@ -224,7 +224,7 @@ jobs:
       - run:
           name: Exploration of nonsynonymous filter
           command: ./scripts/run_in_ci.sh bash analyses/snv-callers/explore_variant_classifications/run_explorations.sh
-
+          
       # This analysis was used to explore the TCGA PBTA data when the BED files used to calculate TCGA
       # were incorrect https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/568
       #- run:
@@ -254,9 +254,9 @@ jobs:
           name: TCGA Capture Kit Investigation
           command: ./scripts/run_in_ci.sh bash analyses/tcga-capture-kit-investigation/run-investigation.sh
 
-#      - run:
-#          name: d3b TMB code
-#          command: ./scripts/run_in_ci.sh bash analyses/tmb-compare/TMB_d3b_code/run_tmb_d3b.sh
+      - run:
+          name: d3b TMB code
+          command: ./scripts/run_in_ci.sh bash analyses/tmb-compare/TMB_d3b_code/run_tmb_d3b.sh
 
       - run:
           name: Compare TMB calculations

Dockerfile

@@ -245,8 +245,8 @@ RUN pip3 install \
     "cycler==0.10.0" "kiwisolver==1.1.0" "pyparsing==2.4.5" "python-dateutil==2.8.1" "pytz==2019.3" \
     "cython==0.29.15" \
     "ipykernel==4.8.1" \
+    "jupyter==1.0.0" \
     "matplotlib==3.0.3" \
-    "notebook==6.0.0" \
     "numpy==1.17.3" \
     "pandas==0.25.3" \
     "plotnine==0.3.0" \