[AlexsLemonade#323] update CI file, dockerfile, results file

for comparative-rnaseq-analysis:
- update command lines in CI file; add dependency to dockerfile;
add new version of outlier results tsv.gz file with sample filters applied.

.circleci/config.yml

@@ -129,15 +129,15 @@ jobs:
 
       - 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 --output-prefix rsem-tpm-polya- --verbose
+          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 --output-prefix rsem-tpm-stranded- --verbose
+          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- --verbose
+          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

Dockerfile

@@ -257,9 +257,6 @@ RUN apt-get update -qq && apt-get -y --no-install-recommends install \
 # package required for shatterseek
 RUN R -e "withr::with_envvar(c(R_REMOTES_NO_ERRORS_FROM_WARNINGS='true'), remotes::install_github('parklab/ShatterSeek', ref = '83ab3effaf9589cc391ecc2ac45a6eaf578b5046', dependencies = TRUE))"
 
-#### Please install your dependencies here
-#### Add a comment to indicate what analysis it is required for
-
 # MATLAB Compiler Runtime is required for GISTIC, MutSigCV
 # Install steps are adapted from usuresearch/matlab-runtime
 # https://hub.docker.com/r/usuresearch/matlab-runtime/dockerfile
@@ -292,4 +289,10 @@ RUN mkdir -p gistic_install && \
 RUN chown -R rstudio:rstudio /home/rstudio/gistic_install
 RUN chmod 755 /home/rstudio/gistic_install
 
+# pyarrow for comparative-RNASeq-analysis, to read/write .feather files
+RUN pip3 install "pyarrow==0.16.0"
+
+#### Please install your dependencies here
+#### Add a comment to indicate what analysis it is required for
+
 WORKDIR /rocker-build/