Install MATLAB Compiler Runtime on project Docker container (#531)

* First pass at MCR install

* The xorg step appeared to be hanging

* Needs to be noninteractive

* Forgot RUN

* Try noninteractive another way

* Environmental variables for MCR

* Move up copy number consensus

* Move MCR up

* Revert "Move MCR up"

This reverts commit f840192.

* Don't configure environmental variables

* Unclear if the embryonal subtyping is failure related

* Revert "Unclear if the embryonal subtyping is failure related"

This reverts commit 0895474.

* Revert "Move up copy number consensus"

This reverts commit 1b839c4.

* WIP: push what I have

* add MCR working w/ gistic steps

* hold my container

* Move export LD_LIBRARY_PATH step

* Use ENV instead

* Quiet wget

* Install GISTIC in /home/rstudio

* Add GISTIC proof of concept

Co-authored-by: Casey Greene <[email protected]>

.circleci/config.yml

@@ -20,6 +20,10 @@ jobs:
           name: Sample Distribution Analyses
           command: ./scripts/run_in_ci.sh bash "analyses/sample-distribution-analysis/run-sample-distribution.sh"
 
+      - run:
+          name: GISTIC proof of concept
+          command: ./scripts/run_in_ci.sh bash analyses/gistic-proof-of-concept/gistic-example.sh
+
       # The analysis no longer needs to be tested as it has been retired and is better covered by 'SNV Caller Analysis' below.
       #- run:
       #    name: Mutect2 vs Strelka2

Dockerfile

@@ -60,7 +60,7 @@ RUN R -e "BiocManager::install(c('annotatr', 'TxDb.Hsapiens.UCSC.hg38.knownGene'
 RUN R -e "BiocManager::install(c('preprocessCore', 'sva'), update = FALSE)"
 
 
-## This is deprecated 
+## This is deprecated
 #  # These packages are for single-sample GSEA analysis
 #  RUN R -e "BiocManager::install(c('GSEABase', 'GSVA'), update = FALSE)"
 
@@ -180,7 +180,7 @@ RUN R -e "BiocManager::install(c('TCGAbiolinks'), update = FALSE)"
 
 # Install python3 data science basics (pandas)
 # using pip to get more current versions
-RUN apt-get update -qq && apt-get -y --no-install-recommends install python3-pip  python3-dev 
+RUN apt-get update -qq && apt-get -y --no-install-recommends install python3-pip  python3-dev
 RUN pip3 install "numpy==1.17.3" && \
    pip3 install "six==1.13.0" "setuptools==41.6.0" && \
    pip3 install "cycler==0.10.0" "kiwisolver==1.1.0" "pyparsing==2.4.5" "python-dateutil==2.8.1" "pytz==2019.3" && \
@@ -212,7 +212,7 @@ RUN apt-get update -qq && apt-get -y --no-install-recommends install \
     survival \
     cmprsk \
     survMisc \
-    survminer 
+    survminer
 
 # pyreadr for comparative-RNASeq-analysis
 RUN pip3 install "pyreadr==0.2.1"
@@ -260,3 +260,34 @@ RUN R -e "withr::with_envvar(c(R_REMOTES_NO_ERRORS_FROM_WARNINGS='true'), remote
 #### 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
+
+ENV DEBIAN_FRONTEND noninteractive
+RUN apt-get -q update && \
+    apt-get install -q -y --no-install-recommends \
+    xorg
+
+RUN mkdir /mcr-install && \
+    mkdir /opt/mcr && \
+    cd /mcr-install && \
+    wget https://www.mathworks.com/supportfiles/downloads/R2014a/deployment_files/R2014a/installers/glnxa64/MCR_R2014a_glnxa64_installer.zip && \
+    unzip -q MCR_R2014a_glnxa64_installer.zip && \
+    rm -f MCR_R2014a_glnxa64_installer.zip && \
+    ./install -destinationFolder /opt/mcr -agreeToLicense yes -mode silent && \
+    cd / && \
+    rm -rf mcr-install
+
+WORKDIR /home/rstudio/
+
+# GISTIC installation
+RUN mkdir -p gistic_install && \
+    cd gistic_install && \
+    wget -q ftp://ftp.broadinstitute.org/pub/GISTIC2.0/GISTIC_2_0_23.tar.gz && \
+    tar zxf GISTIC_2_0_23.tar.gz
+
+RUN chown -R rstudio:rstudio /home/rstudio/gistic_install
+RUN chmod 755 /home/rstudio/gistic_install
+
+WORKDIR /rocker-build/

analyses/gistic-proof-of-concept/gistic-example.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+set -e 
+set -o pipefail
+
+export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/mcr/v83/runtime/glnxa64:/opt/mcr/v83/bin/glnxa64:/opt/mcr/v83/sys/os/glnxa64:
+export XAPPLRESDIR=/opt/mcr/v83/X11/app-defaults
+
+cd /home/rstudio/gistic_install && ./run_gistic_example