Use pkgdepends (#20)

* add installer script

* comment lines for testing

* add installer R script that uses pkgdepends

* remove redundant dependendencies and use r-base

* fix file path for battenberg_wgs.R

* add dependencies using conda

* Update CHANGELOG.md

* add apt-get list removal

* add space

---------

Co-authored-by: Mootor <mmootor@ip-0A125967.rhxrlfvjyzbupc03cc22jkch3c.xx.internal.cloudapp.net>
Co-authored-by: Mootor <mmootor@ip-0A125937.rhxrlfvjyzbupc03cc22jkch3c.xx.internal.cloudapp.net>

CHANGELOG.md

@@ -5,6 +5,15 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+---
+## Unreleased
+### Chanded
+- Use the official `r-base:4.4.1` docker image
+- Replace GitHub package installation with `pkgdepends`
+
+### Added
+- Add installer.R that uses `pkgdepends`
+
 ---
 
 ## [2.2.9] - 2023-06-27

Dockerfile

@@ -13,31 +13,50 @@ RUN mamba create -qy -p /usr/local \
     cancerit-allelecount==${ALLELECOUNT_VERSION} \
     impute2==${IMPUTE2_VERSION}
 
-# Deploy the target tools into a base image
 FROM ubuntu:20.04
+FROM r-base:4.4.1
 COPY --from=builder /usr/local /usr/local
 
-ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+        libcurl4-openssl-dev \
+        libbz2-dev \
+        liblzma-dev \
+        libpng-dev \
+        libssl-dev \
+        libxml2-dev \
+        python3 \
+    && apt-get clean && rm -rf /var/lib/apt/lists/*
 
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends libxml2 libxml2-dev libcurl4-gnutls-dev build-essential \
-    libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev r-cran-rgl git libssl-dev r-cran-curl && \
-    apt-get clean && rm -rf /var/lib/apt/lists/*
+# Main tool version
+ARG BATTENBERG_VERSION="2.2.9"
 
-RUN R -q -e 'install.packages("BiocManager")' && \
-    R -q -e 'BiocManager::install(c("curl","cpp11","lifecycle","readr","ellipsis","vctrs",\
-        "GenomicRanges","IRanges","gtools", "optparse", "RColorBrewer","ggplot2",\
-        "gridExtra","doParallel","foreach", "splines", "VariantAnnotation", "copynumber"))'
+# Dependency version or commit ID
+ARG ASCAT_VERSION=3.1.3
+ARG COPYNUMBER_VERSION="b404a4d"
 
-# Install devtools, ASCAT & Battenberg
-RUN R -q -e 'install.packages("devtools", dependencies = TRUE)' && \
-    R -q -e 'devtools::install_github("Crick-CancerGenomics/ascat/[email protected]")' && \
-    R -q -e 'devtools::install_github("Wedge-Oxford/[email protected]")'
+# GitHub repo link
+ARG ASCAT="VanLoo-lab/ascat/ASCAT@v${ASCAT_VERSION}"
+ARG COPYNUMBER="igordot/copynumber@${COPYNUMBER_VERSION}"
+ARG BATTENBERG="Wedge-lab/battenberg@v${BATTENBERG_VERSION}"
+
+# R library path to install the above packages
+ARG LIBRARY="/usr/lib/R/site-library"
+
+# Install Package Dependency toolkit
+RUN library=${LIBRARY} R -e 'install.packages(c("argparse", "BiocManager", "pkgdepends", "optparse"), lib = Sys.getenv("library"))' && \
+    R -q -e 'BiocManager::install(c("ellipsis", "splines", "VariantAnnotation"))'
+
+# Install Battenberg
+COPY installer.R /usr/local/bin/installer.R
+RUN chmod +x /usr/local/bin/installer.R
+
+RUN Rscript /usr/local/bin/installer.R -l ${LIBRARY} -d ${COPYNUMBER} ${ASCAT} ${BATTENBERG}
 
 # Modify paths to reference files
 COPY modify_reference_path.sh /usr/local/bin/modify_reference_path.sh
 RUN chmod +x /usr/local/bin/modify_reference_path.sh && \
-    bash /usr/local/bin/modify_reference_path.sh /usr/local/lib/R/site-library/Battenberg/example/battenberg_wgs.R /usr/local/bin/battenberg_wgs.R
+    bash /usr/local/bin/modify_reference_path.sh /usr/lib/R/site-library/Battenberg/example/battenberg_wgs.R /usr/local/bin/battenberg_wgs.R
 
 RUN ln -sf /usr/local/lib/R/site-library/Battenberg/example/filter_sv_brass.R /usr/local/bin/filter_sv_brass.R && \
     ln -sf /usr/local/lib/R/site-library/Battenberg/example/battenberg_cleanup.sh /usr/local/bin/battenberg_cleanup.sh

installer.R

@@ -0,0 +1,29 @@
+library(argparse);
+library(pkgdepends);
+
+parser <- ArgumentParser();
+
+parser$add_argument(
+    '-l',
+    '--lib',
+    help = 'Library path to install the tools'
+    );
+parser$add_argument(
+    '-d',
+    '--dependencies',
+    nargs = '+',
+    help = 'List dependencies separated by space'
+    );
+
+args <- parser$parse_args();
+
+tools <- args$dependencies;
+lib <- args$lib;
+
+pkg.installation.proposal <- new_pkg_installation_proposal(
+    tools,
+    config = list(library = lib)
+    );
+pkg.installation.proposal$solve();
+pkg.installation.proposal$download();
+pkg.installation.proposal$install();