From 790fde4a98a8e483cdef8c557b8e5b3a23f80118 Mon Sep 17 00:00:00 2001
From: Gregor Rot <gregor.rot@gmail.com>
Date: Mon, 8 Sep 2025 12:37:43 +0200
Subject: [PATCH] Update Dockerfile

---
 Dockerfile | 42 ++++++++++++++++++++----------------------
 1 file changed, 20 insertions(+), 22 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 6d3bdf6..a7bc291 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -8,40 +8,38 @@ RUN apt-get update && apt-get install -y tzdata curl gpg
 
 # nodejs packages
 RUN mkdir -p /etc/apt/keyrings
-RUN curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg
-RUN echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_21.x nodistro main" | tee /etc/apt/sources.list.d/nodesource.list
+RUN curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg && \
+    echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_21.x nodistro main" | tee /etc/apt/sources.list.d/nodesource.list
 
 # R packages
-RUN echo 'deb https://cloud.r-project.org/bin/linux/ubuntu noble-cran40/' | tee -a /etc/apt/sources.list
-RUN apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
+RUN echo 'deb https://cloud.r-project.org/bin/linux/ubuntu noble-cran40/' | tee -a /etc/apt/sources.list && \
+    apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
 
 # update and install
-RUN apt-get update
-RUN apt-get install -y autoconf automake build-essential ca-certificates cmake cpanminus curl curl fort77 gcc gfortran ghostscript git gnupg gnupg2 gzip libblas-dev libbz2-dev libcurl4-openssl-dev libexpat1-dev libgd-dev libgmp3-dev libgs-dev libgsl-dev libhtml-template-compiled-perl liblapack-dev liblzma-dev libmpc-dev libmpfr-dev libncurses5-dev libopenmpi-dev libssl-dev libtool libxml-libxml-debugging-perl libxml-opml-simplegen-perl libxml2 libxml2-dev libxslt1-dev libxslt1.1 nodejs openmpi-bin python-is-python3 python3 python3-dev python3-pip r-base wget zlib1g-dev
-RUN pip3 install deeptools cython --break-system-packages
-RUN npm install -g @jbrowse/cli
+RUN apt-get update && \
+    apt-get install -y libnlopt-dev autoconf automake build-essential ca-certificates cmake cpanminus curl curl fort77 gcc gfortran ghostscript git gnupg gnupg2 gzip libblas-dev libbz2-dev libcurl4-openssl-dev libexpat1-dev libgd-dev libgmp3-dev libgs-dev libgsl-dev libhtml-template-compiled-perl liblapack-dev liblzma-dev libmpc-dev libmpfr-dev libncurses5-dev libopenmpi-dev libssl-dev libtool libxml-libxml-debugging-perl libxml-opml-simplegen-perl libxml2 libxml2-dev libxslt1-dev libxslt1.1 nodejs openmpi-bin python-is-python3 python3 python3-dev python3-pip r-base wget zlib1g-dev && \
+    pip3 install deeptools cython --break-system-packages && \
+    npm install -g @jbrowse/cli
 
 # R with edgeR
-RUN R -e "install.packages('BiocManager')"
-RUN R -e "BiocManager::install('edgeR')"
-RUN R -e "install.packages('data.table')"
-RUN R -e "install.packages('statmod')"
-RUN R -e "install.packages('R.utils')"
+RUN R -e "install.packages('BiocManager', repos='https://cloud.r-project.org')" && \
+    R -e "BiocManager::install('edgeR')" && \
+    R -e "install.packages(c('data.table', 'statmod', 'R.utils', 'doParallel', 'foreach', 'nloptr'), repos='https://cloud.r-project.org')"
 
 # Perl modules
 RUN cpanm XML::Compile::Transport::SOAPHTTP XML::Compile::WSDL11 XML::Compile::SOAP11 XML::Compile XML::LibXML::Simple XML::LibXML Log::Log4perl Math::CDF CGI File::Which Data::Dumper File::Copy File::Spec::Functions HTML::PullParser HTML::Template HTML::TreeBuilder JSON Pod::Usage XML::Simple XML::Parser::Expat
 
 # MEME suite
-RUN wget http://meme-suite.org/meme-software/5.5.6/meme-5.5.6.tar.gz --no-check-certificate
-RUN tar zxf meme-5.5.6.tar.gz
+RUN wget http://meme-suite.org/meme-software/5.5.6/meme-5.5.6.tar.gz --no-check-certificate && \
+    tar zxf meme-5.5.6.tar.gz
 WORKDIR /meme-5.5.6
-RUN ./configure --prefix=/meme --with-url=http://meme-suite.org --enable-build-libxml2 --enable-build-libxslt --disable-dependency-tracking
-RUN make
-RUN make install
+RUN ./configure --prefix=/meme --with-url=http://meme-suite.org --enable-build-libxml2 --enable-build-libxslt --disable-dependency-tracking && \
+    make && \
+    make install
 
 # rmats-turbo
-RUN apt-get update
-RUN apt-get install -y subread bedtools samtools tabix
+RUN apt-get update && \
+    apt-get install -y subread bedtools samtools tabix
 WORKDIR /
 RUN git clone https://github.com/Xinglab/rmats-turbo.git
 WORKDIR rmats-turbo
@@ -56,8 +54,8 @@ RUN pip install . --break-system-packages
 
 # Install STAR read aligner
 WORKDIR /
-RUN wget https://github.com/alexdobin/STAR/archive/2.7.11b.tar.gz
-RUN tar -xzf 2.7.11b.tar.gz
+RUN wget https://github.com/alexdobin/STAR/archive/2.7.11b.tar.gz && \
+    tar -xzf 2.7.11b.tar.gz
 
 # environment variables
 ENV PATH="$PATH:/rmats-turbo:/meme/bin:/usr/local/bin:/STAR-2.7.11b/bin/Linux_x86_64"