updated Dockerfile

Author: lingminhao

Dockerfile

@@ -1,31 +1,54 @@
-FROM debian:bookworm-slim
+FROM debian:latest
 
-MAINTAINER lingminhao 
+# install R 4.4.1 and all CLI tools 
+ENV R_VERSION=4.4.1 \
+    DEBIAN_FRONTEND=noninteractive
 
-# install all required CLI tools 
 RUN apt-get update \ 
  && apt-get install -y wget make g++ git-all zlib1g zlib1g-dev r-base python-is-python3 python3-pip software-properties-common \ 
- ca-certificates gnupg2 libssl-dev libcurl4-gnutls-dev libxml2-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
-
-RUN wget -q https://cloud.r-project.org/bin/linux/debian/key_4.1.2 -O cran-key.asc \
- && gpg --import cran-key.asc \
- && mv cran-key.asc /etc/apt/trusted.gpg.d/cran.gpg
-
-RUN add-apt-repository -y 'deb http://cloud.r-project.org/bin/linux/debian bookworm-cran40/' \ 
+ ca-certificates gnupg2 libssl-dev libcurl4-gnutls-dev libxml2-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev \ 
  && apt update \ 
  && apt-get install -y r-base
 
+RUN apt-get update -qq && apt-get -y install --no-install-recommends \
+    ca-certificates \
+    build-essential \
+    gfortran \
+    libreadline-dev \
+    xorg-dev \
+    libbz2-dev \
+    liblzma-dev \
+    curl \
+    git-all \ 
+    libxml2-dev \
+    libcairo2-dev \
+    libsqlite3-dev \
+    libmariadbd-dev \
+    libpq-dev \
+    libssh2-1-dev \
+    unixodbc-dev \
+    libcurl4-openssl-dev \
+    libssl-dev \
+    libsodium-dev \
+    wget \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN wget -c https://cran.r-project.org/src/base/R-4/R-${R_VERSION}.tar.gz \
+    && tar -xf R-${R_VERSION}.tar.gz \
+    && cd R-${R_VERSION} \
+    && ./configure \
+    && make -j$(nproc) \
+    && make install \
+    && cd .. \
+    && rm -rf R-${R_VERSION} R-${R_VERSION}.tar.gz
+
 # make a directory to store all required softwares
 RUN mkdir mnt/software
-
+    
 # install flexiplex 
 RUN cd mnt/software && wget https://github.com/DavidsonGroup/flexiplex/releases/download/v1.01/flexiplex-1.01.tar.gz \
  && tar -xvf flexiplex-1.01.tar.gz && rm flexiplex-1.01.tar.gz && cd flexiplex-1.01 && make  
 
-# install jaffa
-RUN cd mnt/software && wget https://github.com/Oshlack/JAFFA/releases/download/version-2.3/JAFFA-version-2.3.tar.gz \
- && tar -xvf JAFFA-version-2.3.tar.gz && rm JAFFA-version-2.3.tar.gz && cd JAFFA-version-2.3 $$ ./install_linux64.sh
-
 # install minimap2
 RUN cd mnt/software && git clone https://github.com/lh3/minimap2 \ 
  && cd minimap2 && make 
@@ -37,20 +60,30 @@ RUN cd mnt/software && wget https://github.com/samtools/htslib/releases/download
  && tar -xvf samtools-1.18.tar.bz2 && rm samtools-1.18.tar.bz2 && cd samtools-1.18 && make && make install
 
 # install bambu  
-RUN cd mnt/software && R -e "install.packages('devtools')" 
-RUN cd mnt/software && R -e "install.packages('R.utils')" 
-RUN cd mnt/software && R -e "install.packages('BiocManager')" 
-RUN cd mnt/software && R -e "BiocManager::install('bambu')"
-RUN cd mnt/software && git clone -b messyForest --single-branch https://github.com/GoekeLab/bambu.git
-RUN cd mnt/software && R -e "library('devtools'); load_all('bambu')"
-RUN cd mnt/software && R -e "install.packages('Rcpp')"
+# RUN R -e "install.packages('R.utils', repos = 'http://cran.us.r-project.org')" 
+RUN R -e "install.packages('BiocManager', repos = 'http://cran.us.r-project.org')" 
+RUN R -e "BiocManager::install('bambu')"
+
+# install Seurat 
+RUN R -e "install.packages('SeuratObject', repos = 'http://cran.us.r-project.org')"
+RUN R -e "install.packages('Seurat', repos = 'http://cran.us.r-project.org')"
 
-RUN cd mnt/software && wget https://raw.githubusercontent.com/DavidsonGroup/flexiplex/863a5f3b182a0ee669407406b6cb39ae9f7f0c76/scripts/filter-barcodes.py \ 
- && pip3 install numpy pandas --break-system-packages
+# mischellous setup
+RUN R -e "install.packages('devtools', repos = 'http://cran.us.r-project.org')" 
+RUN cd mnt/software && git clone -b Multiplex_Major_Patch --single-branch https://github.com/GoekeLab/bambu.git
+RUN cd mnt/software && wget https://raw.githubusercontent.com/DavidsonGroup/flexiplex/main/scripts/flexiplex_filter/main.py \ 
+&& pip3 install numpy==1.26.4 pandas --break-system-packages
 
 RUN cd mnt/software/bambu && chmod 777 DESCRIPTION
+RUN R -e "library(devtools); load_all('/mnt/software/bambu')"
+
+# install jaffa 
+RUN cd mnt/software && wget https://github.com/Oshlack/JAFFA/releases/download/version-2.3/JAFFA-version-2.3.tar.gz \
+ && tar -xvf JAFFA-version-2.3.tar.gz && rm JAFFA-version-2.3.tar.gz && cd JAFFA-version-2.3 $$ ./install_linux64.sh
 
-RUN apt-get install -y libopenblas-dev
+#RUN apt-get install -y libopenblas-dev
 
 # environment variables 
 ENV PATH=$PATH:/mnt/software/flexiplex-1.01:/mnt/software/minimap2:/mnt/software/samtools-1.18:/mnt/software/htslib-1.18:/mnt/software/bambu
+ENV R_LIBS_USER="/usr/local/lib/R/site-library"    
+