no message

Author: Jan Winter

docker/Dockerfile

@@ -2,9 +2,7 @@ FROM rocker/r-ver:3.4.3
 
 MAINTAINER Jan Winter "[email protected]"
 
-#### things we need for the crispranalyzer package
-#### and for the crispr reannotator
-#### and another deb pkgs we later need for the R libraries to compile or run
+#### LINUX DEPENDENCIES
 RUN apt-get update && apt-get install -y  \
     wget \
     sudo \
@@ -26,37 +24,39 @@ RUN apt-get update && apt-get install -y  \
     htop \
     ghostscript \
     nginx \
-    libtbb2
+    libtbb2 \
+    libmariadbclient-dev
 
-# again some more things we need to run the crispranalyzer package
+# Add TEX for report and R Markdown
 RUN apt-get update && apt-get -y --no-install-recommends \
    install texlive texlive-xetex
 
 # install the shiny server debian package from r-studio
 RUN wget https://download3.rstudio.org/ubuntu-12.04/x86_64/shiny-server-1.5.3.838-amd64.deb -P /tmp/
-#COPY ./shiny-server-1.5.2.837-amd64.deb /tmp/ss.deb
 RUN gdebi -n /tmp/shiny-server-1.5.3.838-amd64.deb && \
     rm -f /tmp/shiny-server-1.5.3.838-amd64.deb
 
 COPY ./shiny-server.sh /usr/bin/shiny-server.sh
 RUN chmod +x /usr/bin/shiny-server.sh
 
+#### R PACKAGES
 
-# now to the R part...
-
-
-# first we need devtools for all the installation of all further packages
+# First we need devtools for all the installation of all further packages
 RUN R -e 'install.packages("devtools", repos = "http://cloud.r-project.org/")'
 
-# install all the packages we need from cran, bioconductor and github
+# install all the packages we need from CRAN, Bioconductor and GitHub
 
+RUN R -e 'devtools::install_version("RCurl", repos = "http://cloud.r-project.org/")'
+RUN R -e 'devtools::install_version("XML", repos = "http://cloud.r-project.org/")'
 RUN R -e 'source("http://bioconductor.org/biocLite.R");biocLite()'
+RUN R -e 'source("http://bioconductor.org/biocLite.R");biocLite("BiocParallel")'
+RUN R -e 'source("http://bioconductor.org/biocLite.R");biocLite("rtracklayer")'
+
 # We have to retrieve thise package as it is not available anymore, but required by some packages
 RUN wget http://www.omegahat.net/XMLRPC/XMLRPC_0.3-0.tar.gz -P /tmp/
 RUN R -e 'install.packages("/tmp/XMLRPC_0.3-0.tar.gz", repos = NULL, type="source")'
+
 RUN R -e 'source("http://bioconductor.org/biocLite.R");biocLite("RCytoscape")'
-RUN R -e 'source("http://bioconductor.org/biocLite.R");biocLite("BiocParallel")'
-RUN R -e 'source("http://bioconductor.org/biocLite.R");biocLite("rtracklayer")'
 RUN R -e 'source("http://bioconductor.org/biocLite.R");biocLite("RamiGO")'
 RUN R -e 'source("http://bioconductor.org/biocLite.R");biocLite("BiocGenerics")'
 RUN R -e 'source("http://bioconductor.org/biocLite.R");biocLite("limma")'
@@ -74,34 +74,28 @@ RUN R -e 'source("http://bioconductor.org/biocLite.R");biocLite("Gviz")'
 RUN R -e 'source("http://bioconductor.org/biocLite.R");biocLite("STRINGdb")'
 RUN R -e 'devtools::install_version("dplyr", version = "0.7.4", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_github("jyyu/ScreenBEAM", ref = "d6204b3")'
-#RUN R -e 'devtools::install_version("readr", version = "1.1.1", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("shinydashboard", version = "0.5.3", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("jsonlite", version = "1.1", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("shinyBS", version = "0.61", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("highcharter", version = "0.5.0", repos = "http://cloud.r-project.org/")'
-#RUN R -e 'devtools::install_github("jbkunst/highcharter", ref = "cc5f1e0157c50fc67233bc1bad6c3ad906d418c8")'
 RUN R -e 'devtools::install_version("seqinr", version = "3.3-6", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("openxlsx", version = "4.0.17", repos = "http://cloud.r-project.org/")'
-#RUN R -e 'devtools::install_github("awalker89/openxlsx", ref = "6d0fed9")'
 RUN R -e 'devtools::install_version("caTools", version = "1.17.1", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("reshape2", version = "1.4.2", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("MESS", version = "0.4-3", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("igraph", version = "1.0.1", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("data.table", version = "1.10.4", repos = "http://cloud.r-project.org/")'
-RUN R -e 'devtools::install_github("jimhester/gmailr", ref = "59dac01")'
+RUN R -e 'devtools::install_github("jimhester/gmailr", ref = "d5ee3c2")' #OLD d5ee3c2 # new 59dac01
 RUN R -e 'devtools::install_version("d3heatmap", version = "0.6.1.1", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("DEoptim", version = "2.2-3", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("httr", version = "1.3.1", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("sgRSEA", version = "0.1", repos = "http://cloud.r-project.org/")'
-#RUN R -e 'devtools::install_version("plyr", version = "1.8.4", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("VennDiagram", version = "1.6.17", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("tidyverse", version = "1.2.1", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("htmltools", version = "0.3.6", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("DT", version = "0.2", repos = "http://cloud.r-project.org/")'
-#RUN R -e 'devtools::install_version("tidyr", version = "0.6.3", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("sm", version = "2.2-5.4", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("shinyjs", version = "0.9.1", repos = "http://cloud.r-project.org/")'
-#RUN R -e 'devtools::install_version("ggplot2", version = "2.2.1", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("markdown", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("knitr", version = "1.16", repos = "http://cloud.r-project.org/")'
 RUN R -e 'devtools::install_version("shiny", version = "1.0.5", repos = "http://cloud.r-project.org/")'
@@ -114,8 +108,7 @@ RUN R -e 'devtools::install_version("shinyWidgets", repos = "http://cloud.r-proj
 # cleaning up downloaded deb packages for keeping clean our docker image
 RUN apt-get -qq clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-# now install the reannotate-crispr PERL package
-# for CPAN to auto say yes to every question
+# now install the reannotate-crispr PERL package, which is based on the CRISPR LIBRARY DESIGNER
 
 ENV PERL_MM_USE_DEFAULT=1
 RUN perl -MCPAN -e 'CPAN::Shell->install("Bundle::CPAN")'
@@ -138,30 +131,29 @@ RUN perl -MCPAN -e 'CPAN::Shell->install("Getopt::Long")'
 RUN perl -MCPAN -e 'CPAN::Shell->install("File::Grep")'
 RUN perl -MCPAN -e 'CPAN::Shell->install("Text::Wrap")'
 RUN perl -MCPAN -e 'CPAN::Shell->install("Unix::Processors")'
+
 RUN git clone https://github.com/boutroslab/Supplemental-Material.git /tmp/Supplemental-Material
 RUN cp -r /tmp/Supplemental-Material/Rauscher\&Heigwer_2016/crispr-reannotation /opt/
 RUN chmod +x /opt/crispr-reannotation/reannotate_crispr.pl
 env PATH /opt/crispr-reannotation:$PATH
 RUN rm -rf /tmp/Supplemental-Material
-# install intervaltree...another dependency for the crispr reannotator
+
+# install intervaltree...another dependency for  reannotate-crispr
 RUN cd /opt/crispr-reannotation/depends/Set-IntervalTree-0.10-OD; perl Makefile.PL; make; make test && make install
 
 # Install Python NumPy and SciPy required for BAGEL
 RUN apt-get update && apt-get install -y python-numpy python-scipy python-sympy
 
-## Install Software packages and download them
+## Install Software packages, Download and Install them
 
-# install software package bowtie2 which has a difficult license and therefore cannot be packaged or shipped in a docker image
-# TODO: check if this can be used in open source packages at all
+# Bowtie 2
 RUN wget http://www.dkfz.de/signaling/crispranalyzer/bowtie2-2.2.9-linux-x86_64.zip -P /tmp/
-#COPY ./bowtie2-2.3.2-linux-x86_64.zip /tmp/
 RUN unzip /tmp/bowtie2-2.2.9-linux-x86_64.zip -d /opt
 ENV PATH=/opt/bowtie2-2.2.9:$PATH
 RUN echo 'export PATH=/opt/bowtie2-2.2.9/:$PATH' >> /etc/profile
 
-# install bowtie
+# Bowtie 1
 RUN wget http://www.dkfz.de/signaling/crispranalyzer/bowtie-1.2.1.1-linux-x86_64.zip -P /tmp/
-#COPY ./bowtie-1.2-linux-legacy-x86_64.zip /tmp/
 RUN unzip /tmp/bowtie-1.2.1.1-linux-x86_64.zip -d /opt
 ENV PATH=/opt/bowtie-1.2.1.1/:$PATH
 RUN echo 'export PATH=/opt/bowtie-1.2.1.1/:$PATH' >> /etc/profile
@@ -173,9 +165,10 @@ RUN wget http://www.dkfz.de/signaling/crispranalyzer/mageck-0.5.5.tar.gz -P /tmp
 RUN cd /tmp/; tar xvf ./mageck-0.5.5.tar.gz; cd /tmp/mageck-0.5.5; python setup.py install
 RUN rm -rf /tmp/mageck-0.5.5 /tmp/mageck-0.5.5.tar.gz
 
+### RUST-based FASTQ Extraction and SAM Extraction
+# PERL-based backup variants are included in CRISPRAnalyzeR source
 
-# INSTALL RUST-based FASTQ-Extraction and SAM-Extraction
-# install RUST compiler
+# Install RUST compiler
 RUN \
     curl https://sh.rustup.rs > /tmp/sh.rustup.rs && \
          chmod +x /tmp/sh.rustup.rs && \
@@ -184,7 +177,7 @@ RUN \
 
 ENV PATH=/root/.cargo/bin:$PATH
 
-# compile CRISPRAnalyzer mapper and extractor
+# compile CRISPRAnalyzer mapper and extractor from source
 RUN \
      git clone https://github.com/OliPelz/fastq_extractor_proof_of_principle.git \
      /tmp/crispranalyzer-rust-tools
@@ -208,7 +201,7 @@ RUN \
 ENV PATH=/opt/crispranalyzer-tools:$PATH 
 RUN echo 'export PATH=/opt/crispranalyzer-tools/:$PATH' >> /etc/profile
 
-##### end of RUST CODE
+### CRISPRAnalyzeR FROM SOURCE
 
 ## Now we add CRISPRAnalyzeR code directly from Github Repository
 ARG CACHEBUST=1