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update to V 1.40
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Jan Winter committed Nov 2, 2017
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182 changes: 111 additions & 71 deletions docker/Dockerfile
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@@ -1,6 +1,6 @@
FROM rocker/r-ver:3.3.2
FROM rocker/r-ver:3.4.1

MAINTAINER Oliver Pelz "o.pelz@dkfz.de"
MAINTAINER Jan Winter "jan.winter@dkfz.de"

#### things we need for the crispranalyzer package
#### and for the crispr reannotator
Expand All @@ -23,22 +23,25 @@ RUN apt-get update && apt-get install -y \
curl \
libssl-dev \
libtiff5-dev \
htop

RUN apt-get update && apt-get install -y ghostscript
htop \
ghostscript \
nginx \
libtbb2

# again some more things we need to run the crispranalyzer package
RUN apt-get update && apt-get -y --no-install-recommends \
install texlive texlive-xetex

# install the shiny server debian package from r-studio
COPY ./shiny-server-1.5.2.837-amd64.deb /tmp/ss.deb
RUN gdebi -n /tmp/ss.deb && \
rm -f /tmp/ss.deb
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


# now to the R part...


Expand All @@ -63,16 +66,16 @@ RUN R -e 'source("http://bioconductor.org/biocLite.R");biocLite("DESeq2")'
RUN R -e 'source("http://bioconductor.org/biocLite.R");biocLite("edgeR")'
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 = "0.5.0", repos = "http://cloud.r-project.org/")'
RUN R -e 'devtools::install_version("dplyr", version = "0.7.2", repos = "http://cloud.r-project.org/")'
RUN R -e 'devtools::install_github("jyyu/ScreenBEAM", ref = "d6204b3")'
RUN R -e 'devtools::install_version("readr", version = "1.0.0", repos = "http://cloud.r-project.org/")'
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("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 = "4.0.0", 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/")'
Expand All @@ -86,19 +89,19 @@ RUN R -e 'devtools::install_version("httr", version = "1.2.1", repos = "http://c
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 = "1.0.0", repos = "http://cloud.r-project.org/")'
RUN R -e 'devtools::install_version("htmltools", version = "0.3.5", repos = "http://cloud.r-project.org/")'
RUN R -e 'devtools::install_version("tidyverse", version = "1.1.1", 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 = "0.6.1", 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", repos = "http://cloud.r-project.org/")'
RUN R -e 'devtools::install_version("ggplot2", version = "2.2.0", 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 = "1.15.1", repos = "http://cloud.r-project.org/")'
RUN R -e 'devtools::install_version("shiny", version = "1.0.2", repos = "http://cloud.r-project.org/")'
RUN R -e 'devtools::install_version("bookdown", version = "0.3", 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 = "1.0.4", repos = "http://cloud.r-project.org/")'
RUN R -e 'devtools::install_version("bookdown", version = "0.4", repos = "http://cloud.r-project.org/")'
RUN R -e 'devtools::install_version("R.utils", version = "2.5.0", repos = "http://cloud.r-project.org/")'
RUN R -e 'devtools::install_version("htmltools", version = "0.3.5", repos = "http://cloud.r-project.org/")'
RUN R -e 'devtools::install_version("shinyWidgets", repos = "http://cloud.r-project.org/")'



Expand All @@ -107,8 +110,10 @@ 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

ENV PERL_MM_USE_DEFAULT=1
RUN perl -MCPAN -e 'CPAN::Shell->install("Bundle::CPAN")'

# now install all the modules we need for crispr reannotator
RUN perl -MCPAN -e 'CPAN::Shell->install("Bio::DB::Fasta")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Bio::SeqIO")'
Expand All @@ -128,7 +133,7 @@ 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/crispr-reannotation /opt/
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
Expand All @@ -138,98 +143,133 @@ RUN cd /opt/crispr-reannotation/depends/Set-IntervalTree-0.10-OD; perl Makefile.
# Install Python NumPy and SciPy required for BAGEL
RUN apt-get update && apt-get install -y python-numpy python-scipy python-sympy

# install software package bowtie 2 which has a difficult license and therefore cannot be packaged or shipped in a docker image
## Install Software packages and download 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
COPY ./bowtie2-2.2.9-linux-x86_64.zip /tmp/
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:$PATH
ENV PATH=/opt/bowtie2-2.2.9:$PATH
RUN echo 'export PATH=/opt/bowtie2-2.2.9/:$PATH' >> /etc/profile

# install bowtie
COPY ./bowtie-1.2-linux-legacy-x86_64.zip /tmp/
RUN unzip /tmp/bowtie-1.2-linux-legacy-x86_64.zip -d /opt
RUN echo 'export PATH=/opt/bowtie-1.2-legacy/:$PATH' >> /etc/profile
RUN wget http://www.dkfz.de/signaling/crispranalyzer/bowtie-1.2.1.1-linux-x86_64.zip -P /tmp/
#COPY ./bowtie-1.2-linux-legacy-x86_64.zip /tmp/
RUN unzip /tmp/bowtie-1.2.1.1-linux-x86_64.zip -d /opt
ENV PATH=/opt/bowtie-1.2.1.1/:$PATH
RUN echo 'export PATH=/opt/bowtie-1.2.1.1/:$PATH' >> /etc/profile


# install MAGeCK from Sourceforge
COPY ./mageck-0.5.5.tar.gz /tmp/
RUN wget http://www.dkfz.de/signaling/crispranalyzer/mageck-0.5.5.tar.gz -P /tmp/
#COPY ./mageck-0.5.5.tar.gz /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

# Cloning CRISPRAnalyzeR
RUN git clone git@github.com:boutroslab/CRISPRAnalyzeR.git /tmp/

# Copy to the shiny-server
COPY /tmp/CRISPRAnalyzeR-master/source/ /srv/shiny-server/CRISPRAnalyzeR

# we will run crispranalyzer as user
RUN chown -R shiny:shiny /srv/shiny-server/CRISPRAnalyzeR



# add R profile options

RUN echo 'setwd("/srv/shiny-server/CRISPRAnalyzeR")' >> /usr/local/lib/R/etc/Rprofile.site
RUN echo 'options(download.file.method = "libcurl")' >> /usr/local/lib/R/etc/Rprofile.site


# BEGIN RUST CODE
# install RUST compiler with mapper and extractor components
# INSTALL RUST-based FASTQ-Extraction and SAM-Extraction
# install RUST compiler
RUN \
curl https://sh.rustup.rs > /tmp/sh.rustup.rs && \
chmod +x /tmp/sh.rustup.rs && \
/tmp/sh.rustup.rs -y && \
rm /tmp/sh.rustup.rs

chmod +x /tmp/sh.rustup.rs && \
/tmp/sh.rustup.rs -y && \
rm /tmp/sh.rustup.rs
ENV PATH=/root/.cargo/bin:$PATH

# compile CRISPRAnalyzer mapper and extractor
RUN \
git clone https://github.com/OliPelz/fastq_extractor_proof_of_principle.git \
/tmp/crispranalyzer-rust-tools
git clone https://github.com/OliPelz/fastq_extractor_proof_of_principle.git \
/tmp/crispranalyzer-rust-tools
# target dir for compiled executables
RUN \
mkdir -p /opt/crispranalyzer-tools

mkdir -p /opt/crispranalyzer-tools
# source cargo env file so we can use it
RUN \
cd /tmp/crispranalyzer-rust-tools/extractor_in_RUST/fastq_parser && \
cargo build --release && \
cp ./target/release/fastq_parser /opt/crispranalyzer-tools/ && \
chmod +x /opt/crispranalyzer-tools/fastq_parser

cd /tmp/crispranalyzer-rust-tools/extractor_in_RUST/fastq_parser && \
cargo build --release && \
cp ./target/release/fastq_parser /opt/crispranalyzer-tools/ && \
chmod +x /opt/crispranalyzer-tools/fastq_parser
RUN \
cd /tmp/crispranalyzer-rust-tools/sam_mapper_in_RUST/sam_mapper/ && \
cargo build --release && \
cp ./target/release/sam_mapper /opt/crispranalyzer-tools/ && \
chmod +x /opt/crispranalyzer-tools/sam_mapper

cd /tmp/crispranalyzer-rust-tools/sam_mapper_in_RUST/sam_mapper/ && \
cargo build --release && \
cp ./target/release/sam_mapper /opt/crispranalyzer-tools/ && \
chmod +x /opt/crispranalyzer-tools/sam_mapper

ENV PATH=/opt/crispranalyzer-tools:$PATH
ENV PATH=/opt/crispranalyzer-tools:$PATH
RUN echo 'export PATH=/opt/crispranalyzer-tools/:$PATH' >> /etc/profile

##### end of RUST CODE

## Now we add CRISPRAnalyzeR code directly from Github Repository
ARG CACHEBUST=1
# We use CACHEBUST=1 arg to FORCE docker to start from here without caching
# This can be achieved by a build argument as described here : https://github.com/moby/moby/issues/1996#issuecomment-185872769
# docker build --rm --label crispranalyzer --build-arg CACHEBUST=$(date +%s) -t boutroslab/crispranalyzer:latest

# install CRISPRAnalyzeR
RUN mkdir /srv/shiny-server/CRISPRAnalyzeR
RUN git clone https://github.com/boutroslab/CRISPRAnalyzeR.git /tmp/CRISPRAnalyzeR
RUN cp -r /tmp/CRISPRAnalyzeR/source/* /srv/shiny-server/CRISPRAnalyzeR/

# Generate Directories
RUN mkdir /srv/shiny-server/CRISPRAnalyzeR2 \
/srv/shiny-server/CRISPRAnalyzeR3 \
/srv/shiny-server/CRISPRAnalyzeR4 \
/srv/shiny-server/CRISPRAnalyzeR5

RUN cp -r /srv/shiny-server/CRISPRAnalyzeR/multiuser/* /srv/shiny-server/CRISPRAnalyzeR2 && \
cp -r /srv/shiny-server/CRISPRAnalyzeR/multiuser/* /srv/shiny-server/CRISPRAnalyzeR3 && \
cp -r /srv/shiny-server/CRISPRAnalyzeR/multiuser/* /srv/shiny-server/CRISPRAnalyzeR4 && \
cp -r /srv/shiny-server/CRISPRAnalyzeR/multiuser/* /srv/shiny-server/CRISPRAnalyzeR5

# take CSS and web files
RUN cp -r /srv/shiny-server/CRISPRAnalyzeR/www /srv/shiny-server/CRISPRAnalyzeR2 && \
cp -r /srv/shiny-server/CRISPRAnalyzeR/www /srv/shiny-server/CRISPRAnalyzeR3 && \
cp -r /srv/shiny-server/CRISPRAnalyzeR/www /srv/shiny-server/CRISPRAnalyzeR4 && \
cp -r /srv/shiny-server/CRISPRAnalyzeR/www /srv/shiny-server/CRISPRAnalyzeR5

# we will run crispranalyzer as user shiny, so not as root!
RUN chown -R shiny:shiny /srv/shiny-server/CRISPRAnalyzeR
RUN chown -R shiny:shiny /srv/shiny-server/CRISPRAnalyzeR/userdata


# add R profile options
RUN echo 'setwd("/srv/shiny-server/CRISPRAnalyzeR")' >> /usr/local/lib/R/etc/Rprofile.site
RUN echo 'options(download.file.method = "libcurl")' >> /usr/local/lib/R/etc/Rprofile.site


# NGINX (copy the config)
COPY nginx.conf /etc/nginx/nginx.conf

# shiny-server.conf
# shiny-server.conf will be automatically created with default values, which is totally fine

# Copy docker entrypoint and shiny-server.sh, in which is stated how we start shiny and nginx
# Moreover we copy the index.html to do a forward of the base directory to ./CRISPRAnalyzeR/, from which NGINX will do the rest
COPY docker-entrypoint.sh /
COPY index.html /srv/shiny-server
RUN chmod +x /docker-entrypoint.sh
RUN chmod +x /srv/shiny-server/index.html

EXPOSE 3838
EXPOSE 8000

# Add ENV for KiteMatic
# this ENV vars are required to be able to change these settings using Kitematic

ENV websockets_behind_proxy=FALSE
ENV verbose_logfiles=TRUE
ENV verbose_logfiles=FALSE
ENV COSMIC_database="CosmicMutantExport.tsv"
ENV EnrichR_URL="http://amp.pharm.mssm.edu/Enrichr/
ENV EnrichR_URL="http://amp.pharm.mssm.edu/Enrichr/"
ENV EnrichR=TRUE
ENV bowtie_threads=2
ENV proxy_url=
ENV proxy_port=
ENV max_upload=4096
ENV downloadlogs=TRUE

ENTRYPOINT ["/docker-entrypoint.sh"]
# finally run
Expand Down
15 changes: 13 additions & 2 deletions docker/docker-entrypoint.sh
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Expand Up @@ -7,8 +7,6 @@ CRISPR_CFG=/srv/shiny-server/CRISPRAnalyzeR/config.r
# subs definition go here

# usage: key_value_to_cfg key value
# ie: file_env 'car_proxy_url' 'www-int2.dkfz-heidelberg.de'
# (will write the key/value pair car_proxy_url www-int2.dkfz-heidelberg.de
# to the crispranalyzer config file
# example: key_value_to_cfg "car.proxy" "'value'" "/srv/shiny-server/CRISPRAnalyzeR/config.r"
key_value_to_cfg() {
Expand Down Expand Up @@ -74,5 +72,18 @@ if [ "$1" = 'crispranalyzer' ]; then
echo "[CUSTOM] setting PROXY PORT"
key_value_to_cfg "car.proxy.port" "$proxy_port" "$CRISPR_CFG"
fi
if [ "$downloadlogs" ]; then
echo "[CUSTOM] setting Logs"
key_value_to_cfg "downloadlogs" "$downloadlogs" "$CRISPR_CFG"
fi
# Copy config.r to all copies
cp /srv/shiny-server/CRISPRAnalyzeR/config.r /srv/shiny-server/CRISPRAnalyzeR2/config.r
cp /srv/shiny-server/CRISPRAnalyzeR/config.r /srv/shiny-server/CRISPRAnalyzeR3/config.r
cp /srv/shiny-server/CRISPRAnalyzeR/config.r /srv/shiny-server/CRISPRAnalyzeR4/config.r
cp /srv/shiny-server/CRISPRAnalyzeR/config.r /srv/shiny-server/CRISPRAnalyzeR5/config.r

echo "Starting Shiny-Server"
echo "As a default, please navigate to http://localhost:8000/CRISPRAnalyzeR/ to access CRISPRAnalyzeR"
exec /usr/bin/shiny-server.sh
echo "Shiny-Server started"
fi
2 changes: 1 addition & 1 deletion docker/index.html
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@@ -1 +1 @@
<meta http-equiv="refresh" content="0; url=./CRISPRAnalyzeR" />
<meta http-equiv="refresh" content="0; url=./CRISPRAnalyzeR/" />

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