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Commit e0c5a8d0 authored by dchalopi's avatar dchalopi
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change dockerfile with brian Haas dockerfile from Trinity git

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src/docker_modules/Trinity/2.6.6/Dockerfile
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FROM ubuntu:18.04
MAINTAINER Domitille Chalopin
FROM ubuntu:16.04
MAINTAINER bhaas@broadinstitute.org
ENV TRINITY_VERSION=2.6.6
ENV TRINITY_CO="06f284a"
ENV BOWTIE2_VERSION=2.3.4.1
ENV PACKAGES bowtie2=${BOWTIE2_VERSION}* \
ENV SALMON_VERSION=0.7.2
ENV PACKAGES curl=7.58.0* \
ca-certificates=20180409
RUN apt-get update && apt-get install -y gcc g++ perl python automake make \
wget git curl libdb-dev \
zlib1g-dev bzip2 libncurses5-dev \
texlive-latex-base \
default-jre \
python-pip python-dev \
gfortran \
build-essential libghc-zlib-dev libncurses-dev libbz2-dev liblzma-dev libpcre3-dev libxml2-dev \
libblas-dev gfortran git unzip ftp libzmq3-dev nano ftp fort77 libreadline-dev \
libcurl4-openssl-dev libx11-dev libxt-dev \
x11-common libcairo2-dev libpng12-dev libreadline6-dev libjpeg8-dev pkg-config libtbb-dev \
&& apt-get clean
RUN curl -L https://cpanmin.us | perl - App::cpanminus
RUN cpanm install DB_File
RUN cpanm install URI::Escape
## set up tool config and deployment area:
ENV SRC /usr/local/src
ENV BIN /usr/local/bin
#####
# Install R
WORKDIR $SRC
ENV R_VERSION=R-3.4.1
RUN curl https://cran.r-project.org/src/base/R-3/$R_VERSION.tar.gz -o $R_VERSION.tar.gz && \
tar xvf $R_VERSION.tar.gz && \
cd $R_VERSION && \
./configure && make && make install
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLite("tidyverse", dep = TRUE)'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLite("edgeR", dep = TRUE)'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLite("DESeq2", dep = TRUE)'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLite("ape", dep = TRUE)'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLite("ctc", dep = TRUE)'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLite("gplots", dep = TRUE)'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLite("Biobase", dep = TRUE)'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLite("qvalue", dep = TRUE)'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLite("goseq", dep = TRUE)'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLite("Glimma", dep = TRUE)'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLite("ROTS", dep = TRUE)'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLite("GOplot", dep = TRUE)'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLite("argparse", dep = TRUE)'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLite("sm", dep = TRUE)'
RUN apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
## bowtie
WORKDIR $SRC
RUN wget https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.2.1.1/bowtie-1.2.1.1-linux-x86_64.zip/download -O bowtie-1.2.1.1-linux-x86_64.zip && \
unzip bowtie-1.2.1.1-linux-x86_64.zip && \
mv bowtie-1.2.1.1/bowtie* $BIN
RUN curl -k -L https://github.com/COMBINE-lab/salmon/releases/download/v${SALMON_VERSION}/Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz -o Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz && \
tar xzf Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz && \
mv Salmon-${SALMON_VERSION}_linux_x86_64/bin/* /usr/bin/ && \
rm -Rf Salmon-${SALMON_VERSION}*
## RSEM
RUN mkdir /usr/local/lib/site_perl
WORKDIR $SRC
RUN wget https://github.com/deweylab/RSEM/archive/v1.3.0.tar.gz && \
tar xvf v1.3.0.tar.gz && \
cd RSEM-1.3.0 && \
make && \
cp rsem-* $BIN && \
cp rsem_perl_utils.pm /usr/local/lib/site_perl/ && \
cd ../ && rm -r RSEM-1.3.0
## Kallisto
WORKDIR $SRC
RUN wget https://github.com/pachterlab/kallisto/releases/download/v0.43.1/kallisto_linux-v0.43.1.tar.gz && \
tar xvf kallisto_linux-v0.43.1.tar.gz && \
mv kallisto_linux-v0.43.1/kallisto $BIN
## FASTQC
WORKDIR $SRC
RUN wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip && \
unzip fastqc_v0.11.5.zip && \
chmod 755 /usr/local/src/FastQC/fastqc && \
ln -s /usr/local/src/FastQC/fastqc $BIN/.
# blast
WORKDIR $SRC
RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.5.0/ncbi-blast-2.5.0+-x64-linux.tar.gz && \
tar xvf ncbi-blast-2.5.0+-x64-linux.tar.gz && \
cp ncbi-blast-2.5.0+/bin/* $BIN && \
rm -r ncbi-blast-2.5.0+
## Bowtie2
WORKDIR $SRC
RUN wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.1/bowtie2-2.3.4.1-linux-x86_64.zip/download -O bowtie2-2.3.4.1-linux-x86_64.zip && \
unzip bowtie2-2.3.4.1-linux-x86_64.zip && \
mv bowtie2-2.3.4.1-linux-x86_64/bowtie2* $BIN && \
rm *.zip && \
rm -r bowtie2-2.3.4.1-linux-x86_64
## Samtools
RUN wget https://github.com/samtools/samtools/releases/download/1.7/samtools-1.7.tar.bz2 && \
tar xvf samtools-1.7.tar.bz2 && \
cd samtools-1.7/ && \
./configure && make && make install
## Jellyfish
RUN wget https://github.com/gmarcais/Jellyfish/releases/download/v2.2.7/jellyfish-2.2.7.tar.gz && \
tar xvf jellyfish-2.2.7.tar.gz && \
cd jellyfish-2.2.7/ && \
./configure && make && make install
tar xvf jellyfish-2.2.7.tar.gz && \
cd jellyfish-2.2.7/ && \
./configure && make && make install
## Salmon
WORKDIR $SRC
RUN wget https://github.com/COMBINE-lab/salmon/releases/download/v0.9.1/Salmon-0.9.1_linux_x86_64.tar.gz && \
tar xvf Salmon-0.9.1_linux_x86_64.tar.gz && \
ln -s $SRC/Salmon-latest_linux_x86_64/bin/salmon $BIN/.
ENV LD_LIBRARY_PATH=/usr/local/lib
RUN pip install numpy
##########
## Trinity
WORKDIR $SRC
ENV TRINITY_VERSION="2.6.6"
ENV TRINITY_CO="06f284a"
WORKDIR $SRC
RUN git clone https://github.com/trinityrnaseq/trinityrnaseq.git && \
cd trinityrnaseq && \
git checkout $TRINITY_CO && \
make && make plugins && \
make install && \
cd ../ && rm -r trinityrnaseq
cd ../ && rm -r trinityrnaseq
ENV TRINITY_HOME /usr/local/bin/trinityrnaseq
ENV PATH=${TRINITY_HOME}:${PATH}
COPY Dockerfile $SRC/Dockerfile.$TRINITY_VERSION
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLite("fastcluster", dep = TRUE)'
## patch the RSEM install... need convert-sam-for-rsem too!
WORKDIR $SRC
RUN wget https://github.com/deweylab/RSEM/archive/v1.3.0.tar.gz && \
tar xvf v1.3.0.tar.gz && \
cd RSEM-1.3.0 && \
make && \
cp rsem-* $BIN && \
cp convert-sam-for-rsem $BIN && \
cp rsem_perl_utils.pm /usr/local/lib/site_perl/ && \
cd ../ && rm -r RSEM-1.3.0
# adding multiqc
RUN pip install git+https://github.com/ewels/MultiQC.git
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