From e0c5a8d04443b46b3798eb2b1fe345fef4ba85ec Mon Sep 17 00:00:00 2001
From: dchalopi <domitille.chalopin@ens-lyon.fr>
Date: Wed, 20 Jun 2018 13:51:55 +0000
Subject: [PATCH] change dockerfile with brian Haas dockerfile from Trinity git
---
src/docker_modules/Trinity/2.6.6/Dockerfile | 201 ++++++++++++++++++--
1 file changed, 181 insertions(+), 20 deletions(-)
diff --git a/src/docker_modules/Trinity/2.6.6/Dockerfile b/src/docker_modules/Trinity/2.6.6/Dockerfile
index 2ec07ec..909a84e 100644
--- a/src/docker_modules/Trinity/2.6.6/Dockerfile
+++ b/src/docker_modules/Trinity/2.6.6/Dockerfile
@@ -1,35 +1,196 @@
-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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