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Dockerfile
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FROM continuumio/anaconda
MAINTAINER Brian Schlining <[email protected]>
# Install Qiime
RUN conda create -n qiime1 python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda
# Install JDK
RUN apt-get update && \
apt-get -y install default-jdk
# Install blast
RUN mkdir -p /opt/temp/ && \
cd /opt/temp && \
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.22/ncbi-blast-2.2.22+-x64-linux.tar.gz && \
tar -xzvf ncbi-blast-2.2.22+-x64-linux.tar.gz -C /opt && \
rm ncbi-blast-2.2.22+-x64-linux.tar.gz
RUN apt-get -y install unzip
# Install RDP Classifier
RUN cd /opt/temp && \
wget -O rdp.zip "https://downloads.sourceforge.net/project/rdp-classifier/rdp-classifier/rdp_classifier_2.2.zip?r=http%3A%2F%2Fqiime.org%2Finstall%2Falternative.html&ts=1489181761&use_mirror=svwh" && \
unzip rdp.zip -d /opt && \
rm rdp.zip
# Install ChimeraSlayer
RUN cd /opt/temp && \
wget -O microbio.tar.gz "https://downloads.sourceforge.net/project/microbiomeutil/__OLD_VERSIONS/microbiomeutil_2010-04-29.tar.gz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fmicrobiomeutil%2Ffiles%2F__OLD_VERSIONS%2F&ts=1489182721&use_mirror=svwh" && \
tar -xzvf microbio.tar.gz -C /opt && \
rm microbio.tar.gz
# Install Mothur
RUN apt-get -y install build-essential gfortran
# Install muscle
RUN cd /opt/temp && \
wget http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz && \
mkdir -p /opt/muscle && \
tar -xzvf muscle3.8.31_i86linux64.tar.gz -C /opt/muscle && \
rm muscle3.8.31_i86linux64.tar.gz
# RUN cd /opt/temp && \
# wget http://www.mothur.org/w/images/6/6d/Mothur.1.25.0.zip && \
# unzip Mothur.1.25.0.zip -d /opt/temp && \
# cd /opt/temp/Mothur.source && \
# make && \
# rm Mothur.1.25.0.zip && \
# mkdir /opt/mothur && \
# cp /opt/temp/Mothur.source/mothor /opt/mothur && \
# cp /opt/temp/Mothur.source/uchime /opt/mothur && \
# rm -rf /opt/temp/Mothor.source && \
# cd /opt/temp && \
# rm Mothur.1.25.0.zip
RUN cd /opt/temp && \
wget http://static.davidsoergel.com/rtax-0.984.tgz && \
mkdir -p /opt/rtax && \
tar -xzvf rtax-0.984.tgz -C /opt/rtax && \
rm rtax-0.984.tgz
# Install swarm
RUN cd /opt/temp && \
wget -O swarm.tar.gz https://github.com/torognes/swarm/archive/1.2.19.tar.gz && \
tar -xzvf swarm.tar.gz && \
cd swarm-1.2.19 && \
make && \
mkdir -p /opt/swarm && \
cp swarm /opt/swarm && \
cd /opt/temp && \
rm -rf swarm-1.2.19 && \
rm swarm.tar.gz
# Install sumatra
# RUN cd /opt/temp && \
# wget ftp://ftp.microbio.me/pub/QIIME-v1.9.0-dependencies/suma_package_V_1.0.00.tar.gz && \
# tar -xzvf suma_package_V_1.0.00.tar.gz && \
# cd suma_package_V_1.0.00/sumatra && \
# make
RUN apt-get -y install r-base r-base-dev
#RUN apt-get -y remove build-essential unzip gfortran
ENV RDP_JAR_PATH="/opt/rdp_classifier_2.2/rdp_classifier-2.2.jar"
ENV PATH="/opt/ncbi-blast-2.2.22+/bin:/opt/mothur:/opt/muscle:/opt/rtax:/opt/rtax/greengenes:/opt/microbiomeutil_2010-04-29/ChimeraSlayer:/opt/swarm:${PATH}"
CMD [ "/bin/bash" ]