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Dockerfile tweaks for singularity support and download url updates #5

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Dockerfile tweaks for singularity support and download url updates #5

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de06730
Fix Dockerfile download urls
javh Apr 4, 2019
fbebb7e
Fix typo in Dockerfile
javh Apr 4, 2019
226f6c1
Dockerfile cleanup
javh Apr 4, 2019
9842278
Minor
javh Apr 4, 2019
14d8010
Minor
javh Apr 4, 2019
d693cf6
Change nextflow install method in Dockerfile
javh Apr 4, 2019
af10c41
Run nextflow
javh Apr 4, 2019
1f62b9b
More nextflow install tweaks
javh Apr 5, 2019
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63 changes: 28 additions & 35 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,54 +1,47 @@
FROM ubuntu:latest
MAINTAINER Dave Roe <droe@nmdp.org>

# install stuff
RUN apt-get update && apt-get install -qyy curl git make vim cmake \
# apt stuff
RUN apt-get update \
&& apt-get install -qyy curl git make vim cmake \
gcc g++ unzip subversion gzip openjdk-8-jdk openjdk-8-doc groovy wget \
zlib1g-dev gnuplot lynx maven \
bzip2 libbz2-dev liblzma-dev libncurses5-dev libncursesw5-dev \
&& apt-get clean \
&& cd /opt && git clone https://github.com/droe-nmdp/kpi.git \
&& mkdir -p /opt/kpi/raw \
&& mkdir -p /opt/bin \
&& cd /opt/bin && curl -fsSL get.nextflow.io | /bin/bash \
&& cd /opt/bin && wget https://github.com/refresh-bio/KMC/releases/download/v3.0.0/KMC3.linux.tar.gz \
&& gunzip KMC3.linux.tar.gz && tar -xvf KMC3.linux.tar && rm -f KMC3.linux.tar \
# && cd /opt && wget https://sourceforge.net/projects/bbmap/files/latest/download \
# && mv download BBMap.tar && tar -xvzf BBMap.tar && rm BBMap.tar \
&& mkdir -p /opt/jars \
# && cd /opt && git clone https://github.com/marbl/canu.git && cd canu/src \
# && make -j 2 \
&& cd /opt/jars \
&& wget http://mirrors.sorengard.com/apache//commons/math/binaries/commons-math3-3.6.1-bin.tar.gz \
&& gunzip commons-math3-3.6.1-bin.tar.gz && tar -xvf commons-math3-3.6.1-bin.tar \
&& rm -f /opt/jars/commons-math3-3.6.1-bin.tar \
# && cd /opt/ && wget https://github.com/samtools/htslib/releases/download/1.8/htslib-1.8.tar.bz2 \
# && tar -xjvf htslib-1.8.tar.bz2 && cd htslib-1.8 && make && make install \
# && cd /opt/ && wget https://github.com/samtools/bcftools/releases/download/1.8/bcftools-1.8.tar.bz2 \
# && tar -xjvf bcftools-1.8.tar.bz2 && cd bcftools-1.8 && make && make install \
# && cd /opt/ && wget https://github.com/samtools/samtools/releases/download/1.8/samtools-1.8.tar.bz2 \
# && bunzip2 samtools-1.8.tar.bz2 \
# && tar -xvf samtools-1.8.tar && cd samtools-1.8 && make && make install \
# && rm -f /opt/*.bz2 /opt/*.tar* \
bzip2 libbz2-dev liblzma-dev libncurses5-dev libncursesw5-dev \
&& apt-get clean

# install stuff
ENV TMPDIR /tmp
RUN cd /opt \
&& git clone https://github.com/droe-nmdp/kpi.git \
&& mkdir -p /opt/kpi/raw /opt/bin \
&& cd /opt/bin \
&& wget -qO- http://get.nextflow.io | bash \
&& sed -i s/"curl -fsSL"/"curl -fsSLk"/ /opt/bin/nextflow \
&& chmod 755 /opt/bin/nextflow \
&& /opt/bin/nextflow \
&& wget https://github.com/refresh-bio/KMC/releases/download/v3.0.0/KMC3.linux.tar.gz \
&& tar -zxvf KMC3.linux.tar.gz \
&& rm -f KMC3.linux.tar.gz \
&& mkdir -p /opt/jars \
&& cd /opt/jars \
&& wget http://www.apache.org/dist/commons/math/binaries/commons-math3-3.6.1-bin.tar.gz \
&& tar -zxvf commons-math3-3.6.1-bin.tar.gz \
&& rm -f /opt/jars/commons-math3-3.6.1-bin.tar.gz

# google guava
ENV JAVA_HOME /usr/lib/jvm/java-8-openjdk-amd64/
RUN cd /opt && git clone https://github.com/google/guava.git \
&& cd guava/guava/ && mvn install
RUN cd /opt \
&& git clone https://github.com/google/guava.git \
&& cd guava/guava \
&& mvn install

# env vars
ENV NXF_OPTS "-Xms4G -Xmx20G"
ENV LD_LIBRARY_PATH /opt/lib:$LD_LIBRARY_PATH

# kpi source
RUN mkdir -p /opt/kpi/input /opt/kpi/output /opt/kpi/src
ENV PATH /opt/bin:$PATH
ENV PATH /opt/kpi:$PATH
ENV PATH /opt/kpi/src:$PATH
ENV PATH /opt/bbmap:$PATH
ENV PATH /opt/canu/Linux-amd64/bin:$PATH
ENV PATH /opt/bin:/opt/kpi:/opt/kpi/src:/opt/bbmap:/opt/canu/Linux-amd64/bin:$PATH
ENV CLASSPATH /opt/guava/guava/target/guava-HEAD-jre-SNAPSHOT.jar:/opt/jars/commons-math3-3.6.1/commons-math3-3.6.1.jar:$CLASSPATH

#CMD ["/bin/bash"]
CMD ["/opt/kpi/main.nf"]