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updating biscuit version, adding flexbar and picard to container #4

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merged 3 commits into from
Jan 28, 2021
Merged

updating biscuit version, adding flexbar and picard to container #4

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58e6f74
updating biscuit version, adding flexbar
chrisamiller Jan 13, 2021
39cd547
updating biscuit, adding picard and flexbar
chrisamiller Jan 13, 2021
9a68434
cleanup
chrisamiller Jan 27, 2021
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147 changes: 102 additions & 45 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,16 +1,54 @@
FROM zhouwanding/biscuit_v0.3.8
FROM ubuntu:latest
MAINTAINER "Chris Miller" <[email protected]>

####################
#Biscuit QC scripts#
####################
RUN cd /opt && \
git clone https://github.com/zwdzwd/biscuit.git
## Adding QC_scripts
ADD Bisulfite_QC_bisulfiteconversion.sh /opt/biscuit/scripts
ADD Bisulfite_QC_Coveragestats.sh /opt/biscuit/scripts
ADD Bisulfite_QC_CpGretentiondistribution.sh /opt/biscuit/scripts
ADD Bisulfite_QC_mappingsummary.sh /opt/biscuit/scripts
ARG DEBIAN_FRONTEND=noninteractive

RUN apt-get update -y && \
apt-get install \
build-essential \
bzip2 \
cmake \
default-jre \
g++ \
git \
libbz2-dev \
liblzma-dev \
libncurses5 \
libtbb2 \
libtbb-dev \
make \
ncurses-dev \
wget \
xz-utils \
zlib1g-dev -y

##################
# Biscuit 0.3.16 #
##################
RUN mkdir /opt/biscuit_binary && cd /opt/biscuit_binary && \
wget https://github.com/huishenlab/biscuit/releases/download/v0.3.16.20200420/biscuit_0_3_16_linux_amd64 && \
chmod +x /opt/biscuit_binary/biscuit_0_3_16_linux_amd64 && \
ln -s /opt/biscuit_binary/biscuit_0_3_16_linux_amd64 biscuit && \
ln -s /opt/biscuit_binary/biscuit_0_3_16_linux_amd64 /usr/bin/biscuit

###############
# Flexbar 3.5 #
###############

RUN mkdir -p /opt/flexbar/tmp \
&& cd /opt/flexbar/tmp \
&& wget https://github.com/seqan/flexbar/archive/v3.5.0.tar.gz \
&& wget https://github.com/seqan/seqan/releases/download/seqan-v2.4.0/seqan-library-2.4.0.tar.xz \
&& tar xzf v3.5.0.tar.gz \
&& tar xJf seqan-library-2.4.0.tar.xz \
&& mv seqan-library-2.4.0/include flexbar-3.5.0 \
&& cd flexbar-3.5.0 \
&& cmake . \
&& make \
&& cp flexbar /opt/flexbar/ \
&& cd / \
&& rm -rf /opt/flexbar/tmp


##############
#HTSlib 1.3.2#
Expand All @@ -25,6 +63,17 @@ RUN wget https://github.com/samtools/htslib/releases/download/1.3.2/htslib-1.3.2
make install && \
cp $HTSLIB_INSTALL_DIR/lib/libhts.so* /usr/lib/

#################
# Picard #
#################

RUN mkdir /opt/picard-2.18.1/ \
&& cd /tmp/ \
&& wget --no-check-certificate https://github.com/broadinstitute/picard/releases/download/2.18.1/picard.jar \
&& mv picard.jar /opt/picard-2.18.1/ \
&& ln -s /opt/picard-2.18.1 /opt/picard \
&& ln -s /opt/picard-2.18.1 /usr/picard

#################
#Sambamba v0.6.4#
#################
Expand All @@ -41,43 +90,51 @@ RUN mkdir /opt/sambamba/ \
#Samtools 1.3.1#
################
ENV SAMTOOLS_INSTALL_DIR=/opt/samtools

WORKDIR /tmp
RUN wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 && \
tar --bzip2 -xf samtools-1.3.1.tar.bz2

WORKDIR /tmp/samtools-1.3.1
RUN ./configure --with-htslib=$HTSLIB_INSTALL_DIR --prefix=$SAMTOOLS_INSTALL_DIR && \
RUN cd /tmp && wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 && \
tar --bzip2 -xf samtools-1.3.1.tar.bz2 && cd /tmp/samtools-1.3.1 && \
./configure --with-htslib=$HTSLIB_INSTALL_DIR --prefix=$SAMTOOLS_INSTALL_DIR && \
make && \
make install

WORKDIR /
RUN rm -rf /tmp/samtools-1.3.1




make install && \
cd / && rm -rf /tmp/samtools-1.3.1 && ln -s /opt/samtools/bin/samtools /usr/bin/samtools

##########
#Bedtools#
##########

ARG PACKAGE_VERSION=2.27.1
ARG BUILD_PACKAGES="git openssl python build-essential zlib1g-dev"
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get update && \
apt-get install --yes \
$BUILD_PACKAGES && \
cd /tmp && \
git clone https://github.com/arq5x/bedtools2.git && \
cd bedtools2 && \
git checkout v$PACKAGE_VERSION && \
make && \
mv bin/* /usr/local/bin && \
cd / && \
rm -rf /tmp/* && \
apt remove --purge --yes \
$BUILD_PACKAGES && \
apt autoremove --purge --yes && \
apt clean && \
rm -rf /var/lib/apt/lists/*
RUN mkdir /opt/bedtools && cd /opt/bedtools && wget https://github.com/arq5x/bedtools2/releases/download/v2.29.2/bedtools.static.binary && \
chmod +x /opt/bedtools/bedtools.static.binary && \
ln -s /opt/bedtools/bedtools.static.binary /usr/bin/bedtools

# ARG PACKAGE_VERSION=2.27.1
# ARG BUILD_PACKAGES="git openssl python build-essential zlib1g-dev"
# ARG DEBIAN_FRONTEND=noninteractiveq
# RUN apt-get update && \
# apt-get install --yes \
# $BUILD_PACKAGES && \
# cd /tmp && \
# git clone https://github.com/arq5x/bedtools2.git && \
# cd bedtools2 && \
# git checkout v$PACKAGE_VERSION && \
# make && \
# mv bin/* /usr/local/bin && \
# cd / && \
# rm -rf /tmp/* && \
# apt remove --purge --yes \
# $BUILD_PACKAGES && \
# apt autoremove --purge --yes && \
# apt clean && \
# rm -rf /var/lib/apt/lists/*
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####################
#Biscuit QC scripts#
####################
RUN cd /opt && \
git clone https://github.com/zwdzwd/biscuit.git
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Should this point to a particular release or commit?

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That's complicated, because the latest release doesn't have some updates. Furthermore, the repo has been forked and this one isn't under active development anymore. In the next 6 months, we're going to have to grab the other version and update to the new QC tools, but that's a separate PR, so I'm going to leave this as-is for now. There's already an issue in to update these scripts at genome/analysis-workflows#993

## Adding QC_scripts
ADD Bisulfite_QC_bisulfiteconversion.sh /opt/biscuit/scripts
ADD Bisulfite_QC_Coveragestats.sh /opt/biscuit/scripts
ADD Bisulfite_QC_CpGretentiondistribution.sh /opt/biscuit/scripts
ADD Bisulfite_QC_mappingsummary.sh /opt/biscuit/scripts

RUN apt-get update -y && \
apt-get install
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