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Dockerfile
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# Dfam TE Tools container including RepeatMasker, RepeatModeler, coseg
FROM debian:12 AS builder
ARG TARGETARCH
RUN apt-get -y update && apt-get -y install \
gcc \
g++ \
make \
zlib1g-dev \
libgomp1 \
perl \
python3-h5py \
libfile-which-perl \
libtext-soundex-perl \
libjson-perl liburi-perl libwww-perl \
libdevel-size-perl \
aptitude && aptitude install -y ~pstandard ~prequired \
curl wget \
vim nano \
procps strace \
libpam-systemd- \
python3-setuptools \
locales
COPY src/* /opt/src/
COPY sha256sums.txt /opt/src/
WORKDIR /opt/src
RUN if [ "$TARGETARCH" = "amd64" ]; then \
sha256sum -c sha256sums.txt; \
elif [ "$TARGETARCH" = "arm64" ]; then \
mv sha256sums.txt /opt; \
cat /opt/sha256sums.txt | shasum -a 256 -c; \
rm /opt/sha256sums.txt; \
fi
# Extract RMBlast
RUN mkdir /opt/rmblast && \
if [ "$TARGETARCH" = "amd64" ]; then \
tar --strip-components=1 -x -f /opt/src/rmblast-2.14.1+-x64-linux.tar.gz -C /opt/rmblast; \
elif [ "$TARGETARCH" = "arm64" ]; then \
tar --strip-components=1 -x -f /opt/src/rmblast-2.14.1+-arm64-macosx.tar.gz -C /opt/rmblast; \
fi
# Compile HMMER
RUN tar -x -f hmmer-3.4.tar.gz \
&& cd hmmer-3.4 \
&& ./configure --prefix=/opt/hmmer && make && make install \
&& make clean
# Compile TRF
RUN tar -x -f trf-4.09.1.tar.gz \
&& cd TRF-4.09.1 \
&& mkdir build && cd build \
&& ../configure && make && cp ./src/trf /opt/trf \
&& cd .. && rm -r build
# Compile RepeatScout
RUN tar -x -f RepeatScout-1.0.6.tar.gz \
&& cd RepeatScout-1.0.6 \
&& sed -i 's#^INSTDIR =.*#INSTDIR = /opt/RepeatScout#' Makefile \
&& make && make install
# Compile and configure RECON
RUN tar -x -f RECON-1.08.tar.gz \
&& mv RECON-1.08 ../RECON \
&& cd ../RECON \
&& make -C src && make -C src install \
&& cp 00README bin/ \
&& sed -i 's#^\$path =.*#$path = "/opt/RECON/bin";#' scripts/recon.pl
# Compile cd-hit
RUN tar -x -f cd-hit-v4.8.1-2019-0228.tar.gz \
&& cd cd-hit-v4.8.1-2019-0228 \
&& make && mkdir /opt/cd-hit && PREFIX=/opt/cd-hit make install
# Compile genometools (for ltrharvest)
RUN tar -x -f gt-1.6.4.tar.gz \
&& cd genometools-1.6.4 \
&& make -j4 cairo=no && make cairo=no prefix=/opt/genometools install \
&& make cleanup
# Configure LTR_retriever
RUN cd /opt \
&& tar -x -f src/LTR_retriever-2.9.0.tar.gz \
&& mv LTR_retriever-2.9.0 LTR_retriever \
&& cd LTR_retriever \
&& sed -i \
-e 's#BLAST+=#BLAST+=/opt/rmblast/bin#' \
-e 's#RepeatMasker=#RepeatMasker=/opt/RepeatMasker#' \
-e 's#HMMER=#HMMER=/opt/hmmer/bin#' \
-e 's#CDHIT=#CDHIT=/opt/cd-hit#' \
-e 's#TEsorter=#TEsorter=/opt/TEsorter/dist#' \
paths
# Compile MAFFT
RUN tar -x -f mafft-7.471-without-extensions-src.tgz \
&& cd mafft-7.471-without-extensions/core \
&& sed -i 's#^PREFIX =.*#PREFIX = /opt/mafft#' Makefile \
&& make clean && make && make install \
&& make clean
# Compile NINJA
RUN cd /opt \
&& tar --strip-components=1 -x -f src/NINJA-cluster.tar.gz \
&& cd NINJA \
&& make clean && make all \
&& cd .. \
&& mv LICENSE ./NINJA \
&& mv README.md ./NINJA
# Move UCSC tools
RUN mkdir /opt/ucsc_tools && \
if [ "$TARGETARCH" = "amd64" ]; then \
mv /opt/src/faToTwoBit_x86 /opt/ucsc_tools/faToTwoBit; \
mv /opt/src/twoBitInfo_x86 /opt/ucsc_tools/twoBitInfo; \
mv /opt/src/twoBitToFa_x86 /opt/ucsc_tools/twoBitToFa; \
elif [ "$TARGETARCH" = "arm64" ]; then \
mv /opt/src/faToTwoBit_arm64 /opt/ucsc_tools/faToTwoBit; \
mv /opt/src/twoBitInfo_arm64 /opt/ucsc_tools/twoBitInfo; \
mv /opt/src/twoBitToFa_arm64 /opt/ucsc_tools/twoBitToFa; \
fi
COPY LICENSE.ucsc /opt/ucsc_tools/LICENSE
# Compile and configure coseg
RUN cd /opt \
&& mkdir coseg \
&& tar -x -f src/coseg-0.2.3.tar.gz -C ./coseg \
&& cd coseg/coseg-coseg-0.2.3 \
&& mv * ../ \
&& cd ../ \
&& sed -i 's@#!.*perl@#!/usr/bin/perl@' preprocessAlignments.pl runcoseg.pl refineConsSeqs.pl \
&& sed -i 's#use lib "/usr/local/RepeatMasker";#use lib "/opt/RepeatMasker";#' preprocessAlignments.pl \
&& make
# Configure RepeatMasker
# With Minimal TE Library
# - Also with full Dfam curated RepeatMasker.lib for RepeatClassifier
RUN cd /opt \
&& tar -x -f src/RepeatMasker-4.1.7-p1.tar.gz \
&& chmod a+w RepeatMasker/Libraries \
&& chmod a+w RepeatMasker/Libraries/famdb \
&& cd RepeatMasker \
&& perl configure \
-hmmer_dir=/opt/hmmer/bin \
-rmblast_dir=/opt/rmblast/bin \
-libdir=/opt/RepeatMasker/Libraries \
-trf_prgm=/opt/trf \
-default_search_engine=rmblast \
&& gunzip -c /opt/src/Dfam-RepeatMasker.lib.gz > Libraries/RepeatMasker.lib \
&& /opt/rmblast/bin/makeblastdb -dbtype nucl -in Libraries/RepeatMasker.lib \
&& cd ..
# With Dfam root partition
#RUN cd /opt \
# && tar -x -f src/RepeatMasker-4.1.6.tar.gz \
# && chmod a+w RepeatMasker/Libraries \
# && chmod a+w RepeatMasker/Libraries/famdb \
# && gunzip src/dfam38_full.0.h5.gz \
# && mv src/dfam38_full.0.h5 /opt/RepeatMasker/Libraries/famdb/dfam38_full.0.h5 \
# && cd RepeatMasker \
# && perl configure \
# -hmmer_dir=/opt/hmmer/bin \
# -rmblast_dir=/opt/rmblast/bin \
# -libdir=/opt/RepeatMasker/Libraries \
# -trf_prgm=/opt/trf \
# -default_search_engine=rmblast \
# && gunzip -c src/Dfam-RepeatMasker.lib.gz > RepeatMasker/Libraries/RepeatMasker.lib \
# && /opt/rmblast/bin/makeblastdb -dbtype nucl -in RepeatMasker/Libraries/RepeatMasker.lib \
# && cd ..
# Include config update
COPY tetoolsDfamUpdate.pl /opt/RepeatMasker/tetoolsDfamUpdate.pl
# Configure RepeatModeler
RUN cd /opt \
&& tar -x -f src/RepeatModeler-2.0.5.tar.gz \
&& mv RepeatModeler-2.0.5 RepeatModeler \
&& cd RepeatModeler \
&& perl configure \
-cdhit_dir=/opt/cd-hit -genometools_dir=/opt/genometools/bin \
-ltr_retriever_dir=/opt/LTR_retriever -mafft_dir=/opt/mafft/bin \
-ninja_dir=/opt/NINJA -recon_dir=/opt/RECON/bin \
-repeatmasker_dir=/opt/RepeatMasker \
-rmblast_dir=/opt/rmblast/bin -rscout_dir=/opt/RepeatScout \
-trf_dir=/opt \
-ucsctools_dir=/opt/ucsc_tools
RUN echo "PS1='(dfam-tetools \$(pwd))\\\$ '" >> /etc/bash.bashrc
# Set the locale
RUN sed -i '/en_US.UTF-8/s/^# //g' /etc/locale.gen && \
locale-gen
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US:en
ENV LC_ALL en_US.UTF-8
ENV PYTHONIOENCODING=utf8
ENV PATH=/opt/RepeatMasker:/opt/RepeatMasker/util:/opt/RepeatModeler:/opt/RepeatModeler/util:/opt/coseg:/opt/ucsc_tools:/opt:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/opt/rmblast/bin:/bin
RUN chmod +x /opt/ucsc_tools/* \
&& rm -r /opt/src