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# Distributed under the terms of the Modified BSD License.
ARG OWNER=jupyter
ARG BASE_CONTAINER=$OWNER/minimal-notebook
FROM $BASE_CONTAINER as base
# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
USER root
RUN apt-get update --yes && \
apt-get install --yes --no-install-recommends \
# for cython: https://cython.readthedocs.io/en/latest/src/quickstart/install.html
build-essential \
# for latex labels
cm-super \
dvipng \
# for matplotlib anim
ffmpeg \
time && \
apt-get clean && rm -rf /var/lib/apt/lists/*
RUN apt update && \
apt-get install -y --no-install-recommends \
man-db \
g++ \
less \
zlib1g-dev \
&& \
apt-get clean && rm -rf /var/lib/apt/lists/*
RUN cd /opt && \
git clone --recursive https://github.com/clwgg/seqstats && \
cd seqstats && \
make
ENV PATH=${PATH}:/opt/seqstats
# cdbfasta
RUN cd /opt && \
git clone https://github.com/gpertea/cdbfasta.git && \
cd cdbfasta && \
make
ENV PATH=${PATH}:/opt/cdbfasta
# hisat2
#RUN cd /opt && \
# git clone https://github.com/DaehwanKimLab/hisat2.git && \
# cd hisat2 && \
# make -j 16
#ENV PATH=${PATH}:/opt/hisat2
# stringtie2 (ETP+)
#RUN cd /opt && \
# wget http://ccb.jhu.edu/software/stringtie/dl/stringtie-2.2.1.Linux_x86_64.tar.gz && \
# tar -xvf stringtie-2.2.1.Linux_x86_64.tar.gz
#ENV PATH=${PATH}:/opt/stringtie-2.2.1.Linux_x86_64
# gffread (ETP+)
#RUN cd /opt && \
# git clone https://github.com/gpertea/gffread.git && \
# cd gffread && \
# make
#ENV PATH=${PATH}:/opt/gffread
# diamond
#RUN cd /opt && \
# mkdir diamond && \
# cd diamond && \
# wget http://github.com/bbuchfink/diamond/releases/download/v2.0.15/diamond-linux64.tar.gz && \
# tar -xf diamond-linux64.tar.gz && \
# rm diamond-linux64.tar.gz
#ENV PATH=${PATH}:/opt/diamond
# tsebra
RUN cd /opt && \
git clone https://github.com/Gaius-Augustus/TSEBRA
ENV PATH=${PATH}:/opt/TSEBRA/bin
# makehub
RUN cd /opt && \
git clone https://github.com/Gaius-Augustus/MakeHub.git && \
cd MakeHub && \
git checkout braker3 && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/bedToBigBed && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/genePredCheck && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/faToTwoBit && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/gtfToGenePred && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/hgGcPercent && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/ixIxx && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/twoBitInfo && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/wigToBigWig && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/genePredToBed && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/genePredToBigGenePred && \
chmod u+x bedToBigBed genePredCheck faToTwoBit gtfToGenePred hgGcPercent ixIxx twoBitInfo wigToBigWig genePredToBed genePredToBigGenePred make_hub.py
ENV PATH=${PATH}:/opt/MakeHub
# augustus
ENV AUGUSTUS_CONFIG_PATH=/usr/share/augustus/config/
ENV AUGUSTUS_BIN_PATH=/usr/bin/
ENV AUGUSTUS_SCRIPTS_PATH=/usr/share/augustus/scripts/
RUN apt update && \
apt install -yq augustus augustus-data augustus-doc && \
apt clean all && \
fix-permissions "${AUGUSTUS_CONFIG_PATH}"
# perl dependencies of BRAKER and GeneMark-ETP+
RUn apt update && \
apt install -yq libyaml-perl libhash-merge-perl libparallel-forkmanager-perl libscalar-util-numeric-perl libclass-data-inheritable-perl libexception-class-perl libtest-pod-perl libfile-which-perl libmce-perl libthread-queue-perl libmath-utils-perl libscalar-list-utils-perl && \
apt clean all
# bedtools (ETP+)
#RUN apt update && \
# apt install -yq bedtools && \
# apt clean all
# sratools (ETP+)
#RUN cd /opt && \
# wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz && \
# tar -xvf sratoolkit.current-ubuntu64.tar.gz
#ENV PATH=${PATH}:/opt/sratoolkit.3.0.1-ubuntu64/bin/
# patch Augustus scripts (because Debian package is often outdated, this way we never need to worry)
RUN cd /usr/share/augustus/scripts && \
rm optimize_augustus.pl && \
wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/optimize_augustus.pl && \
rm aa2nonred.pl && \
wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/aa2nonred.pl && \
rm gff2gbSmallDNA.pl && \
wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/gff2gbSmallDNA.pl && \
rm new_species.pl && \
wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/new_species.pl && \
rm filterGenesIn.pl && \
wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/filterGenesIn.pl && \
rm filterGenesIn_mRNAname.pl && \
wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/filterGenesIn_mRNAname.pl && \
rm filterGenes.pl && \
wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/filterGenes.pl && \
rm join_mult_hints.pl && \
wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/join_mult_hints.pl && \
rm randomSplit.pl && \
wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/randomSplit.pl && \
rm join_aug_pred.pl && \
wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/join_aug_pred.pl && \
rm getAnnoFastaFromJoingenes.py && \
wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/getAnnoFastaFromJoingenes.py && \
rm gtf2gff.pl && \
wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/gtf2gff.pl && \
rm splitMfasta.pl && \
wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/splitMfasta.pl && \
rm createAugustusJoblist.pl && \
wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/createAugustusJoblist.pl && \
chmod a+x optimize_augustus.pl aa2nonred.pl gff2gbSmallDNA.pl new_species.pl filterGenesIn_mRNAname.pl filterGenes.pl filterGenesIn.pl join_mult_hints.pl randomSplit.pl join_aug_pred.pl getAnnoFastaFromJoingenes.py gtf2gff.pl splitMfasta.pl createAugustusJoblist.pl
# bamtools (ETP+)
RUN apt update && \
apt install -yq bamtools && \
apt clean all
USER ${NB_UID}
RUN mamba install --quiet -c bioconda -c anaconda --yes \
biopython && \
mamba clean --all -f -y && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
WORKDIR "${HOME}"
USER root
# braker including RNAseq test file
RUN cd /opt && \
git clone https://github.com/Gaius-Augustus/BRAKER.git && \
cd BRAKER && \
cd example && \
wget http://bioinf.uni-greifswald.de/augustus/datasets/RNAseq.bam
ENV PATH=${PATH}:/opt/BRAKER/scripts
# include ETP
RUN cd /opt && \
wget http://topaz.gatech.edu/GeneMark/etp.for_braker.tar.gz && \
tar -xzf etp.for_braker.tar.gz && \
mv etp.for_braker ETP && \
chmod a+x /opt/ETP/bin/*py /opt/ETP/bin/*pl /opt/ETP/tools/*
ENV GENEMARK_PATH=/opt/ETP/bin
ENV PATH=${PATH}:/opt/ETP/bin:/opt/ETP/tools:/opt/ETP/bin/gmes/ProtHint/bin
USER ${NB_UID}