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‎Dockerfile‎

Lines changed: 31 additions & 261 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,10 @@
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# This Dockerfile is based on https://github.com/ahmedmoustafa/bioinformatics-toolbox
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FROM ubuntu:22.04
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LABEL description="Bioinformatics Docker Container"
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LABEL description="ECRRM Genomics Commons Docker Image"
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LABEL maintainer="amoustafa@aucegypt.edu"
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LABEL version="1.0"
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RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections
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@@ -18,7 +21,7 @@ add-apt-repository restricted
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##########################################################################################
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##########################################################################################
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ARG SETUPDIR=/tmp/bioinformatics-toolbox-setup/
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ARG SETUPDIR=/tmp/genomics-commons-setup/
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RUN mkdir -p $SETUPDIR
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WORKDIR $SETUPDIR
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@@ -406,179 +409,6 @@ chmod +x /usr/local/bin/sambamba
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##########################################################################################
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##########################################################################################
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# Assemblers
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############
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############
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# SPAdes
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########
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RUN cd $SETUPDIR/ && \
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wget -t 0 http://cab.spbu.ru/files/release3.15.5/SPAdes-3.15.5-Linux.tar.gz && \
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tar zxvf SPAdes-3.15.5-Linux.tar.gz && \
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mv SPAdes-3.15.5-Linux/bin/* /usr/local/bin/ && \
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mv SPAdes-3.15.5-Linux/share/* /usr/local/share/
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# ABySS
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#######
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# RUN cd $SETUPDIR/ && \
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# git clone https://github.com/sparsehash/sparsehash.git && \
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# cd $SETUPDIR/sparsehash && \
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# ./autogen.sh && ./configure && make && make install
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# RUN cd $SETUPDIR/ && \
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# git clone https://github.com/bcgsc/btllib.git && \
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# btllib/compile && \
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# mv $SETUPDIR/btllib/install/bin/ /usr/local/bin/ && \
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# mv $SETUPDIR/btllib/install/include/ /usr/local/include/ && \
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# mv $SETUPDIR/btllib/install/lib/ /usr/local/lib/
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# RUN cd $SETUPDIR/ && \
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# git clone https://github.com/bcgsc/abyss.git && \
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# cd $SETUPDIR/abyss && \
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# ./autogen.sh && ./configure && make && make install
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# Velvet
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########
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RUN cd $SETUPDIR/ && \
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git clone https://github.com/dzerbino/velvet.git && \
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cd $SETUPDIR/velvet/ && \
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make && mv velvet* /usr/local/bin/
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# MEGAHIT
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#########
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RUN cd $SETUPDIR/ && \
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git clone https://github.com/voutcn/megahit.git && \
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cd $SETUPDIR/megahit && \
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git submodule update --init && \
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mkdir build && \
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cd $SETUPDIR/megahit/build && \
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cmake .. -DCMAKE_BUILD_TYPE=Release && make -j4 && make simple_test && make install
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# MetaVelvet
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############
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RUN cd $SETUPDIR/ && \
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git clone https://github.com/hacchy/MetaVelvet.git && \
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cd $SETUPDIR/MetaVelvet && \
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make && mv meta-velvetg /usr/local/bin/
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##########################################################################################
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##########################################################################################
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# Phylogenetics
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###############
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###############
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# TreeTime
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##########
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RUN pip3 install phylo-treetime
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# FastTree
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##########
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RUN cd $SETUPDIR/ && \
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wget -t 0 http://www.microbesonline.org/fasttree/FastTree.c && \
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gcc -O3 -finline-functions -funroll-loops -Wall -o FastTree FastTree.c -lm && \
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gcc -DOPENMP -fopenmp -O3 -finline-functions -funroll-loops -Wall -o FastTreeMP FastTree.c -lm && \
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mv FastTree /usr/local/bin && \
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mv FastTreeMP /usr/local/bin
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# RAxML
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#######
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RUN cd $SETUPDIR/ && \
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git clone https://github.com/stamatak/standard-RAxML.git && \
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cd $SETUPDIR/standard-RAxML && \
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rm -fr *.o && make -f Makefile.gcc && cp raxmlHPC /usr/local/bin/ && \
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rm -fr *.o && make -f Makefile.SSE3.gcc && cp raxmlHPC-SSE3 /usr/local/bin/ && \
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rm -fr *.o && make -f Makefile.PTHREADS.gcc && cp raxmlHPC-PTHREADS /usr/local/bin/ && \
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rm -fr *.o && make -f Makefile.SSE3.PTHREADS.gcc && cp raxmlHPC-PTHREADS-SSE3 /usr/local/bin/ && \
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rm -fr *.o && make -f Makefile.MPI.gcc && cp raxmlHPC-MPI /usr/local/bin/ && \
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rm -fr *.o && make -f Makefile.SSE3.MPI.gcc && cp raxmlHPC-MPI-SSE3 /usr/local/bin/
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# RAxML NG
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##########
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RUN cd $SETUPDIR/ && \
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git clone --recursive https://github.com/amkozlov/raxml-ng && \
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cd $SETUPDIR/raxml-ng && \
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mkdir build && \
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cd $SETUPDIR/raxml-ng/build && \
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cmake .. && make && mv ../bin/raxml-ng /usr/local/bin/ && \
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cmake -DSTATIC_BUILD=ON -DENABLE_RAXML_SIMD=OFF -DENABLE_PLLMOD_SIMD=OFF .. && make && mv ../bin/raxml-ng-static /usr/local/bin/ && \
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cmake -DUSE_MPI=ON .. && make && mv ../bin/raxml-ng-mpi /usr/local/bin/
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# PhyML
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#######
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RUN cd $SETUPDIR/ && \
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git clone https://github.com/stephaneguindon/phyml.git && \
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cd $SETUPDIR/phyml/ && \
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sh ./autogen.sh && ./configure && make && make install
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# Pplacer
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#########
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RUN cd $SETUPDIR/ && \
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wget -t 0 https://github.com/matsen/pplacer/releases/download/v1.1.alpha19/pplacer-linux-v1.1.alpha19.zip && \
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unzip pplacer-linux-v1.1.alpha19.zip && \
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cd $SETUPDIR/pplacer-Linux-v1.1.alpha19/ && \
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mv guppy /usr/local/bin/ && \
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mv pplacer /usr/local/bin/ && \
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mv rppr /usr/local/bin/ && \
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cd $SETUPDIR/pplacer-Linux-v1.1.alpha19/scripts/ && \
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python setup.py install
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##########################################################################################
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##########################################################################################
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# Gene Prediction
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#################
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#################
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RUN cd $SETUPDIR/ && \
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wget -t 0 https://github.com/hyattpd/Prodigal/releases/download/v2.6.3/prodigal.linux && \
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mv prodigal.linux /usr/local/bin/prodigal && \
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chmod +x /usr/local/bin/prodigal
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# GlimmerHMM
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############
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RUN cd $SETUPDIR/ && \
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wget -t 0 http://ccb.jhu.edu/software/glimmerhmm/dl/GlimmerHMM-3.0.4.tar.gz && \
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tar zxvf GlimmerHMM-3.0.4.tar.gz && \
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mv $SETUPDIR/GlimmerHMM/bin/glimmerhmm_linux_x86_64 /usr/local/bin/glimmerhmm && \
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chmod +x /usr/local/bin/glimmerhmm
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# Infernal
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##########
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RUN cd $SETUPDIR/ && \
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wget -t 0 http://eddylab.org/infernal/infernal-1.1.4.tar.gz && \
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tar zxvf infernal-1.1.4.tar.gz && \
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cd $SETUPDIR/infernal-1.1.4/ && \
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./configure && make && make install
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# GECCO
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#######
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RUN pip install gecco-tool
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# DeepBGC
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#########
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RUN apt-get update && \
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apt-get -y install software-properties-common && \
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add-apt-repository ppa:deadsnakes/ppa && \
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apt-get install -y python3-distutils python3-apt
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RUN pip install kiwisolver --force
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RUN pip install deepbgc
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RUN pip install deepbgc[hmm]
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# RUN deepbgc download
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# antiSMASH
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###########
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# RUN apt-get update && apt-get -y install hmmer2 hmmer fasttree
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RUN wget http://dl.secondarymetabolites.org/antismash-stretch.list -O /etc/apt/sources.list.d/antismash.list && \
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wget -q -O- http://dl.secondarymetabolites.org/antismash.asc | apt-key add -
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RUN cd $SETUPDIR/ && \
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wget https://dl.secondarymetabolites.org/releases/7.0.0/antismash-7.0.0.tar.gz && tar -zxf antismash-7.0.0.tar.gz && \
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pip install ./antismash-7.0.0
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# RUN download-antismash-databases
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##########################################################################################
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##########################################################################################
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# Misc
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######
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######
@@ -627,78 +457,36 @@ mv IGV_Linux_snapshot IGV
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# VEP
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#####
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# RUN cd /apps/ && \
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# apt-get -y install cpanminus libtry-tiny-perl libperl4-corelibs-perl && \
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# cpanm autodie && \
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# cpanm Module::Build && \
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# cpanm Bio::DB::HTS::Tabix && \
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# git clone https://github.com/Ensembl/ensembl-vep.git && \
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# cd ensembl-vep && \
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# perl INSTALL.pl --NO_HTSLIB --AUTO alcfp --SPECIES homo_sapiens --ASSEMBLY GRCh38 --PLUGINS all
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RUN cd /apps/ && \
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apt-get -y install cpanminus libtry-tiny-perl libperl4-corelibs-perl && \
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cpanm autodie && \
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cpanm Module::Build && \
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cpanm Bio::DB::HTS::Tabix && \
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git clone https://github.com/Ensembl/ensembl-vep.git && \
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cd ensembl-vep
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# RUN cd /apps/ensembl-vep && perl INSTALL.pl --NO_HTSLIB --AUTO alcfp --SPECIES homo_sapiens --ASSEMBLY GRCh38 --PLUGINS all
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##########################################################################################
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##########################################################################################
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# Taxonomic Classification & Microbiome
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#######################################
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#######################################
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# Population Genetics
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#####################
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#####################
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# Centrifuge
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# PLINK 1.90
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############
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RUN cd $SETUPDIR/ && \
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git clone https://github.com/DaehwanKimLab/centrifuge.git && \
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cd $SETUPDIR/centrifuge/ && \
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make && make install
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# Pavian
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########
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RUN R -e "remotes::install_github('fbreitwieser/pavian')"
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# Kraken2
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#########
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RUN cd $SETUPDIR/ && \
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git clone https://github.com/DerrickWood/kraken2.git && \
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cd $SETUPDIR/kraken2/src/ && \
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make && \
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cd $SETUPDIR/kraken2/ && \
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bash install_kraken2.sh /usr/local/bin/
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wget -t 0 https://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20230116.zip && \
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unzip plink_linux_x86_64_20230116.zip && \
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mv plink /usr/local/bin/ && \
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mv prettify /usr/local/bin/ && \
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RUN cd $SETUPDIR/ && \
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git clone https://github.com/jenniferlu717/Bracken.git && \
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cd $SETUPDIR/Bracken && \
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bash install_bracken.sh && \
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mv bracken /usr/local/bin/ && \
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mv bracken-build /usr/local/bin/
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# MetaPhlAn
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###########
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RUN pip install metaphlan graphlan panphlan humann
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# RUN metaphlan --install
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# mothur
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########
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RUN apt-get -y install libreadline*
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RUN cd $SETUPDIR/ && \
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wget -t 0 http://drive5.com/uchime/uchime4.2.40_i86linux32 && \
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mv uchime4.2.40_i86linux32 /usr/local/bin/uchime && \
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chmod a+x /usr/local/bin/uchime
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RUN cd $SETUPDIR/ && \
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wget -t 0 https://github.com/mothur/mothur/releases/download/v1.48.0/Mothur.linux_8.zip && \
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unzip Mothur.linux_8.zip && \
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mv $SETUPDIR/mothur/mothur /usr/local/bin/
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# QIIME2
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########
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RUN cd $SETUPDIR/ && \
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wget https://data.qiime2.org/distro/core/qiime2-2023.5-py38-linux-conda.yml && \
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/usr/local/miniconda3/bin/conda env create -n qiime2-2023.5 --file qiime2-2023.5-py38-linux-conda.yml
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##########################################################################################
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##########################################################################################
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# Finishing
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###########
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###########
@@ -713,28 +501,25 @@ RUN echo "#!/usr/bin/bash" > $SETUPDIR/init.sh
713501
RUN echo "export PATH=$PATH:/usr/local/ncbi/sra-tools/bin/:/usr/local/ncbi/ngs-tools/bin/:/usr/local/ncbi/ncbi-vdb/bin:/usr/local/miniconda3/bin:/apps/gatk:/apps/IGV:/apps/ensembl-vep:" >> $SETUPDIR/init.sh
714502
RUN echo "source /etc/profile.d/*" >> $SETUPDIR/init.sh
715503
RUN echo "echo '****************************************'" >> $SETUPDIR/init.sh
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RUN echo "echo 'Welcome to Bioinformatics Toolbox (v1.3)'" >> $SETUPDIR/init.sh
504+
RUN echo "echo 'Welcome to ECRRM Genomics Commons (v1.0)'" >> $SETUPDIR/init.sh
717505
RUN echo "echo '****************************************'" >> $SETUPDIR/init.sh
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RUN echo "echo 'Bioinformatics Toolbox is a docker container for bioinformatics'" >> $SETUPDIR/init.sh
506+
RUN echo "echo 'CRRM Genomics Commons is a docker container for bioinformatics'" >> $SETUPDIR/init.sh
719507
RUN echo "echo " >> $SETUPDIR/init.sh
720508
RUN echo "echo 'For a list of installed tools, please visit: '" >> $SETUPDIR/init.sh
721-
RUN echo "echo 'https://github.com/ahmedmoustafa/bioinformatics-toolbox/blob/master/Tools.md'" >> $SETUPDIR/init.sh
509+
RUN echo "echo 'https://github.com/ECRRM/genomics-commons/blob/master/Tools.md'" >> $SETUPDIR/init.sh
722510
RUN echo "echo " >> $SETUPDIR/init.sh
723511
RUN echo "echo 'If you would like to request adding certain tools or report a problem,'" >> $SETUPDIR/init.sh
724-
RUN echo "echo 'please submit an issue https://github.com/ahmedmoustafa/bioinformatics-toolbox/issues'" >> $SETUPDIR/init.sh
512+
RUN echo "echo 'please submit an issue https://github.com/ECRRM/genomics-commons/issues'" >> $SETUPDIR/init.sh
725513
RUN echo "echo " >> $SETUPDIR/init.sh
726-
RUN echo "echo 'If you use Bioinformatics Toolbox in your work, please cite: '" >> $SETUPDIR/init.sh
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RUN echo "echo '10.5281/zenodo.8103969'" >> $SETUPDIR/init.sh
728514
RUN echo "echo 'Have fun!'" >> $SETUPDIR/init.sh
729515
RUN echo "echo ''" >> $SETUPDIR/init.sh
730516
RUN echo "echo ''" >> $SETUPDIR/init.sh
731-
RUN echo "/usr/bin/bash" >> $SETUPDIR/init.sh
732517
RUN echo "" >> $SETUPDIR/init.sh
733-
RUN mv $SETUPDIR/init.sh /etc/bioinformatics-toolbox.sh
734-
RUN chmod a+x /etc/bioinformatics-toolbox.sh
518+
RUN mv $SETUPDIR/init.sh /etc/genomics-commons.sh
519+
RUN chmod a+x /etc/genomics-commons.sh
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736521
WORKDIR /root/
737-
ENTRYPOINT ["/etc/bioinformatics-toolbox.sh"]
522+
CMD ["/etc/genomics-commons.sh"]
738523
RUN rm -fr $SETUPDIR
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# Versions
@@ -754,37 +539,22 @@ STAR --version ; \
754539
salmon --version ; \
755540
bbmap.sh --version ; \
756541
hts_Stats --version ; \
757-
treetime --version ; \
758-
raxmlHPC -v ; \
759-
raxml-ng --version ; \
760-
pplacer --version ; \
761542
samtools --version ; \
762543
bcftools --version ; \
763544
bamtools --version ; \
764545
vcftools --version ; \
765546
bedtools --version ; \
766547
deeptools --version ; \
767548
bedops --version ; \
768-
spades.py --version ; \
769-
megahit --version ; \
770-
spades.py --version ; \
771549
seqkit version ; \
772550
fastp --version ; \
773551
fqtrim -V ; \
774552
seqmagick --version ; \
775-
gecco --version ; \
776-
deepbgc info ; \
777553
/apps/gatk/gatk --list ; \
778554
/apps/IGV/igv.sh --version ; \
779-
centrifuge --version ; \
780-
kraken2 --version ; \
781-
bracken -v ; \
782-
metaphlan --version ; \
783-
humann --version ; \
784-
uchime --version ; \
785-
mothur --version ; \
786555
/usr/local/miniconda3/bin/conda --version ; \
787-
nextflow -version
556+
nextflow -version ;\
557+
plink --version
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##########################################################################################
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##########################################################################################

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