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Dockerfile
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Dockerfile
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# Base image
FROM omicsclass/biocontainer-base:latest
################## METADATA ######################
LABEL base.image="omicsclass/biocontainer-base:latest" \
version="v0.0.1" \
software="rnaseq" \
software.version="20200324" \
about.summary="rnaseq analysis software packages" \
about.home="www.omicsclass.com" \
about.documentation="" \
license=" " \
about.tags="Genomics,Proteomics,Transcriptomics,General,Metabolomics"
################## MAINTAINER ######################
MAINTAINER huangls <huang2002003@qq.com>
#COPY Miniconda3-latest-Linux-x86_64.sh /tmp/miniconda.sh
#ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
ENV PATH /biosoft/hisat2-2.1.0:/biosoft/stringtie-2.1.1.Linux_x86_64:~/.aspera/connect/bin/:/biosoft/gffread-0.11.8.Linux_x86_64/:/biosoft/gffcompare-0.11.5.Linux_x86_64/:$PATH
RUN cd /biosoft && wget -qO- https://download.asperasoft.com/download/sw/connect/3.9.9/ibm-aspera-connect-3.9.9.177872-linux-g2.12-64.tar.gz |tar xvz \
&& chmod +x ibm-aspera-connect-3.9.9.177872-linux-g2.12-64.sh && ./ibm-aspera-connect-3.9.9.177872-linux-g2.12-64.sh && rm ibm-aspera-connect-3.9.9.177872-linux-g2.12-64.sh \
&& wget -qO- http://ccb.jhu.edu/software/stringtie/dl/gffread-0.11.8.Linux_x86_64.tar.gz|tar xvz \
&& wget -qO- http://ccb.jhu.edu/software/stringtie/dl/gffcompare-0.11.5.Linux_x86_64.tar.gz |tar xvz \
&& wget -qO- http://ccb.jhu.edu/software/stringtie/dl/stringtie-2.1.1.Linux_x86_64.tar.gz |tar zvx \
&& wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.1.0-Linux_x86_64.zip && unzip hisat2-2.1.0-Linux_x86_64.zip && rm hisat2-2.1.0-Linux_x86_64.zip \
&& cd /biosoft/biotools && wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred && chmod a+x gtfToGenePred \
&& wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/gff3ToGenePred && chmod a+x gff3ToGenePred
RUN yum -y install epel-release && \
yum -y install R && \
yum -y remove epel-release && \
yum clean all
#COPY .Rprofile /root
RUN R -e "install.packages(c('BiocManager', 'ggplot2','devtools','dplyr','gplots','RColorBrewer','tidyverse','argparse', 'getopt','reshape2','pheatmap','cowplot','R.utils'),dependencies=TRUE,repos='http://cran.wustl.edu/')" \
&& R -e "BiocManager::install(c('DESeq2','GenomicRanges','genefilter','ballgown','biomaRt','rhdf5','clusterProfiler','EBSeq','edgeR','topGO','pathview','AnnotationHub','GSEABase','enrichplot'))"
RUN R -e "BiocManager::install(c('org.Hs.eg.db','org.Mm.eg.db','org.Rn.eg.db','org.Sc.sgd.db','org.Dm.eg.db','org.At.tair.db','org.Dr.eg.db','org.Ce.eg.db','org.Bt.eg.db','org.Gg.eg.db','org.Cf.eg.db','org.Ss.eg.db','org.Mmu.eg.db','org.EcK12.eg.db','org.Xl.eg.db','org.Ag.eg.db','org.Pt.eg.db','org.Pf.plasmo.db','org.EcSakai.eg.db','org.Mxanthus.db'))"
RUN echo "alias R=\"/usr/bin/R \"" >> ~/.bashrc \
&& echo "alias Rscript=\"/usr/bin/Rscript \"" >> ~/.bashrc
RUN conda update -y -n base -c defaults conda \
&& conda install -y samtools=1.10 \
&& conda install -y bamtools=2.5.1 \
&& conda install -y sra-tools=2.10.3 \
&& conda install -y matplotlib \
&& conda install -y pandas \
#&& conda install -y hisat2=2.2.0 \
&& conda install -y rseqc=3.0.1 \
#&& conda install -y -c r r-essentials r-base \
#&& conda install -y htseq=0.11.3 \
&& conda install -y htseq \
#&& conda install -y bowtie2=2.3.5.1 \
#&& conda install -y bowtie=1.2.3 \
#&& conda install -y stringtie=2.1.1 \
&& conda install -y fastqc=0.11.9 \
&& conda install -y fastp=0.20.0 \
&& conda install -y eggnog-mapper=2.1.3 diamond=2.0.9 hmmer \
&& conda install -y perl-bioperl blast \
#&& conda install -y trim-galore=0.6.5 \
#&& conda install -y gffcompare=0.11.2 \
#&& conda install -y gffread=0.11.7 \
#&& conda install -y picard=2.22.1 \
#&& conda install -y flexbar=3.5.0 \
#&& conda install -y regtools=0.5.2 \
#&& conda install -y bedops=2.4.37 \
#&& conda install -y gffutils=0.10.1 \
#&& conda install -y ea-utils=1.1.2.779 \
#&& conda install -y ucsc-gff3togenepred=377 \
#&& conda install -y ucsc-gtftogenepred=377 \
#&& conda install -y ucsc-bedtogenepred=377 \
#&& conda install -y trinity=2.9.1 \
#&& conda install -y star=2.7.3a \
#&& conda install -y rsem=1.3.3 \
#&& conda install -y transdecoder=5.5.0 \
#&& conda install -y blast=2.9.0 \
#&& conda install -y hmmer=3.3 \
#&& pip install tmhmm.py \
&& conda clean --all --yes
COPY welcome.sh /root/.welcome.sh
WORKDIR /work