FROM ****
RUN dnf install -y R openssl-devel && \
R -e "install.packages(c('getopt','BiocManager'), repos='https://cran.r-project.org/')" && \
R -e "BiocManager::install('org.Mm.eg.db')" && \
R -e "BiocManager::install('org.Hs.eg.db')" && \
R -e "BiocManager::install('clusterProfiler')" && \
R -e "remove.packages('rvcheck')" && \
R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/rvcheck/rvcheck_0.1.8.tar.gz', repos=NULL, type='source')" && \
R -e "BiocManager::install('clusterProfiler')"
RUN dnf install -y libcurl-devel R-rgeos && \
R -e "install.packages(c('httr','plotly','SeuratObject','Seurat','tidyverse','extrafont','ggplot2','data.table'),repos='https://cran.r-project.org/')" && \
R -e "BiocManager::install('monocle')" && \
R -e "install.packages('pheatmap', repos='https://cran.r-project.org/')"
COPY ./tools/ /usr/lib/
RUN pip install cutadapt && \
dnf install -y java-1.8.0-openjdk.x86_64 perl htslib samtools && \
chmod a+x /usr/lib/FastQC/fastqc && \
ln -s /usr/lib/FastQC/fastqc /usr/local/bin/fastqc && \
ln -s /usr/lib/TrimGalore-0.6.6/trim_galore /usr/local/bin/trim_galore && \
ln -s /usr/lib/hisat2-2.2.1/hisat2 /usr/local/bin/hisat2 && \
ln -s /usr/lib/hisat2-2.2.1/hisat2-build /usr/local/bin/hisat2-build && \
ln -s /usr/lib/stringtie-2.2.1.Linux_x86_64/stringtie /usr/local/bin/stringtie && \
ln -s /usr/lib/stringtie-2.2.1.Linux_x86_64/prepDE.py3 /usr/local/bin/prepDE.py3 && \
ln -s /usr/lib/STAR-2.7.10a/STAR /usr/local/bin/STAR && \
export PATH=$PATH:/usr/lib/sratoolkit.3.0.0
RUN R -e "install.packages(c('gplots','RColorBrewer'),repos='https://cran.r-project.org/')" && \
R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/locfit/locfit_1.5-9.2.tar.gz', repos=NULL)" && \
R -e "BiocManager::install('DESeq2')"
RUN R -e "BiocManager::install('org.Mm.eg.db')" && \
R -e "BiocManager::install('MAST')" && \
R -e "BiocManager::install('optparse')"