conda_config.sh

# conda deactivate
# rm -Rf /summer/epistorage/miniconda3/*
# ~/Miniconda3-latest-Linux-x86_64.sh -u -p /summer/epistorage/miniconda3 -b
# conda update -n base -c defaults conda

__conda_setup="$('/summer/epistorage/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
   eval "$__conda_setup"
else
   if [ -f "/summer/epistorage/miniconda3/etc/profile.d/conda.sh" ]; then
       . "/summer/epistorage/miniconda3/etc/profile.d/conda.sh"
   else
       export PATH="/summer/epistorage/miniconda3/bin:$PATH"
   fi
fi
unset __conda_setup


# conda create --name rnaseq_env
conda activate rnaseq_env


conda install  -c bioconda snakemake fastqc samtools star htseq deeptools
pip install --upgrade snakemake
conda install -c bioconda -c conda-forge multiqc 

conda install -c r -c bioconda \
  r-base=3.6.1     \
  r-rmarkdown      \
  r-devtools       \
  r r-xml \
  bioconductor-Biobase    \
  bioconductor-affy       \
  bioconductor-GEOquery

conda install -c bioconda bioconductor-deseq2

install.packages("https://cran.r-project.org/src/contrib/Archive/locfit/locfit_1.5-9.tar.gz")


# # https://github.com/fchuffar/epimedtools
# Sys.setenv(TAR = "/bin/tar") ; devtools::install_github("fchuffar/epimedtools")