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Requirements

Software

Configure conda channels

conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/mro/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/pro/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/

Install Python packages using conda

conda install -y numpy scipy scikit-learn pandas matplotlib seaborn tqdm snakemake h5py bokeh

Install Bioconda packages

List of all available Bioconda packages: (https://bioconda.github.io/recipes.html)

conda install -y bedtools samtools star subread bowtie2
conda install -y rsem bamtools cutadapt picard gffread gffcompare
conda install -y ucsc-bedtogenepred ucsc-genepredtogtf ucsc-bedgraphtobigwig
conda install -y htseq fastx_toolkit biopython rpy2

Install Ubuntu packages

sudo apt-get install -y gzip pigz openjdk-8-jdk

Install R packages

Install by running the following code in an R interactive session:

options("repos" = c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))
options(BioC_mirror="https://mirrors.tuna.tsinghua.edu.cn/bioconductor")
# From CRAN
install.packages(c('devtools', 'sva', 'VGAM', 'argparse', 'magrittr', 'readr'))
# From Bioconductor
source('https://bioconductor.org/biocLite.R')
biocLite(c('SingleCellExperiment', 'scater', 'scran', 'SCnorm',
    'EDASeq', 'RUVSeq', 'DESeq2', 'edgeR'))
# From R-forge
install.packages('countreg', repos = c('http://R-Forge.R-project.org', 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/'), dep = TRUE)
# From GitHub
library(devtools)
install_github('ChenMengjie/VIPER')
install_github('kassambara/easyGgplot2')
install_github("Vivianstats/scImpute")
install_github("hemberg-lab/scRNA.seq.funcs")

Other packages

Singularity

Build image

singularity build singularity/exseek.img singularity/Singularity

Make wrappers for singularity executables

bin/make_singularity_wrappers.py \
    --image singularity/exseek.simg \
    --list-file singularity/exports.txt \
    --singularity-path $(which singularity) \
    -o singularity/wrappers

Add wrappers to PATH

export PATH="$PWD/singularity/wrappers:$PATH"