Singularity.scRNAseq

BootStrap: docker
From: ubuntu:16.04


%post

    # install some stuff
    #-------------------
    apt-get -y update
    apt-get -y install curl unzip wget 
    apt-get clean

    # download and install miniconda3
    #---------------------------------
    curl -sSL -O https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
    bash Miniconda3-latest-Linux-x86_64.sh -p /opt/miniconda3 -b
    rm -fr Miniconda3-latest-Linux-x86_64.sh
    export PATH=/opt/miniconda3/bin:$PATH
    conda update -n base conda
    conda config --add channels conda-forge
    conda config --add channels bioconda

    # install what i need from Bioconda
    #---------------------------------
    conda install -y -c bioconda salmon
    conda install -y -c bioconda bioawk
    
    # prepare reference files for alevin (https://combine-lab.github.io/alevin-tutorial/2018/setting-up-resources/)
    #---------------------------------------------------------------------------------------------------------------
    wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.pc_transcripts.fa.gz
    salmon index -i index -k 31 --gencode -p 1 -t gencode.v32.pc_transcripts.fa.gz
    wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.primary_assembly.annotation.gtf.gz
    gunzip -c gencode.v32.primary_assembly.annotation.gtf.gz > gencode.v32.primary_assembly.annotation.gtf
    bioawk -c gff '$feature=="transcript" {print $group}' gencode.v32.primary_assembly.annotation.gtf | awk -F ' ' '{print substr($4,2,length($4)-3) "\t" substr($2,2,length($2)-3)}' - > txp2gene.tsv

    mkdir /scRNAseq_refs
    mv gencode.v32.pc_transcripts.fa.gz index gencode.v32.primary_assembly.annotation.gtf* txp2gene.tsv /scRNAseq_refs/.


%environment
    export LC_ALL=C
    export PATH=/opt/miniconda3/bin:$PATH