Corrected singularity definition file for RNA-Seq analysis. The original file is available from https://hpc.nih.gov/apps/singularity.html. Especially, From: is changed to use miniconda3. I have to comment out sailfish installation.

build_singularity

# Test on Debian 12/Ubuntu 22.04 (Desktop/server, LXC has a mksquashfs issue)
# Assume to install by a user with sudo right
#   Eg. apt update; apt install sudo; adduser USERNAME; usermod -aG sudo USERNAME
# 2024/4/19

# Install Dependencies

# Ensure repositories are up-to-date
sudo apt-get update
# Install debian packages for dependencies
sudo apt-get install -y \
   autoconf \
   automake \
   cryptsetup \
   fuse \
   fuse2fs \
   git \
   libfuse-dev \
   libglib2.0-dev \
   libseccomp-dev \
   libtool \
   make \
   pkg-config \
   runc \
   squashfs-tools \
   squashfs-tools-ng \
   uidmap \
   wget \
   zlib1g-dev

# Install Go    
   
export VERSION=1.22.2 OS=linux ARCH=amd64 && \
    wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz && \
    sudo tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz && \
    rm go$VERSION.$OS-$ARCH.tar.gz

echo 'export GOPATH=${HOME}/go' >> ~/.bashrc && \
    echo 'export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin' >> ~/.bashrc && \
    source ~/.bashrc

# Download SingularityCE from a release    
export VERSION=4.1.0 && # adjust this as necessary \
    wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-ce-${VERSION}.tar.gz && \
    tar -xzf singularity-ce-${VERSION}.tar.gz && \
    cd singularity-ce-${VERSION}
    
./mconfig && \
    make -C ./builddir && \
    sudo make -C ./builddir install

# singularity run docker://hello-world    

rnaseq3.def

Bootstrap: docker
From: continuumio/miniconda3
IncludeCmd: yes

%post
    apt-get -y update
    apt-get -y install wget libncurses5-dev libbz2-dev liblzma-dev zlib1g-dev \
          autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev \
          libcurl4-gnutls-dev libssl-dev libdeflate-dev

    # Install samtools
    wget https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2
    tar -vxjf samtools-1.10.tar.bz2
    cd samtools-1.10
    make
    make install
    cd ..

    export PATH=/opt/conda/bin:$PATH
    conda install --yes -c conda-forge -c bioconda \
        star=2.5.2b \
        # sailfish \
        fastqc=0.12.1 \
        kallisto=0.50.1 \
        subread=2.0.6
    conda clean --index-cache --tarballs --packages --yes
    mkdir /data /resources

%runscript
#!/bin/bash
    # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    # this text code will run whenever the container
    # is called as an executable or with `singularity run`
function usage() {
        cat <<EOF
NAME
    rnaseq - rnaseq pipeline tools 0.1
SYNOPSIS
    rnaseq tool [tool options]
    rnaseq list
    rnaseq help
DESCRIPTION
    Singularity container with tools to build rnaseq pipeline.
EOF
    }

function tools() {
    echo "conda: $(which conda)"
    echo "---------------------------------------------------------------"
    conda list
    echo "---------------------------------------------------------------"
    echo "samtools: $(samtools --version | head -n1)"
}

arg="${1:-none}"

case "$arg" in
    none) usage; exit 1;;
    help) usage; exit 0;;
    list) tools; exit 0;;
    # just try to execute it then
    *)    $@;;
esac

%environment
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# This sets global environment variables for anything run within the container
export PATH="/opt/conda/bin:/usr/local/bin:/usr/bin:/bin:"
unset CONDA_DEFAULT_ENV
export ANACONDA_HOME=/opt/conda

Singularity

sudo singularity build rnaseq3 rnaseq3.def
./rnaseq3 cat /etc/os-release  # debian 11, host=ubuntu 2204
./rnaseq3 samtools --version # 1.10
./rnaseq3 STAR --version # 2.5.2b
./rnaseq3 fastqc -v # v0.12.1
./rnaseq3 kallisto | head 1 # 0.50.1
./rnaseq3 subread  # command not found
./rnaseq3 featureCounts -v | head # v2.0.6  
./rnaseq3 ls /opt/conda/bin
./rnaseq3 which gcc  # 10.2.1