Install and configure Docker for 'nextflow run nf-core/rnaseq'

Install and configure that the packages for Docker (docker-ce, docker-ce-cli, and containerd.io):

1. Update your system's package information:

   sudo apt-get update
   

2. Uninstall any old versions of Docker:

   sudo apt-get remove docker docker-engine docker.io containerd runc
   

3. Set up the Docker repository to get the latest version of Docker. First, install packages to allow apt to use a repository over HTTPS:

   sudo apt-get install apt-transport-https ca-certificates curl gnupg lsb-release
   

4. Add Docker’s official GPG key:

   curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg
   

5. Use the following command to set up the stable repository (Note the use of the signed-by option to point to the keyring file that you have just downloaded):

   echo \
     "deb [arch=amd64 signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/ubuntu \
     $(lsb_release -cs) stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
   

6. Update the apt package index again, and then install Docker:

   sudo apt-get update
   sudo apt-get install docker-ce docker-ce-cli containerd.io
   

   The Docker installation includes the Docker service (daemon), which allows you to start containers, and the Docker CLI client. The Docker CLI uses the Docker API to interact with the Docker service.

7. Finally, add your user to the Docker group with the command. The following command cannot solve permission errors, rather than running step 8 can solve the problem.

   sudo usermod -aG docker ${USER}
   

8. Run nf-core/rnaseq under dock

   sudo chmod 666 /var/run/docker.sock
   xxxxx@xxx:~/DATA/Data_Manja_RNAseq_Organoids$ nextflow run nf-core/rnaseq --input samplesheet.csv --outdir results_GRCh38 --with_umi --umitools_bc_pattern 'NNNNNNNNNNNN' --fasta "/home/jhuang/REFs/Homo_sapiens/Ensembl/GRCh38/Sequence/WholeGenomeFasta/genome.fa" --gtf "/home/jhuang/REFs/Homo_sapiens/Ensembl/GRCh38/Annotation/Genes/genes.gtf"  --skip_rseqc --skip_dupradar --skip_preseq -profile docker -resume
   

9. During the installation of singularity, we got a error as follows.

   sudo apt-get update && sudo apt-get instal -y \
   build-essential \
   libssl-dev \
   uuid-dev \
   libgpgme11-dev \
   squashfs-tools \
   libseccomp-dev \
   wget \
   pkg-config \
   git \
   cryptsetup
   ...
   Processing triggers for initramfs-tools (0.130ubuntu3.6) ...
   update-initramfs: Generating /boot/initrd.img-5.4.0-150-generic
   I: The initramfs will attempt to resume from /dev/dm-9
   I: (UUID=698e2e03-7762-4764-b890-86d234beb938)
   I: Set the RESUME variable to override this.
   

   The changes here are related to enabling your system to resume from a specific device after suspend. The line "The initramfs will attempt to resume from /dev/dm-9" indicates that if your system goes into a suspend or hibernate state, it'll try to resume the system state from the device /dev/dm-9. This setting is typically safe and should not cause any problems.

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