[BUG] Permission denied in installation

[ssqd2022]

Permission denied when installing

To Reproduce

./pgap.py --update # required files are downloaded and extracted The latest version of PGAP is 2022-02-10.build5872, you have nothing installed locally. Downloading (as needed) Docker image ncbi/pgap:2022-02-10.build5872 Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post "http://%2Fvar%2Frun%2Fdocker.sock/v1.24/images/create?fromImage=ncbi%2Fpgap&tag=2022-02-10.build5872": dial unix /var/run/docker.sock: connect: permission denied None

Expected behavior A clear and concise description of what you expected to happen.

Software versions (please complete the following information):

• Ubuntu 20.04
  • Docker (or other container runner) version. [e.g. docker --version]
  • sudo apt-get install docker-ce=5:20.10.13~3-0~ubuntu-focal docker-ce-cli=5:20.10.13~3-0~ubuntu-focal containerd.io

Log Files Please rerun pgap.py with the --debug flag and attach an archive (e.g. zip or tarball) of the logs in the directory: debug/tmp-outdir/*/*.log.

Additional context Add any other context about the problem here.

[azat-badretdin]

Thank you for your report! We had a similar message in the past (#172) which was related to SLURM or parallel running of more than one job at a time, but your message seems to be happening very early (during installation).

I wonder if you will be able to download our image from a command line.

docker pull ncbi/pgap:2022-02-10.build5872

Could you please try that?

[ssqd2022]

Thank you for your prompt response. Unfortunately, I got the similar message

mubil@bioinfo-64:~/pgap$ docker pull ncbi/pgap:2022-02-10.build5872 Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post "http://%2Fvar%2Frun%2Fdocker.sock/v1.24/images/create?fromImage=ncbi%2Fpgap&tag=2022-02-10.build5872": dial unix /var/run/docker.sock: connect: permission denied.

[ssqd2022]

I have Ubuntu 20.04. Here is what I did before install pgap:

$ sudo apt-get update $ sudo apt-get install \ ca-certificates \ curl \ gnupg \ lsb-release $ curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg $ echo \ "deb [arch=$(dpkg --print-architecture) 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 $ sudo apt-get update $ sudo apt-get install docker-ce docker-ce-cli containerd.io

List the versions available in your repo, then choose one for installation

$ apt-cache madison docker-ce

docker-ce | 5:18.09.1~3-0~ubuntu-xenial | https://download.docker.com/linux/ubuntu xenial/stable amd64 Packages docker-ce | 5:18.09.0~3-0~ubuntu-xenial | https://download.docker.com/linux/ubuntu xenial/stable amd64 Packages …… sudo apt-get install docker-ce=5:20.10.13~3-0~ubuntu-focal docker-ce-cli=5:20.10.13~3-0~ubuntu-focal containerd.io

[azat-badretdin]

Thanks, can you try docker pull hello-world?

[ssqd2022]

I tried docker pull hello-world. I also had a permission problem. Then, I used "sudo su" and pull pgap again. It works this time. Do we have to use sudo to install pgap locally? What is the way around this?

[azat-badretdin]

Do we have to use sudo to install pgap locally?

Worth a try. Looks like you have a sudo access... Could you please try that?

[azat-badretdin]

The downside is that it will create reference data in your current directory with root ownership. From the other hand, you can be root, so it should not be a big deal, hopefully.