databio / bulker

Manager for multi-container computing environments
https://bulker.io
BSD 2-Clause "Simplified" License
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user id not working in container on MacOS #30

Closed nsheff closed 4 years ago

nsheff commented 5 years ago

I have a different problem now:

Levis-Air:~ lw391$ bulker activate waldronlab/levi
Bulker config: /Users/lw391/bulker_config.yaml
Activating bulker crate: waldronlab/levi

bulker-3.2$ cd git/hub.bulker.io/
bulker-3.2$ git pull
No user exists for uid 501
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
bulker-3.2$ _git
Starting interactive docker shell for image 'samueldebruyn/debian-git' and command 'git'
I have no name!@docker-desktop:/Users/lw391/git/hub.bulker.io$ ls .git
COMMIT_EDITMSG  FETCH_HEAD  HEAD  ORIG_HEAD  config  description  hooks  index  info  logs  objects  packed-refs  refs
I have no name!@docker-desktop:/Users/lw391/git/hub.bulker.io$ whoami
whoami: cannot find name for user ID 501
I have no name!@docker-desktop:/Users/lw391/git/hub.bulker.io$ 

Here is my bulker_config.yaml:

bulker:
  volumes: ['/tmp', '$HOME']
  envvars: ['DISPLAY']
  registry_url: http://hub.bulker.io/
  default_crate_folder: ${HOME}/bulker_crates
  singularity_image_folder: ${HOME}/simages
  container_engine: docker
  default_namespace: bulker
  executable_template: templates/docker_executable.jinja2
  shell_template: templates/docker_shell.jinja2
  build_template: templates/docker_build.jinja2
  crates:
    bulker:
      demo:
        default: /Users/lw391/bulker_crates/bulker/demo/default
    bioconductor:
      bioconductor_full:
        default:
          docker_args: --volume=${HOME}/.local/lib/R:/usr/local/lib/R/host-site-library
        devel:
          docker_args: --volume=${HOME}/.local/lib/Rdev:/usr/local/lib/R/host-site-library
      levi:
        default: /Users/lw391/bulker_crates/bulker/levi/default
    waldronlab:
      bioconductor:
        default: /Users/lw391/bulker_crates/waldronlab/bioconductor/default
      levi:
        default: /Users/lw391/bulker_crates/waldronlab/levi/default

Originally posted by @lwaldron in https://github.com/databio/bulker/issues/28#issuecomment-544713067

Kmrouj commented 4 years ago

Ok. Thank you