SARS-CoV-2 tutorial Docker default issue

Help and Getting Started
1

Dear Nextstrain team,
before I discovered the SARS-CoV-2 tutorial Docker, I followed the Zika tutorial. So I guess all my installation and set-up uses Docker as default. In order to also get the native set-up for following the “ncov-tutorial” as recommended, I just conducted all the “getting started” steps of this tutorial. Running nextstrain check-setup --set-default says : “Supported Nextstrain environments: docker, native. Setting default environment to docker.” I can’t figure out how to “close Docker” as recommended in the yellow highlighted block nor can I find a way to run the “nextstrain build” using --native. Please, advise. Thanks a lot. Katharina

2

I think I might have found a solution:

  1. Run: nextstrain build --native . --cores 4 --use-conda --configfile ./my_profiles/getting_started/builds.yaml
    This gave a lot of error messages, probable reason as stated:
    CreateCondaEnvironmentException:
    Could not create conda environment from /home/…/SARS-CoV2-tutorial/ncov/workflow/envs/nextstrain.yaml:
    Package Version Build Channel Size
    ────────────────────────────────────────────────────────────────────────────────────────────
    Install:
    ────────────────────────────────────────────────────────────────────────────────────────────
  • _libgcc_mutex 0.1 conda_forge conda-forge/linux-64 Cached
  • _openmp_mutex 4.5 1_gnu conda-forge/linux-64 Cached

But then obviously installed all missing programs.

  1. Run above command line again. Seemed to have worked.