install dependencies via Conda

• add 3 separate Conda environment files for installing
  • essential dependencies without Singularity (most users)
  • essential dependencies including Singularity (root users on Linux only)
  • non-essential dependencies (required for tests etc.)
• install Python dependencies via pip within Conda environment to avoid #56 (closed)
• update Conda-based installation instructions
  • describe usage of different environment files
  • add supported OS versions (macOS not yet added, because only installation works)
• update CI config to use same setup (based on Miniconda Docker image)

Closes #56 (closed)

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• 73675fab - get VM OS version

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• 40b21d69 - add Debian 10 to tested OS

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Installation tested successfully on my laptop (Ubuntu 18.04), on login node (CentOS 7.5; local and Slurm-based) and on VM (Debian 10).

@gypas & @herrmchr : Please check installation instructions (README.md in branch conda_env) and see if it works for you; you can try the tests as well, but on Mac do not bother with the integration test because of #55 (closed); please let me know your OS versions and status below. Thanks!

• Ubuntu 16.04
• conda 4.8.2
• root user installation: OK.
  (Snakemake part of integration test successful. Test only breaks later because of the missing test dependencies.)
• root user PLUS test dependencies: OK.
  (Integration test success.)
• non-root user: OK.
  Singularity 2.4.5-dist
  (Snakemake part of integration test successful. Test only breaks later because of the missing test dependencies.)

macOS Mojave v10.14.6 and conda 4.8.1:

I cloned the branch conda_env and executed:
conda env create -f install/environment.yml

What I got is:

Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound:
  - singularity=3.5.2

@bakma Thanks. Well, apparently Singularity for Conda is only available for Linux. I didn't know but will add this info to the instructions.

Could you please try again? I have set this as the default now, the version of the environment file that includes Singularity is called environment.root.yml now and the one without was renamed from environment.no_root.yml to environment.yml, as this is likely the more common usage.

closed

reopened

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• 4bdf70e8 - update docs and set 'no root' install as default

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• 8d0c6a97 - use root installer on VM

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I have executed the same command as previously on the same machine - the build was successful and the ENV can be activated/deactivated with no problems.

I have performed one more test upon activation:
conda env update -f install/environment.dev.yml
It works fine, no errors.

Awesome - thanks a lot! One final thing: if you have Singularity installed on your system, you could also run the integration test and see if you get the same error as Foivos.

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• 6c66197c - add Ubuntu 16.04 as supported OS

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Actually, given that @gypas uses the same macOS version, I will merge this issue now as Conda-based installation generally seems to work, with or without Singularity, depending on the system (as documented in README.md)

changed the description

merged

mentioned in commit 885c5692