Conda: Usage Example

Creating and Using Ecosystem

Flight Env provides quick setup methods to create a conda software ecosystem.

To install and use conda:

  • Activate the flight system

  • Create the conda installation for the user:

    [flight@gateway1 ~]$ flight env create conda
    Creating environment conda@default
       > ✅ Verifying prerequisites
       > ✅ Fetching prerequisite (miniconda)
       > ✅ Creating environment (conda@default)
    Environment conda@default has been created
    
  • Activate the conda ecosystem:

    [flight@gateway1 ~]$ flight env activate conda
    (base) <conda> [flight@gateway1 ~]$
    
  • Check that conda can be run:

    (base) <conda> [flight@gateway1 ~]$ conda --version
    conda 4.7.10
    

Installing and Running Perl

An example workflow using perl is demonstrated below.

  • View available versions:

    (base) <conda> [flight@gateway1 ~]$ conda search perl
    Loading channels: done
    # Name                       Version           Build  Channel
    perl                          5.26.0      hae598fd_0  pkgs/main
    perl                          5.26.2      h14c3975_0  pkgs/main
    
  • Install specific version:

    (base) <conda> [flight@gateway1 ~]$ conda install perl=5.26.2
    Collecting package metadata (current_repodata.json): done
    Solving environment: done
    
    ## Package Plan ##
    
      environment location: /home/flight/.local/share/flight/env/conda+default
    
      added / updated specs:
        - perl=5.26.2
    
    
    The following packages will be downloaded:
    
        package                    |            build
        ---------------------------|-----------------
        ca-certificates-2019.5.15  |                1         134 KB
        certifi-2019.6.16          |           py37_1         156 KB
        conda-4.7.11               |           py37_0         3.0 MB
        perl-5.26.2                |       h14c3975_0        10.5 MB
        ------------------------------------------------------------
                                               Total:        13.7 MB
    
    The following NEW packages will be INSTALLED:
    
      perl               pkgs/main/linux-64::perl-5.26.2-h14c3975_0
    
    The following packages will be UPDATED:
    
      ca-certificates                               2019.5.15-0 --> 2019.5.15-1
      certifi                                  2019.6.16-py37_0 --> 2019.6.16-py37_1
      conda                                       4.7.10-py37_0 --> 4.7.11-py37_0
    
    
    Proceed ([y]/n)? y
    
    
    Downloading and Extracting Packages
    conda-4.7.11         | 3.0 MB    | ############################################################################################ | 100%
    certifi-2019.6.16    | 156 KB    | ############################################################################################ | 100%
    perl-5.26.2          | 10.5 MB   | ############################################################################################ | 100%
    ca-certificates-2019 | 134 KB    | ############################################################################################ | 100%
    Preparing transaction: done
    Verifying transaction: done
    Executing transaction: done
    
  • Check installation location:

    (base) <conda> [flight@gateway1 ~]$ which perl
    ~/.local/share/flight/env/conda+default/bin/perl
    
  • Install perl library (this may prompt for initial cpan configuration, once configuration is complete then the library will be installed):

    (base) <conda> [flight@gateway1 ~]$ cpan File::Slurp
    Loading internal null logger. Install Log::Log4perl for logging messages
    Reading '/home/flight/.cpan/Metadata'
      Database was generated on Mon, 09 Sep 2019 15:17:03 GMT
    Running install for module 'File::Slurp'
    <-- snip -->
    
  • Check installation worked:

    (base) <conda> [flight@gateway1 ~]$ cpan File::Slurp
    Loading internal null logger. Install Log::Log4perl for logging messages
    Reading '/home/flight/.cpan/Metadata'
      Database was generated on Mon, 09 Sep 2019 15:17:03 GMT
    File::Slurp is up to date (9999.27).