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).