Class: MiGA::Cli::Action::Env

Inherits:
MiGA::Cli::Action show all
Defined in:
lib/miga/cli/action/env.rb

Instance Attribute Summary

Attributes inherited from MiGA::Cli::Action

#cli

Instance Method Summary collapse

Methods inherited from MiGA::Cli::Action

#complete, #initialize, #launch, load, #name

Constructor Details

This class inherits a constructor from MiGA::Cli::Action

Instance Method Details

#empty_action ⇒ Object 



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# File 'lib/miga/cli/action/env.rb', line 28

def empty_action
end

#parse_cli ⇒ Object 



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# File 'lib/miga/cli/action/env.rb', line 7

def parse_cli
  cli.parse { |_| }
end

#perform ⇒ Object 



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# File 'lib/miga/cli/action/env.rb', line 11

def perform
  puts <<~BASH
    export MIGA="#{MiGA::MiGA.root_path}"
    export MIGA_HOME=${MIGA_HOME:-"$HOME"}
    . "$MIGA_HOME/.miga_rc"
    # Ensure MiGA & submodules are first in PATH
    export PATH="$MIGA/bin:$PATH"
    for util in enveomics/Scripts FastAAI/fastaai multitrim ; do
      export PATH="$MIGA/utils/$util:$PATH"
    done
    # Override gzip with pigz (if available)
    if command -v pigz &>/dev/null ; then
      gzip() { pigz -p ${CORES:-2} "$@" ; }
    fi
  BASH
end