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

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

Constant Summary

Constants included from MiGA

MiGA::CITATION, VERSION, VERSION_DATE, VERSION_NAME

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

Methods inherited from MiGA

CITATION, CITATION_ARRAY, DEBUG, DEBUG_OFF, DEBUG_ON, DEBUG_TRACE_OFF, DEBUG_TRACE_ON, FULL_VERSION, LONG_VERSION, VERSION, VERSION_DATE, #advance, debug?, debug_trace?, initialized?, #like_io?, #num_suffix, rc_path, #result_files_exist?, #say

Methods included from MiGA::Common::Path

#root_path, #script_path

Methods included from MiGA::Common::Format

#clean_fasta_file, #seqs_length, #tabulate

Methods included from MiGA::Common::Net

#download_file_ftp, #known_hosts, #remote_connection

Methods included from MiGA::Common::SystemCall

#run_cmd, #run_cmd_opts

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 24

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
    MIGA="#{MiGA::MiGA.root_path}"
    MIGA_HOME=${MIGA_HOME:-"$HOME"}
    . "$MIGA_HOME/.miga_rc"
    # Ensure MiGA & submodules are first in PATH
    export PATH="$MIGA/bin:$PATH"
    for util in enveomics/Scripts FastAAI/FastAAI FastAAI multitrim ; do
      export PATH="$MIGA/utils/$util:$PATH"
    done
  BASH
end