miga-base 1.0.0.1 → 1.0.5.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: b4d9aad1ec5368e6cce82c4385a1d40839e948115e7749709a51e9c517d762f0
-  data.tar.gz: dc7b6500cbd85a1c50ef92fd41c0436dbbc16273ad245f730f8c2beb684db587
+  metadata.gz: bc2d6a45a59d47e3490d1e6bbe728961abfc28002c945c0fc371b24277f7abcd
+  data.tar.gz: c20265a37c53e403858c592a72b2de801ab6ce12e48f0fe88d886cea41a94413
 SHA512:
-  metadata.gz: 5973a0b393ff61b1065b74ae36f580be0e80467c8c5b281e82541539b9a97d37b553d82d4d284ec041be72937f7de1274cfa94f2f1c8593a3dcb4c97d3820eff
-  data.tar.gz: 60388895b6d864154ff94cd70ae7959f2ac80688a6f46c1d092fc8b08c7597ef3814bdf947bcc05a9832a9a54136c61a4a1970c4aefa3b05d57ad9c6bb670c1d
+  metadata.gz: 91804137814911287b5f1395e79b28e2805a0584dfb5ff234ca51a2366d17d497acf8a88ee80e18a1b8dd27a1b159ab3433471f82b389fd741825a1f5da57da5
+  data.tar.gz: 97d932379e302a22b2c0f489b5dd6cdd5efe4408c77e9cd32bb3b89efff3bc5f3787d167bc8f46720777dcc4d2efa06fb9b82f77e1903735a4b6e631e20be6f9

data/lib/miga/cli/action/daemon.rb

@@ -74,6 +74,11 @@ class MiGA::Cli::Action::Daemon < MiGA::Cli::Action
 
   def perform
     cli.operation or raise 'Please specify a daemon operation'
+
+    # Cleanup environment
+    %w[PROJECT RUNTYPE CORES DATASET].each { |i| ENV[i] = nil }
+
+    # Configure and run daemon
     p = cli.load_project
     d = MiGA::Daemon.new(p, cli[:json])
     dopts = %i[latency maxjobs nodelist ppn shutdown_when_done]

data/lib/miga/cli/action/env.rb

@@ -0,0 +1,26 @@
+# @package MiGA
+# @license Artistic-2.0
+
+require 'miga/cli/action'
+
+class MiGA::Cli::Action::Env < MiGA::Cli::Action
+  def parse_cli
+    cli.parse { |_| }
+  end
+
+  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:$PATH"
+      for util in enveomics/Scripts FastAAI/FastAAI multitrim ; do
+        export PATH="$MIGA/utils/$util:$PATH"
+      done
+    BASH
+  end
+
+  def empty_action
+  end
+end

data/lib/miga/cli/action/run.rb

@@ -34,7 +34,7 @@ class MiGA::Cli::Action::Run < MiGA::Cli::Action
     if cli[:env]
       cli[:project] ||= ENV['PROJECT']
       cli[:dataset] ||= ENV['DATASET']
-      cli[:thr] ||= ENV['CORES'].to_i unless ENV['CORES'].nil?
+      cli[:thr] = ENV['CORES'].to_i unless ENV['CORES'].nil?
       cli[:result] = File.basename(cli[:result].to_s, '.bash').to_sym
     end
     %i[project dataset result].each do |i|

data/lib/miga/cli/action/wf.rb

@@ -183,6 +183,7 @@ module MiGA::Cli::Action::Wf
     cmd += ['--json', cli[:daemon_json]] unless cli[:daemon_json].nil?
     cmd += ['--max-jobs', cli[:jobs]] unless cli[:jobs].nil?
     cmd += ['--ppn', cli[:threads]] unless cli[:threads].nil?
+    cmd += ['--debug', MiGA::MiGA.debug_trace? ? '2' : '1'] if MiGA::MiGA.debug?
     cwd = Dir.pwd
     call_cli(cmd)
     Dir.chdir(cwd)

data/lib/miga/cli/base.rb

@@ -41,6 +41,7 @@ module MiGA::Cli::Base
     lair: 'Control groups of daemons for several MiGA projects',
     date: 'Return the current date in standard MiGA format',
     console: 'Open an IRB console with MiGA',
+    env: 'Shell code to load MiGA environment',
     # Taxonomy
     tax_set: 'Register taxonomic information for datasets',
     tax_test: 'Return test of taxonomic distributions for query datasets',

data/lib/miga/common/base.rb

@@ -29,10 +29,18 @@ class MiGA::MiGA
     ##
     # Send debug message
     def DEBUG(*args)
-      $stderr.puts(*args) if @@DEBUG
+      $stderr.puts(*args) if debug?
       $stderr.puts(
         caller.map { |v| v.gsub(/^/, '     ') }.join("\n")
-      ) if @@DEBUG_TRACE
+      ) if debug_trace?
+    end
+
+    def debug?
+      @@DEBUG ||= false
+    end
+
+    def debug_trace?
+      @@DEBUG_TRACE ||= false
     end
   end
 end

data/lib/miga/daemon.rb

@@ -329,6 +329,7 @@ class MiGA::Daemon < MiGA::MiGA
   def launch_job(job, hostk = nil)
     # Execute job
     job[:cmd] = job_cmd(job)
+    MiGA::MiGA.DEBUG "CMD: #{job[:cmd]}"
     case runopts(:type)
     when 'ssh'
       # Remote job

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.0, 0, 1].freeze
+  VERSION = [1.0, 5, 0].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2021, 4, 13)
+  VERSION_DATE = Date.new(2021, 8, 26)
 
   ##
   # References of MiGA

data/scripts/miga.bash

@@ -1,21 +1,21 @@
 #!/bin/bash
 
+###
 # Setup environment
 set -e
-MIGA_HOME=${MIGA_HOME:-"$HOME"}
+eval "$("$MIGA/bin/miga" env)"
 SCRIPT=${SCRIPT:-$(basename "$0" .bash)}
-# shellcheck source=/dev/null
-. "$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
 
+###
 # Ancillary functions
+
+# Evaluates if the first passed argument is an existing file
 function exists { [[ -e "$1" ]] ; }
+
+# Evaluates if the first passed argument is a function
 function fx_exists { [[ $(type -t "$1") == "function" ]] ; }
+
+# Initiate a project-wide run
 function miga_start_project_step {
   local dir="$1"
   local dir_r="${dir}.running"
@@ -24,6 +24,8 @@ function miga_start_project_step {
   cd "$dir_r"
   miga date > "miga-project.start"
 }
+
+# Finalize a project-wide run
 function miga_end_project_step {
   local dir="$1"
   local dir_r="${dir}.running"

data/utils/subclade/pipeline.rb

@@ -17,10 +17,10 @@ module MiGA::SubcladeRunner::Pipeline
       metric_res = project.result(par[0]) or raise "Incomplete step #{par[0]}"
       Zlib::GzipReader.open(metric_res.file_path(:matrix)) do |ifh|
         ifh.each_line do |ln|
-          next if ln =~ /^metric\t/
+          next if ln =~ /^a\tb\tvalue\t/
 
           r = ln.chomp.split("\t")
-          ofh.puts "G>#{r[1]}\tG>#{r[2]}\t#{r[3]}" if r[3].to_f >= par[1]
+          ofh.puts "G>#{r[0]}\tG>#{r[1]}\t#{r[2]}" if r[2].to_f >= par[1]
         end
       end
       ofh.close

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.0.0.1
+  version: 1.0.5.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-04-13 00:00:00.000000000 Z
+date: 2021-08-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -141,6 +141,7 @@ files:
 - lib/miga/cli/action/doctor.rb
 - lib/miga/cli/action/doctor/base.rb
 - lib/miga/cli/action/edit.rb
+- lib/miga/cli/action/env.rb
 - lib/miga/cli/action/files.rb
 - lib/miga/cli/action/find.rb
 - lib/miga/cli/action/generic.rb