miga-base 0.7.21.0 → 0.7.24.0

data/utils/index_metadata.rb

@@ -17,8 +17,7 @@ def searchable(db, d, k, v)
 end
 
 p.each_dataset do |d|
-  next unless d.is_ref?
-  next unless d.is_active?
+  next unless d.ref? && d.active?
 
   searchable(db, d, :name, d.name)
   d.metadata.each do |k, v|

data/utils/requirements.txt

@@ -1,10 +1,12 @@
 Software	Test exec	Website								Notes
 --------	---------	-------								-----
 Ruby		ruby		https://www.ruby-lang.org/					Required version: 2.3+
-Python		python		https://www.python.org/
+Python		python		https://www.python.org/						Required version: 3+
 R		R		http://www.r-project.org/
 SQLite3		sqlite3		https://www.sqlite.org/
 NCBI BLAST+	blastp		ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST
+DIAMOND		diamond		http://ab.inf.uni-tuebingen.de/software/diamond			Required version: v0.9.20+
+FastANI		fastANI		https://github.com/ParBLiSS/FastANI				Required version: 1.1+
 HMMer 3.0+	hmmsearch	http://hmmer.janelia.org/software
 Bedtools	bedtools	http://bedtools.readthedocs.org/en/latest/
 Prodigal	prodigal	http://prodigal.ornl.gov
@@ -14,7 +16,6 @@ Barrnap		barrnap		http://www.vicbioinformatics.com/software.barrnap.shtml
 Scythe		scythe		https://github.com/vsbuffalo/scythe				Required version: 0.991+
 FastQC		fastqc		http://www.bioinformatics.babraham.ac.uk/projects/fastqc
 SolexaQA++	SolexaQA++	http://solexaqa.sourceforge.net					Required version: v3.1.3+
-DIAMOND (opt)	diamond		http://ab.inf.uni-tuebingen.de/software/diamond			Required version: v0.9.20+
-MyTaxa (opt)	MyTaxa		http://enve-omics.ce.gatech.edu/mytaxa				The folder must contain the db and utils dirs, and the AllGenomes.faa.dmnd database
-Krona (opt)	ktImportText	https://github.com/marbl/Krona/wiki
-FastANI (opt)	fastANI		https://github.com/ParBLiSS/FastANI				Required version: 1.1+
+OpenJDK (rdp)	java		https://adoptopenjdk.net/					Any Java VM would work
+MyTaxa (mytaxa)	MyTaxa		http://enve-omics.ce.gatech.edu/mytaxa
+Krona (mytaxa)	ktImportText	https://github.com/marbl/Krona/wiki

data/utils/subclade/runner.rb

@@ -15,22 +15,21 @@ class MiGA::SubcladeRunner
     @step = step.to_sym
     @home = File.join(
       File.join(project.path, 'data', '10.clades'),
-      @step == :clade_finding ? '01.find' : '02.ani'
+      @step == :clade_finding ? '01.find.running' : '02.ani.running'
     )
     @opts[:thr] ||= ENV.fetch('CORES') { 2 }.to_i
-    @opts[:run_clades] = !!@project.metadata.data.fetch(:run_clades) { true }
-    @opts[:gsp_ani] = @project.metadata.data.fetch(:gsp_ani) { 95.0 }.to_f
-    @opts[:gsp_aai] = @project.metadata.data.fetch(:gsp_aai) { 90.0 }.to_f
-    @opts[:gsp_metric] =
-      @project.metadata.data.fetch(:gsp_metric) { 'ani' }.to_s
+    @opts[:run_clades] = @project.option(:run_clades)
+    @opts[:gsp_ani] = @project.option(:gsp_ani)
+    @opts[:gsp_aai] = @project.option(:gsp_aai)
+    @opts[:gsp_metric] = @project.option(:gsp_metric)
   end
 
   # Launch the appropriate analysis
   def go!
     return if project.type == :metagenomes
 
-    unless @project.dataset_names.any? { |i| @project.dataset(i).is_ref? }
-      FileUtils.touch(File.expand_path('miga-project.empty', @home))
+    unless @project.dataset_names.any? { |i| @project.dataset(i).ref? }
+      FileUtils.touch(File.join(@home, 'miga-project.empty'))
       return
     end
     Dir.chdir home
@@ -44,15 +43,15 @@ class MiGA::SubcladeRunner
   # Launch analysis for clade_finding
   def go_clade_finding!
     cluster_species
-    unless project.is_clade?
-      subclades :aai
+    unless project.clade?
+      subclades(:aai)
       compile
     end
   end
 
   # Launch analysis for subclades
   def go_subclades!
-    subclades :ani
+    subclades(:ani)
     compile
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.21.0
+  version: 0.7.24.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-01-13 00:00:00.000000000 Z
+date: 2021-02-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -145,12 +145,14 @@ files:
 - lib/miga/cli/action/index_wf.rb
 - lib/miga/cli/action/init.rb
 - lib/miga/cli/action/init/daemon_helper.rb
+- lib/miga/cli/action/init/files_helper.rb
 - lib/miga/cli/action/lair.rb
 - lib/miga/cli/action/ln.rb
 - lib/miga/cli/action/ls.rb
 - lib/miga/cli/action/ncbi_get.rb
 - lib/miga/cli/action/new.rb
 - lib/miga/cli/action/next_step.rb
+- lib/miga/cli/action/option.rb
 - lib/miga/cli/action/preproc_wf.rb
 - lib/miga/cli/action/quality_wf.rb
 - lib/miga/cli/action/rm.rb
@@ -169,9 +171,11 @@ files:
 - lib/miga/common/base.rb
 - lib/miga/common/format.rb
 - lib/miga/common/hooks.rb
+- lib/miga/common/net.rb
 - lib/miga/common/path.rb
 - lib/miga/common/with_daemon.rb
 - lib/miga/common/with_daemon_class.rb
+- lib/miga/common/with_option.rb
 - lib/miga/common/with_result.rb
 - lib/miga/daemon.rb
 - lib/miga/daemon/base.rb
@@ -235,6 +239,7 @@ files:
 - test/json_test.rb
 - test/lair_test.rb
 - test/metadata_test.rb
+- test/net_test.rb
 - test/project_test.rb
 - test/remote_dataset_test.rb
 - test/result_stats_test.rb
@@ -244,6 +249,7 @@ files:
 - test/taxonomy_test.rb
 - test/test_helper.rb
 - test/with_daemon_test.rb
+- test/with_option_test.rb
 - utils/adapters.fa
 - utils/cleanup-databases.rb
 - utils/core-pan-plot.R
@@ -563,7 +569,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.2
+rubygems_version: 3.1.4
 signing_key:
 specification_version: 4
 summary: MiGA