miga-base 0.7.25.1 → 0.7.26.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 5190950602fd859e89ef657912d5749879cd99dfd561e7bd0d1d571683abedfa
-  data.tar.gz: b3e436fde3f35a5b85a52f62d33460eb8ab627fe5d2b63c9270f74432a78d339
+  metadata.gz: 8a4edaaac424eb59fe5956b98c74b6926bfd57b90fd80e0dff9556c5ec75aae5
+  data.tar.gz: 0d2bba4f71074ef9efbeb03482a2d860b3c56ecd6734e7e8aeb82a928c2eec7d
 SHA512:
-  metadata.gz: 5d81f5d53204903b62a55b82ef817751c9c1950b13f4bd20a8120bc5c4abddbc8f2c7f4c3c0c8dabbc00342d8cc85e752a993fdd43d24b0fc66a1c74f8763594
-  data.tar.gz: 763e2bfe0b3c50b385637185b94f4703c9d5a72241b8dd9d9de51412d89eec943e3c62253dd7c47ccd3d09080ebacb46f534c6a05f600b65d6cd271eb4da833c
+  metadata.gz: '0052068c9d5a055d2c13694f1bacf755a37aa294d6db76ea8ed10a1464ddd58f6a536513f8d3f8817cf2491b7f2b01825fcf891bea75e72d699b0d2b9b82804e'
+  data.tar.gz: bbef9fa36b8b8900a3c9de38b3e69daf23fddf2fea59d0899d2781edecd96d32c6f612945ed8f32c373ea669ee7ee02c9c0d9db5db8b13cd92c95c94601494ca

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

@@ -14,6 +14,8 @@ class MiGA::Cli::Action::Init < MiGA::Cli::Action
     cli.defaults = {
       mytaxa: nil,
       rdp: nil,
+      reads: nil,
+      optional: nil,
       config: File.join(ENV['MIGA_HOME'], '.miga_modules'),
       ask: false,
       auto: false,
@@ -35,6 +37,16 @@ class MiGA::Cli::Action::Init < MiGA::Cli::Action
         'Should I try setting up the RDP classifier?',
         'By default: interactive (true if --auto)'
       ) { |v| cli[:rdp] = v }
+      opt.on(
+        '--[no-]read-processing',
+        'Should I try setting up read processing software?',
+        'By default: interactive (true if --auto)'
+      ) { |v| cli[:reads] = v }
+      opt.on(
+        '--[no-]optional',
+        'Should I try setting up the optional software?',
+        'Automatically sets answers for mytaxa, rdp, and reads'
+      ) { |v| cli[:optional] = v }
       opt.on(
         '--daemon-type STRING',
         'Type of daemon launcher, one of: bash, ssh, qsub, msub, slurm',
@@ -104,6 +116,8 @@ class MiGA::Cli::Action::Init < MiGA::Cli::Action
     rc_fh.puts "export MIGA_MYTAXA='#{cli[:mytaxa] ? 'yes' : 'no'}'"
     ask_for_optional(:rdp, 'RDP classifier')
     rc_fh.puts "export MIGA_RDP='#{cli[:rdp] ? 'yes' : 'no'}'"
+    ask_for_optional(:reads, 'read processing')
+    rc_fh.puts "export MIGA_READS='#{cli[:reads] ? 'yes' : 'no'}'"
     paths = {}
     rc_fh.puts 'MIGA_PATH=""'
     req_path = File.expand_path('utils/requirements.txt', MiGA.root_path)
@@ -123,20 +137,20 @@ class MiGA::Cli::Action::Init < MiGA::Cli::Action
   def define_software(ln)
     r = ln.chomp.split(/\t+/)
     return if %w[Software --------].include?(r[0])
-    return if r[0] =~ /\(mytaxa\)$/ && !cli[:mytaxa]
-    return if r[0] =~ /\(rdp\)$/ && !cli[:rdp]
+    %i[mytaxa rdp reads].each { |i| return if r[0] =~ /\(#{i}\)$/ && !cli[i] }
 
     r
   end
 
   def ask_for_optional(symbol, name)
-    if cli[symbol].nil?
-      cli[symbol] =
-        cli.ask_user(
-          "Should I include #{name} modules?",
-          'yes', %w(yes no)
-        ) == 'yes'
-    end
+    cli[symbol] = cli[:optional] if !cli[:optional].nil? && cli[symbol].nil?
+    return cli[symbol] unless cli[symbol].nil?
+
+    cli[symbol] =
+      cli.ask_user(
+        "Should I include #{name} modules?",
+        'yes', %w(yes no)
+      ) == 'yes'
   end
 
   def find_software(exec)

data/lib/miga/version.rb

@@ -10,7 +10,7 @@ module MiGA
   # - Float representing the major.minor version.
   # - Integer representing gem releases of the current version.
   # - Integer representing minor changes that require new version number.
-  VERSION = [0.7, 25, 1].freeze
+  VERSION = [0.7, 26, 2].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2021, 2, 22)
+  VERSION_DATE = Date.new(2021, 3, 1)
 
   ##
   # Reference of MiGA.

data/utils/distance/pipeline.rb

@@ -15,7 +15,7 @@ module MiGA::DistanceRunner::Pipeline
     values = send(metric, sbj_datasets)
     max_idx = values.map(&:to_f).each_with_index.max[1]
     max_val = values[max_idx]
-    val_med = sbj_dataset[max_idx].name
+    val_med = sbj_datasets[max_idx].name
     val_cls = max_idx + 1
     puts "[#{classif}] New max: #{val_med} (#{val_cls}): #{max_val}"
 

data/utils/distance/runner.rb

@@ -102,7 +102,8 @@ class MiGA::DistanceRunner
     cl_path = res.file_path :clades_ani95
     if !cl_path.nil? && File.size?(cl_path) && tsk[0] == :clade_finding
       clades = File.foreach(cl_path).map { |i| i.chomp.split(',') }
-      sbj_datasets = clades.find { |i| i.include?(closest[:ds]) }
+      sbj_dataset_names = clades.find { |i| i.include?(closest[:ds]) }
+      sbj_datasets = sbj_dataset_names&.map { |i| ref_project.dataset(i) }
       ani_after_aai(sbj_datasets, 80.0) if sbj_datasets
     end
 

data/utils/requirements.txt

@@ -10,12 +10,12 @@ 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
-IDBA		idba_ud		http://i.cs.hku.hk/~alse/hkubrg/projects/idba
 MCL		mcl		http://micans.org/mcl/
 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+
+IDBA (reads)	idba_ud		http://i.cs.hku.hk/~alse/hkubrg/projects/idba
+Scythe (reads)	scythe		https://github.com/vsbuffalo/scythe				Required version: 0.991+
+FastQC (reads)	fastqc		http://www.bioinformatics.babraham.ac.uk/projects/fastqc
+SolexaQA++ (reads)	SolexaQA++	http://solexaqa.sourceforge.net				Required version: v3.1.3+
 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

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.25.1
+  version: 0.7.26.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-02-22 00:00:00.000000000 Z
+date: 2021-03-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -554,7 +554,7 @@ homepage: http://enve-omics.ce.gatech.edu/miga
 licenses:
 - Artistic-2.0
 metadata: {}
-post_install_message:
+post_install_message: 
 rdoc_options:
 - lib
 - README.md
@@ -576,7 +576,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubygems_version: 3.1.4
-signing_key:
+signing_key: 
 specification_version: 4
 summary: MiGA
 test_files: []