miga-base 0.7.25.3 → 0.7.26.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 47313defda91b1a031e7700e193fadf688a0115deedf77e40013c16e79bb8b49
-  data.tar.gz: ab6ea787eee6aed1c28ca09a97c8d580b23985fb3961dbf3fa7a33fb2a14f4e5
+  metadata.gz: dda80476da72166bd5eb6bc22a5ae7afc94285a58afe312633a06115e7336d80
+  data.tar.gz: 176c5a3c167232bb221b778b2bb3762c6795893171740dbff83b899d68034cd9
 SHA512:
-  metadata.gz: b152125992f0ece34a0a1d59ccd3d69ed5c931c5fada4a167a12bf3e53054505bde9974fc7e43d32c1164a8d9f89b69135638d71c572b015b04a311bb38540a4
-  data.tar.gz: 9a5493e2d025a4c245ed9b33a2059f529b6ff265274685d602869180538895807034cb24d1628a2f7ed2a9e9124f9b6097d49ad845f736c7c05355cc4bcf7add
+  metadata.gz: 90b69b23c515e7f8ce2508b5c719856112e2b874876c81bc18767fa5b384d3d6b2e1b819b313f7afbc6d9260ddbaf9b143bd3503c641eed29f1738197837c13b
+  data.tar.gz: f25b7224d1b37c386e0d4776a40be0a05496bfa9fd9715c59722794e298405280b3043ac26f7cbd5d033090673776b93a7744610aa24fd0bf7331329f0561e64

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, 3].freeze
+  VERSION = [0.7, 26, 0].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, 26)
+  VERSION_DATE = Date.new(2021, 3, 1)
 
   ##
   # Reference of MiGA.

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: 0.7.25.3
+  version: 0.7.26.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-02-26 00:00:00.000000000 Z
+date: 2021-03-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons