miga-base 1.2.8.2 → 1.2.10.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 6605edc35cd0b2aec6d095653ff1d9604df81d6a57e341a290cbd213bb18fee3
-  data.tar.gz: 2f811051db25da424bdf9f9c89390a4e0cac33fb3c6330e255b369d171e8a4b9
+  metadata.gz: 22d59bdb8dee84becd895fa7cd7be47912f3b895025494e55fb46b7125ac5560
+  data.tar.gz: d7213e012fa9b110d5391f5957cd3b2336e41a7ad84775471beca7da3c9510e3
 SHA512:
-  metadata.gz: 252fe9abe5ce14ebe86c5250716b9ce541f1faf510bd36ae2d33f4f15f964f3ec735a66db9fa11503b74fb82f16d6a2a5c43d6df3a71b67dacec65462425d759
-  data.tar.gz: ef734003e57818b155347ce591e9683420ecfa00cd5b4398c0ed1485fc23108a74d9bd91980d6a2bb4c2481c3d1027805b9083fb9add802b5a30f140926c996d
+  metadata.gz: ecfd6595931a7fb0fd9b924a8a7cc64535a78ab97a1a978a65f0861e719d8570ef4ac34da8587a23664e84c215b67efdaac059d1aa159da318750dd75ebab04d
+  data.tar.gz: cda07a76118f2cba313deb974d8f6397612e11dd619332a707e12898afbb1d199bb8eeef07485c95826ddaa7b15adb617475168b668b201f59b7acc424afff84

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

@@ -60,13 +60,16 @@ class MiGA::Cli::Action::ClassifyWf < MiGA::Cli::Action
     )
     p.set_option(:ref_project, ref_db.path)
     p.set_option(:tax_pvalue, cli[:pvalue])
+
     # Run
     run_daemon
     summarize(%w[cds assembly essential_genes]) if cli[:summaries]
-    summarize(['taxonomy'])
-    cli.say "Summary: classification"
-    ofile = File.expand_path('classification.tsv', cli[:outdir])
-    call_cli(['ls', '-P', cli[:outdir], '-m', 'tax', '--tab', '-o', ofile])
+    summarize(%w[taxonomy])
+    unless cli[:prepare_and_exit]
+      cli.say "Summary: classification"
+      ofile = File.expand_path('classification.tsv', cli[:outdir])
+      call_cli(['ls', '-P', cli[:outdir], '-m', 'tax', '--tab', '-o', ofile])
+    end
     cleanup
   end
 

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

@@ -68,6 +68,8 @@ class MiGA::Cli::Action::DerepWf < MiGA::Cli::Action
   private
 
   def dereplicate(p)
+    return if cli[:prepare_and_exit]
+
     cli.say 'Extracting genomospecies clades'
     r = p.result(:clade_finding) or raise 'Result unavailable: run failed'
     c_f = r.file_path(:clades_gsp) or raise 'Result incomplete: run failed'

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

@@ -26,6 +26,7 @@ class MiGA::Cli::Action::IndexWf < MiGA::Cli::Action
   def perform
     # Input data
     p = create_project(:assembly, {}, run_mytaxa_scan: cli[:mytaxa])
+
     # Run
     run_daemon
     summarize

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

@@ -52,6 +52,12 @@ class MiGA::Cli::Action::Init < MiGA::Cli::Action
         'Type of daemon launcher, one of: bash, ssh, qsub, msub, slurm',
         "By default: interactive (#{cli[:dtype]} if --auto)"
       ) { |v| cli[:dtype] = v.to_sym }
+      %w[R ruby python].each do |bin|
+        opt.on(
+          "--path-to-#{bin} STRING",
+          "Use this path to #{bin} instead of testing for executables"
+        ) { |v| cli[:"path_to_#{bin}"] = v }
+      end
       opt.on(
         '--ask-all',
         'Ask for the location of all software',
@@ -130,8 +136,13 @@ class MiGA::Cli::Action::Init < MiGA::Cli::Action
       fh.each_line do |ln|
         r = define_software(ln) or next
         cli.print "Testing #{r[0]}#{" (#{r[3]})" if r[3]}... "
-        path = find_software(r[1])
-        paths[r[1]] = File.expand_path(r[1], path).shellescape
+        if cli[:"path_to_#{r[1]}"]
+          paths[r[1]] = cli[:"path_to_#{r[1]}"]
+          cli.puts "user-provided: #{paths[r[1]]}"
+        else
+          path = find_software(r[1])
+          paths[r[1]] = File.expand_path(r[1], path).shellescape
+        end
       end
     end
     rc_fh.puts 'export PATH="$MIGA_PATH$PATH"'

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

@@ -41,6 +41,7 @@ class MiGA::Cli::Action::PreprocWf < MiGA::Cli::Action
       d_metadata[:run_mytaxa] = false
     end
     p = create_project(cli[:input_type], p_metadata, d_metadata)
+
     # Run
     run_daemon
     summarize

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

@@ -28,10 +28,11 @@ class MiGA::Cli::Action::QualityWf < MiGA::Cli::Action
     d_metadata = { run_distances: false }
     d_metadata[:run_mytaxa_scan] = false unless cli[:mytaxa]
     p = create_project(:assembly, p_metadata, d_metadata)
+
     # Run
     run_daemon
     summarize
-    if cli[:mytaxa]
+    if cli[:mytaxa] && !cli[:prepare_and_exit]
       dir = File.expand_path('mytaxa_scan', cli[:outdir])
       Dir.mkdir(dir)
       p.each_dataset do |d|

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

@@ -8,7 +8,8 @@ module MiGA::Cli::Action::Wf
     cli.expect_files = true
     cli.defaults = {
       clean: false, project_type: :genomes, dataset_type: :popgenome,
-      ncbi_draft: true, min_qual: MiGA::Project.OPTIONS[:min_qual][:default]
+      ncbi_draft: true, min_qual: MiGA::Project.OPTIONS[:min_qual][:default],
+      prepare_and_exit: false
     }
   end
 
@@ -83,6 +84,10 @@ module MiGA::Cli::Action::Wf
       'Number of CPUs to use per project-wide job',
       'By default controlled by the daemon configuration (ppn_project or ppn)'
     ) { |v| cli[:threads_project] = v }
+    opt.on(
+      '--prepare-and-exit',
+      'Create project and import datasets, but do not run any analyses'
+    ) { |v| cli[:prepare_and_exit] = v }
   end
 
   def opts_for_wf_distances(opt)
@@ -159,6 +164,8 @@ module MiGA::Cli::Action::Wf
   end
 
   def summarize(which = %w[cds assembly essential_genes ssu])
+    return if cli[:prepare_and_exit]
+
     which.each do |r|
       cli.say "Summary: #{r}"
       call_cli(
@@ -173,6 +180,7 @@ module MiGA::Cli::Action::Wf
   end
 
   def cleanup
+    return if cli[:prepare_and_exit]
     return unless cli[:clean]
 
     cli.say 'Cleaning up intermediate files'
@@ -188,6 +196,8 @@ module MiGA::Cli::Action::Wf
   end
 
   def run_daemon
+    return if cli[:prepare_and_exit]
+
     cmd  = ['daemon', 'run', '-P', cli[:outdir], '--shutdown-when-done']
     cmd += ['--json', cli[:daemon_json]] if cli[:daemon_json]
     cmd += ['--max-jobs', cli[:jobs]] if cli[:jobs]

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 = [1.2, 8, 2].freeze
+  VERSION = [1.2, 10, 0].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2022, 8, 14)
+  VERSION_DATE = Date.new(2022, 11, 28)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.8.2
+  version: 1.2.10.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-08-14 00:00:00.000000000 Z
+date: 2022-11-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons