miga-base 1.2.15.2 → 1.2.15.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 02ee43a4f918d4adb45bc28c20386965eeea6a6a7447a7bb56efbd7017c4ee54
-  data.tar.gz: c7d16aff20c61fd64833a3aa2f9ca66aaa6f3caedc19a03ae08cd1b9bd08b720
+  metadata.gz: 8ee87db325ab9759e42953f999099553c0921eca9fc6739db3b132f624b93177
+  data.tar.gz: e423b05412fba8256e0b3d9a6b8411c70b1f45d6addfe01129e842319d24baf9
 SHA512:
-  metadata.gz: 94ca45cab979c73e767cd05dfaceca410b6cedef44a5d9b0d16e4439651d872013fadc23a54d3ed6355bf6ed045f673e8e80424979e17af7dae0a32cd22e89d7
-  data.tar.gz: 0d83195dcbe7afb4fbfce02d492ed63c93776f1756037aa6412ab94b6378ae54d983a0583c3cf1c27e5c9a9b2dca108d386a60aaabce80a7af083d53a9cf0648
+  metadata.gz: 8e473e720985fc09ac49e26f13c2734150fbbaf72422185de7982502e042ae1629e824ae0a2c50fe5cd2f0bfc642ceb6f79dc55cfb13d44be1ca828a639bb16d
+  data.tar.gz: 7692908ef9e69de7526955956a9c6c4d74d3939d69509ac1bfb1a4981248fab6fc2b54091ea56a380f80c913ceddb6179b09f4f1fef37a10cfe1b50bd7e8e74b

data/lib/miga/cli/action/download/gtdb.rb

@@ -43,7 +43,10 @@ module MiGA::Cli::Action::Download::Gtdb
           remote_row_name(acc),
           {
             ids: [acc], db: :assembly, universe: :gtdb,
-            md: { type: :genome, gtdb_assembly: acc }
+            md: {
+              type: :genome, gtdb_assembly: acc,
+              get_ncbi_taxonomy: cli[:get_ncbi_taxonomy]
+            }
           }
         ]
       end

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

@@ -19,6 +19,10 @@ class MiGA::Cli::Action::GtdbGet < MiGA::Cli::Action
         '(Mandatory) Taxon name in GTDB format (e.g., g__Escherichia)'
       ) { |v| cli[:taxon] = v }
       cli_base_flags(opt)
+      opt.on(
+        '--ncbi-taxonomy',
+        'Retrieve NCBI taxonomy instead of GTDB taxonomy'
+      ) { |v| cli[:get_ncbi_taxonomy] = v }
       cli_task_flags(opt)
       cli_name_modifiers(opt)
       cli_filters(opt)

data/lib/miga/daemon.rb

@@ -128,7 +128,10 @@ class MiGA::Daemon < MiGA::MiGA
     say(*msg) if verbosity >= level
   end
 
-  alias miga_say say
+  ##
+  # Rename the orginal MiGA::MiGA.say as +miga_say+, allowing
+  # external reporting since MiGA::Daemon overwrites +say+
+  alias_method :miga_say, :say
 
   ##
   # Same as +l_say+ with +level = 1+

data/lib/miga/lair.rb

@@ -143,14 +143,16 @@ class MiGA::Lair < MiGA::MiGA
   end
 
   ##
-  # Launch daemon for the MiGA::Project +project+
+  # Launch daemon for the MiGA::Project +project+ and returns the corresponding
+  # MiGA::Daemon object
   def launch_daemon(project)
     say "Launching daemon: #{project.path}"
-    d = MiGA::Daemon.new(project, options[:json])
-    d.runopts(:shutdown_when_done, true) unless options[:keep_inactive]
+    daemon = MiGA::Daemon.new(project, options[:json])
+    daemon.runopts(:shutdown_when_done, true) unless options[:keep_inactive]
     unless options[:dry]
-      d.start
+      daemon.start
       sleep(1) # <- to make sure the daemon started up (it takes about 0.1 secs)
     end
+    daemon
   end
 end

data/lib/miga/remote_dataset/download.rb

@@ -42,7 +42,7 @@ class MiGA::RemoteDataset
     # +extra+: Array, passed to download
     # +format+: String, passed to download
     def ncbi_asm_rest(opts)
-      url_dir = opts[:obj].ncbi_asm_json_doc['ftppath_genbank']
+      url_dir = opts[:obj].ncbi_asm_json_doc&.dig('ftppath_genbank')
       if url_dir.nil? || url_dir.empty?
         raise MiGA::RemoteDataMissingError.new(
           "Missing ftppath_genbank in NCBI Assembly JSON"
@@ -60,7 +60,8 @@ class MiGA::RemoteDataset
     # Download data from NCBI GenBank (nuccore) database using the REST method.
     # Supported +opts+ (Hash) are the same as #download_rest and #ncbi_asm_rest.
     def ncbi_gb_rest(opts)
-      o = download_rest(opts)
+      # Simply use defaults, but ensure that the URL can be properly formed
+      o = download_rest(opts.merge(universe: :ncbi, db: :nuccore, format: :gb))
       return o unless o.strip.empty?
 
       MiGA::MiGA.DEBUG 'Empty sequence, attempting download from NCBI assembly'

data/lib/miga/remote_dataset.rb

@@ -30,7 +30,14 @@ class MiGA::RemoteDataset < MiGA::MiGA
         )
       end
       return out
-    rescue MiGA::RemoteDataMissingError => e
+    rescue JSON::ParserError, MiGA::RemoteDataMissingError => e
+      # Note that +JSON::ParserError+ is being rescued because the NCBI backend
+      # may in some cases return a malformed JSON response indicating that the
+      # "Search Backend failed". The issue with the JSON payload is that it
+      # includes two tab characters (\t\t) in the error message, which is not
+      # allowed by the JSON specification and causes a parsing error
+      # (see https://www.rfc-editor.org/rfc/rfc4627#page-4)
+
       if retrials <= 0
         raise e
       else
@@ -118,6 +125,7 @@ class MiGA::RemoteDataset < MiGA::MiGA
   # Get metadata from the remote location.
   def get_metadata(metadata_def = {})
     metadata_def.each { |k, v| @metadata[k] = v }
+
     case universe
     when :ebi, :ncbi, :web
       # Get taxonomy
@@ -126,14 +134,20 @@ class MiGA::RemoteDataset < MiGA::MiGA
       # Get taxonomy
       @metadata[:tax] = get_gtdb_taxonomy
     end
+
+    if metadata[:get_ncbi_taxonomy]
+      tax = get_ncbi_taxonomy
+      tax&.add_alternative(@metadata[:tax].dup, false) if @metadata[:tax]
+      @metadata[:tax] = tax
+    end
+    @metadata[:get_ncbi_taxonomy] = nil
     @metadata = get_type_status(metadata)
   end
 
   ##
   # Get NCBI Taxonomy ID.
   def get_ncbi_taxid
-    origin = (universe == :ncbi and db == :assembly) ? :web : universe
-    send("get_ncbi_taxid_from_#{origin}")
+    send("get_ncbi_taxid_from_#{universe}")
   end
 
   ##
@@ -141,9 +155,9 @@ class MiGA::RemoteDataset < MiGA::MiGA
   # +metadata+ hash.
   def get_type_status(metadata)
     if metadata[:ncbi_asm]
-      get_type_status_ncbi_asm metadata
+      get_type_status_ncbi_asm(metadata)
     elsif metadata[:ncbi_nuccore]
-      get_type_status_ncbi_nuccore metadata
+      get_type_status_ncbi_nuccore(metadata)
     else
       metadata
     end
@@ -218,7 +232,9 @@ class MiGA::RemoteDataset < MiGA::MiGA
   end
 
   def get_ncbi_taxid_from_ncbi
-    doc = self.class.download(universe, db, ids, :gb).split(/\n/)
+    return get_ncbi_taxid_from_web if db == :assembly
+
+    doc = self.class.download(:ncbi, db, ids, :gb, nil, [], self).split(/\n/)
     ln = doc.grep(%r{^\s+/db_xref="taxon:}).first
     return nil if ln.nil?
 
@@ -228,8 +244,10 @@ class MiGA::RemoteDataset < MiGA::MiGA
     ln
   end
 
+  alias :get_ncbi_taxid_from_gtdb :get_ncbi_taxid_from_ncbi
+
   def get_ncbi_taxid_from_ebi
-    doc = self.class.download(universe, db, ids, :annot).split(/\n/)
+    doc = self.class.download(:ebi, db, ids, :annot).split(/\n/)
     ln = doc.grep(%r{^FT\s+/db_xref="taxon:}).first
     ln = doc.grep(/^OX\s+NCBI_TaxID=/).first if ln.nil?
     return nil if ln.nil?

data/lib/miga/taxonomy.rb

@@ -168,6 +168,12 @@ class MiGA::Taxonomy < MiGA::MiGA
     hsh.to_json(*a)
   end
 
+  ##
+  # Generate a duplicate of the current object
+  def dup
+    self.class.new(to_s, nil, alternative.map(&:dup))
+  end
+
   private
 
   def initialize_by_str(str)

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, 15, 2].freeze
+  VERSION = [1.2, 15, 4].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2023, 1, 25)
+  VERSION_DATE = Date.new(2023, 2, 7)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.15.2
+  version: 1.2.15.4
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-01-25 00:00:00.000000000 Z
+date: 2023-02-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -271,13 +271,6 @@ files:
 - test/test_helper.rb
 - test/with_daemon_test.rb
 - test/with_option_test.rb
-- utils/FastAAI/00.Libraries/01.SCG_HMMs/Archaea_SCG.hmm
-- utils/FastAAI/00.Libraries/01.SCG_HMMs/Bacteria_SCG.hmm
-- utils/FastAAI/00.Libraries/01.SCG_HMMs/Complete_SCG_DB.hmm
-- utils/FastAAI/FastAAI
-- utils/FastAAI/FastAAI-legacy/FastAAI
-- utils/FastAAI/FastAAI-legacy/kAAI_v1.0_virus.py
-- utils/FastAAI/README.md
 - utils/adapters.fa
 - utils/cleanup-databases.rb
 - utils/core-pan-plot.R
@@ -289,297 +282,8 @@ files:
 - utils/distance/temporal.rb
 - utils/distances.rb
 - utils/domain-ess-genes.rb
-- utils/enveomics/Docs/recplot2.md
-- utils/enveomics/Examples/aai-matrix.bash
-- utils/enveomics/Examples/ani-matrix.bash
-- utils/enveomics/Examples/essential-phylogeny.bash
-- utils/enveomics/Examples/unus-genome-phylogeny.bash
-- utils/enveomics/LICENSE.txt
-- utils/enveomics/Makefile
-- utils/enveomics/Manifest/Tasks/aasubs.json
-- utils/enveomics/Manifest/Tasks/blasttab.json
-- utils/enveomics/Manifest/Tasks/distances.json
-- utils/enveomics/Manifest/Tasks/fasta.json
-- utils/enveomics/Manifest/Tasks/fastq.json
-- utils/enveomics/Manifest/Tasks/graphics.json
-- utils/enveomics/Manifest/Tasks/mapping.json
-- utils/enveomics/Manifest/Tasks/ogs.json
-- utils/enveomics/Manifest/Tasks/other.json
-- utils/enveomics/Manifest/Tasks/remote.json
-- utils/enveomics/Manifest/Tasks/sequence-identity.json
-- utils/enveomics/Manifest/Tasks/tables.json
-- utils/enveomics/Manifest/Tasks/trees.json
-- utils/enveomics/Manifest/Tasks/variants.json
-- utils/enveomics/Manifest/categories.json
-- utils/enveomics/Manifest/examples.json
-- utils/enveomics/Manifest/tasks.json
-- utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash
-- utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl
-- utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl
-- utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl
-- utils/enveomics/Pipelines/assembly.pbs/README.md
-- utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash
-- utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash
-- utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash
-- utils/enveomics/Pipelines/assembly.pbs/RUNME.bash
-- utils/enveomics/Pipelines/assembly.pbs/kSelector.R
-- utils/enveomics/Pipelines/assembly.pbs/newbler.pbs
-- utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl
-- utils/enveomics/Pipelines/assembly.pbs/soap.pbs
-- utils/enveomics/Pipelines/assembly.pbs/stats.pbs
-- utils/enveomics/Pipelines/assembly.pbs/velvet.pbs
-- utils/enveomics/Pipelines/blast.pbs/01.pbs.bash
-- utils/enveomics/Pipelines/blast.pbs/02.pbs.bash
-- utils/enveomics/Pipelines/blast.pbs/03.pbs.bash
-- utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl
-- utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash
-- utils/enveomics/Pipelines/blast.pbs/FastA.split.pl
-- utils/enveomics/Pipelines/blast.pbs/README.md
-- utils/enveomics/Pipelines/blast.pbs/RUNME.bash
-- utils/enveomics/Pipelines/blast.pbs/TASK.check.bash
-- utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash
-- utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash
-- utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash
-- utils/enveomics/Pipelines/blast.pbs/TASK.run.bash
-- utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash
-- utils/enveomics/Pipelines/idba.pbs/README.md
-- utils/enveomics/Pipelines/idba.pbs/RUNME.bash
-- utils/enveomics/Pipelines/idba.pbs/run.pbs
-- utils/enveomics/Pipelines/trim.pbs/README.md
-- utils/enveomics/Pipelines/trim.pbs/RUNME.bash
-- utils/enveomics/Pipelines/trim.pbs/run.pbs
-- utils/enveomics/README.md
-- utils/enveomics/Scripts/AAsubs.log2ratio.rb
-- utils/enveomics/Scripts/Aln.cat.rb
-- utils/enveomics/Scripts/Aln.convert.pl
-- utils/enveomics/Scripts/AlphaDiversity.pl
-- utils/enveomics/Scripts/BedGraph.tad.rb
-- utils/enveomics/Scripts/BedGraph.window.rb
-- utils/enveomics/Scripts/BlastPairwise.AAsubs.pl
-- utils/enveomics/Scripts/BlastTab.addlen.rb
-- utils/enveomics/Scripts/BlastTab.advance.bash
-- utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl
-- utils/enveomics/Scripts/BlastTab.catsbj.pl
-- utils/enveomics/Scripts/BlastTab.cogCat.rb
-- utils/enveomics/Scripts/BlastTab.filter.pl
-- utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl
-- utils/enveomics/Scripts/BlastTab.metaxaPrep.pl
-- utils/enveomics/Scripts/BlastTab.pairedHits.rb
-- utils/enveomics/Scripts/BlastTab.recplot2.R
-- utils/enveomics/Scripts/BlastTab.seqdepth.pl
-- utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl
-- utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl
-- utils/enveomics/Scripts/BlastTab.subsample.pl
-- utils/enveomics/Scripts/BlastTab.sumPerHit.pl
-- utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl
-- utils/enveomics/Scripts/BlastTab.topHits_sorted.rb
-- utils/enveomics/Scripts/Chao1.pl
-- utils/enveomics/Scripts/CharTable.classify.rb
-- utils/enveomics/Scripts/EBIseq2tax.rb
-- utils/enveomics/Scripts/FastA.N50.pl
-- utils/enveomics/Scripts/FastA.extract.rb
-- utils/enveomics/Scripts/FastA.filter.pl
-- utils/enveomics/Scripts/FastA.filterLen.pl
-- utils/enveomics/Scripts/FastA.filterN.pl
-- utils/enveomics/Scripts/FastA.fragment.rb
-- utils/enveomics/Scripts/FastA.gc.pl
-- utils/enveomics/Scripts/FastA.interpose.pl
-- utils/enveomics/Scripts/FastA.length.pl
-- utils/enveomics/Scripts/FastA.mask.rb
-- utils/enveomics/Scripts/FastA.per_file.pl
-- utils/enveomics/Scripts/FastA.qlen.pl
-- utils/enveomics/Scripts/FastA.rename.pl
-- utils/enveomics/Scripts/FastA.revcom.pl
-- utils/enveomics/Scripts/FastA.sample.rb
-- utils/enveomics/Scripts/FastA.slider.pl
-- utils/enveomics/Scripts/FastA.split.pl
-- utils/enveomics/Scripts/FastA.split.rb
-- utils/enveomics/Scripts/FastA.subsample.pl
-- utils/enveomics/Scripts/FastA.tag.rb
-- utils/enveomics/Scripts/FastA.toFastQ.rb
-- utils/enveomics/Scripts/FastA.wrap.rb
-- utils/enveomics/Scripts/FastQ.filter.pl
-- utils/enveomics/Scripts/FastQ.interpose.pl
-- utils/enveomics/Scripts/FastQ.maskQual.rb
-- utils/enveomics/Scripts/FastQ.offset.pl
-- utils/enveomics/Scripts/FastQ.split.pl
-- utils/enveomics/Scripts/FastQ.tag.rb
-- utils/enveomics/Scripts/FastQ.test-error.rb
-- utils/enveomics/Scripts/FastQ.toFastA.awk
-- utils/enveomics/Scripts/GFF.catsbj.pl
-- utils/enveomics/Scripts/GenBank.add_fields.rb
-- utils/enveomics/Scripts/HMM.essential.rb
-- utils/enveomics/Scripts/HMM.haai.rb
-- utils/enveomics/Scripts/HMMsearch.extractIds.rb
-- utils/enveomics/Scripts/JPlace.distances.rb
-- utils/enveomics/Scripts/JPlace.to_iToL.rb
-- utils/enveomics/Scripts/M5nr.getSequences.rb
-- utils/enveomics/Scripts/MeTaxa.distribution.pl
-- utils/enveomics/Scripts/MyTaxa.fragsByTax.pl
-- utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb
-- utils/enveomics/Scripts/NCBIacc2tax.rb
-- utils/enveomics/Scripts/Newick.autoprune.R
-- utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl
-- utils/enveomics/Scripts/RecPlot2.compareIdentities.R
-- utils/enveomics/Scripts/RefSeq.download.bash
-- utils/enveomics/Scripts/SRA.download.bash
-- utils/enveomics/Scripts/TRIBS.plot-test.R
-- utils/enveomics/Scripts/TRIBS.test.R
-- utils/enveomics/Scripts/Table.barplot.R
-- utils/enveomics/Scripts/Table.df2dist.R
-- utils/enveomics/Scripts/Table.filter.pl
-- utils/enveomics/Scripts/Table.merge.pl
-- utils/enveomics/Scripts/Table.prefScore.R
-- utils/enveomics/Scripts/Table.replace.rb
-- utils/enveomics/Scripts/Table.round.rb
-- utils/enveomics/Scripts/Table.split.pl
-- utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb
-- utils/enveomics/Scripts/VCF.KaKs.rb
-- utils/enveomics/Scripts/VCF.SNPs.rb
-- utils/enveomics/Scripts/aai.rb
-- utils/enveomics/Scripts/ani.rb
-- utils/enveomics/Scripts/anir.rb
-- utils/enveomics/Scripts/clust.rand.rb
-- utils/enveomics/Scripts/gi2tax.rb
-- utils/enveomics/Scripts/in_silico_GA_GI.pl
-- utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz
-- utils/enveomics/Scripts/lib/data/lee_2019_essential.hmm.gz
-- utils/enveomics/Scripts/lib/enveomics.R
-- utils/enveomics/Scripts/lib/enveomics_rb/anir.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/bm_set.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/errors.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/gmm_em.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/match.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/og.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/rbm.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/stats.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/stats/rand.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/stats/sample.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/utils.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb
-- utils/enveomics/Scripts/ogs.annotate.rb
-- utils/enveomics/Scripts/ogs.core-pan.rb
-- utils/enveomics/Scripts/ogs.extract.rb
-- utils/enveomics/Scripts/ogs.mcl.rb
-- utils/enveomics/Scripts/ogs.rb
-- utils/enveomics/Scripts/ogs.stats.rb
-- utils/enveomics/Scripts/rbm-legacy.rb
-- utils/enveomics/Scripts/rbm.rb
-- utils/enveomics/Scripts/sam.filter.rb
-- utils/enveomics/Tests/Makefile
-- utils/enveomics/Tests/Mgen_M2288.faa
-- utils/enveomics/Tests/Mgen_M2288.fna
-- utils/enveomics/Tests/Mgen_M2321.fna
-- utils/enveomics/Tests/Nequ_Kin4M.faa
-- utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata
-- utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt
-- utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv
-- utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv
-- utils/enveomics/Tests/a_mg.cds-go.blast.tsv
-- utils/enveomics/Tests/a_mg.reads-cds.blast.tsv
-- utils/enveomics/Tests/a_mg.reads-cds.counts.tsv
-- utils/enveomics/Tests/alkB.nwk
-- utils/enveomics/Tests/anthrax-cansnp-data.tsv
-- utils/enveomics/Tests/anthrax-cansnp-key.tsv
-- utils/enveomics/Tests/hiv1.faa
-- utils/enveomics/Tests/hiv1.fna
-- utils/enveomics/Tests/hiv2.faa
-- utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv
-- utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim
-- utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec
-- utils/enveomics/Tests/phyla_counts.tsv
-- utils/enveomics/Tests/primate_lentivirus.ogs
-- utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm
-- utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm
-- utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm
-- utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm
-- utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm
-- utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm
-- utils/enveomics/build_enveomics_r.bash
-- utils/enveomics/enveomics.R/DESCRIPTION
-- utils/enveomics/enveomics.R/NAMESPACE
-- utils/enveomics/enveomics.R/R/autoprune.R
-- utils/enveomics/enveomics.R/R/barplot.R
-- utils/enveomics/enveomics.R/R/cliopts.R
-- utils/enveomics/enveomics.R/R/df2dist.R
-- utils/enveomics/enveomics.R/R/growthcurve.R
-- utils/enveomics/enveomics.R/R/prefscore.R
-- utils/enveomics/enveomics.R/R/recplot.R
-- utils/enveomics/enveomics.R/R/recplot2.R
-- utils/enveomics/enveomics.R/R/tribs.R
-- utils/enveomics/enveomics.R/R/utils.R
-- utils/enveomics/enveomics.R/README.md
-- utils/enveomics/enveomics.R/data/growth.curves.rda
-- utils/enveomics/enveomics.R/data/phyla.counts.rda
-- utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd
-- utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd
-- utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd
-- utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd
-- utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd
-- utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd
-- utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd
-- utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd
-- utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd
-- utils/enveomics/enveomics.R/man/enve.__tribs.Rd
-- utils/enveomics/enveomics.R/man/enve.barplot.Rd
-- utils/enveomics/enveomics.R/man/enve.cliopts.Rd
-- utils/enveomics/enveomics.R/man/enve.col.alpha.Rd
-- utils/enveomics/enveomics.R/man/enve.col2alpha.Rd
-- utils/enveomics/enveomics.R/man/enve.df2dist.Rd
-- utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd
-- utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd
-- utils/enveomics/enveomics.R/man/enve.growthcurve.Rd
-- utils/enveomics/enveomics.R/man/enve.prefscore.Rd
-- utils/enveomics/enveomics.R/man/enve.prune.dist.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd
-- utils/enveomics/enveomics.R/man/enve.selvector.Rd
-- utils/enveomics/enveomics.R/man/enve.tribs.Rd
-- utils/enveomics/enveomics.R/man/enve.tribs.test.Rd
-- utils/enveomics/enveomics.R/man/enve.truncate.Rd
-- utils/enveomics/enveomics.R/man/growth.curves.Rd
-- utils/enveomics/enveomics.R/man/phyla.counts.Rd
-- utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd
-- utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd
-- utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd
-- utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd
-- utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd
-- utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd
-- utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd
-- utils/enveomics/globals.mk
-- utils/enveomics/manifest.json
 - utils/find-medoid.R
 - utils/index_metadata.rb
-- utils/multitrim/Multitrim How-To.pdf
-- utils/multitrim/README.md
-- utils/multitrim/multitrim.py
-- utils/multitrim/multitrim.yml
 - utils/mytaxa_scan.R
 - utils/mytaxa_scan.rb
 - utils/plot-taxdist.R
@@ -598,7 +302,7 @@ homepage: http://enve-omics.ce.gatech.edu/miga
 licenses:
 - Artistic-2.0
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options:
 - lib
 - README.md
@@ -619,8 +323,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.6
-signing_key: 
+rubygems_version: 3.2.3
+signing_key:
 specification_version: 4
 summary: MiGA
 test_files: []