miga-base 1.2.17.0 → 1.2.17.2

data/utils/multitrim/multitrim.yml

@@ -0,0 +1,13 @@
+name: multitrim
+dependencies:
+  - faqcs
+  - falco
+  - seqtk
+  - fastp
+  - pigz
+  - multitrim
+  
+channels:
+  - conda-forge
+  - bioconda
+  - kgerhardt

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.17.0
+  version: 1.2.17.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-02-14 00:00:00.000000000 Z
+date: 2023-02-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -273,6 +273,13 @@ 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
@@ -284,8 +291,263 @@ 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/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/low-cov.bg.gz
+- 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
@@ -304,7 +566,7 @@ homepage: http://enve-omics.ce.gatech.edu/miga
 licenses:
 - Artistic-2.0
 metadata: {}
-post_install_message:
+post_install_message: 
 rdoc_options:
 - lib
 - README.md
@@ -325,8 +587,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.3
-signing_key:
+rubygems_version: 3.1.6
+signing_key: 
 specification_version: 4
 summary: MiGA
 test_files: []