miga-base 0.7.25.2 → 0.7.25.3

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Files changed (277) hide show
  1. checksums.yaml +4 -4
  2. data/lib/miga/version.rb +2 -2
  3. data/utils/distance/runner.rb +2 -1
  4. metadata +5 -278
  5. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Archaea_SCG.hmm +0 -41964
  6. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Bacteria_SCG.hmm +0 -32439
  7. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Complete_SCG_DB.hmm +0 -62056
  8. data/utils/FastAAI/FastAAI/FastAAI +0 -1336
  9. data/utils/FastAAI/README.md +0 -84
  10. data/utils/FastAAI/kAAI_v1.0_virus.py +0 -1296
  11. data/utils/enveomics/Docs/recplot2.md +0 -244
  12. data/utils/enveomics/Examples/aai-matrix.bash +0 -66
  13. data/utils/enveomics/Examples/ani-matrix.bash +0 -66
  14. data/utils/enveomics/Examples/essential-phylogeny.bash +0 -105
  15. data/utils/enveomics/Examples/unus-genome-phylogeny.bash +0 -100
  16. data/utils/enveomics/LICENSE.txt +0 -73
  17. data/utils/enveomics/Makefile +0 -52
  18. data/utils/enveomics/Manifest/Tasks/aasubs.json +0 -103
  19. data/utils/enveomics/Manifest/Tasks/blasttab.json +0 -786
  20. data/utils/enveomics/Manifest/Tasks/distances.json +0 -161
  21. data/utils/enveomics/Manifest/Tasks/fasta.json +0 -766
  22. data/utils/enveomics/Manifest/Tasks/fastq.json +0 -243
  23. data/utils/enveomics/Manifest/Tasks/graphics.json +0 -126
  24. data/utils/enveomics/Manifest/Tasks/mapping.json +0 -67
  25. data/utils/enveomics/Manifest/Tasks/ogs.json +0 -382
  26. data/utils/enveomics/Manifest/Tasks/other.json +0 -829
  27. data/utils/enveomics/Manifest/Tasks/remote.json +0 -355
  28. data/utils/enveomics/Manifest/Tasks/sequence-identity.json +0 -501
  29. data/utils/enveomics/Manifest/Tasks/tables.json +0 -308
  30. data/utils/enveomics/Manifest/Tasks/trees.json +0 -68
  31. data/utils/enveomics/Manifest/Tasks/variants.json +0 -111
  32. data/utils/enveomics/Manifest/categories.json +0 -156
  33. data/utils/enveomics/Manifest/examples.json +0 -154
  34. data/utils/enveomics/Manifest/tasks.json +0 -4
  35. data/utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash +0 -69
  36. data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +0 -1
  37. data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +0 -1
  38. data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +0 -1
  39. data/utils/enveomics/Pipelines/assembly.pbs/README.md +0 -189
  40. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash +0 -112
  41. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash +0 -23
  42. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash +0 -44
  43. data/utils/enveomics/Pipelines/assembly.pbs/RUNME.bash +0 -50
  44. data/utils/enveomics/Pipelines/assembly.pbs/kSelector.R +0 -37
  45. data/utils/enveomics/Pipelines/assembly.pbs/newbler.pbs +0 -68
  46. data/utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl +0 -49
  47. data/utils/enveomics/Pipelines/assembly.pbs/soap.pbs +0 -80
  48. data/utils/enveomics/Pipelines/assembly.pbs/stats.pbs +0 -57
  49. data/utils/enveomics/Pipelines/assembly.pbs/velvet.pbs +0 -63
  50. data/utils/enveomics/Pipelines/blast.pbs/01.pbs.bash +0 -38
  51. data/utils/enveomics/Pipelines/blast.pbs/02.pbs.bash +0 -73
  52. data/utils/enveomics/Pipelines/blast.pbs/03.pbs.bash +0 -21
  53. data/utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl +0 -72
  54. data/utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash +0 -98
  55. data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +0 -1
  56. data/utils/enveomics/Pipelines/blast.pbs/README.md +0 -127
  57. data/utils/enveomics/Pipelines/blast.pbs/RUNME.bash +0 -109
  58. data/utils/enveomics/Pipelines/blast.pbs/TASK.check.bash +0 -128
  59. data/utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash +0 -16
  60. data/utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash +0 -22
  61. data/utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash +0 -26
  62. data/utils/enveomics/Pipelines/blast.pbs/TASK.run.bash +0 -89
  63. data/utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash +0 -29
  64. data/utils/enveomics/Pipelines/idba.pbs/README.md +0 -49
  65. data/utils/enveomics/Pipelines/idba.pbs/RUNME.bash +0 -95
  66. data/utils/enveomics/Pipelines/idba.pbs/run.pbs +0 -56
  67. data/utils/enveomics/Pipelines/trim.pbs/README.md +0 -54
  68. data/utils/enveomics/Pipelines/trim.pbs/RUNME.bash +0 -70
  69. data/utils/enveomics/Pipelines/trim.pbs/run.pbs +0 -130
  70. data/utils/enveomics/README.md +0 -42
  71. data/utils/enveomics/Scripts/AAsubs.log2ratio.rb +0 -171
  72. data/utils/enveomics/Scripts/Aln.cat.rb +0 -163
  73. data/utils/enveomics/Scripts/Aln.convert.pl +0 -35
  74. data/utils/enveomics/Scripts/AlphaDiversity.pl +0 -152
  75. data/utils/enveomics/Scripts/BedGraph.tad.rb +0 -93
  76. data/utils/enveomics/Scripts/BedGraph.window.rb +0 -71
  77. data/utils/enveomics/Scripts/BlastPairwise.AAsubs.pl +0 -102
  78. data/utils/enveomics/Scripts/BlastTab.addlen.rb +0 -63
  79. data/utils/enveomics/Scripts/BlastTab.advance.bash +0 -48
  80. data/utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl +0 -55
  81. data/utils/enveomics/Scripts/BlastTab.catsbj.pl +0 -104
  82. data/utils/enveomics/Scripts/BlastTab.cogCat.rb +0 -76
  83. data/utils/enveomics/Scripts/BlastTab.filter.pl +0 -47
  84. data/utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl +0 -194
  85. data/utils/enveomics/Scripts/BlastTab.metaxaPrep.pl +0 -104
  86. data/utils/enveomics/Scripts/BlastTab.pairedHits.rb +0 -157
  87. data/utils/enveomics/Scripts/BlastTab.recplot2.R +0 -48
  88. data/utils/enveomics/Scripts/BlastTab.seqdepth.pl +0 -86
  89. data/utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl +0 -119
  90. data/utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl +0 -86
  91. data/utils/enveomics/Scripts/BlastTab.subsample.pl +0 -47
  92. data/utils/enveomics/Scripts/BlastTab.sumPerHit.pl +0 -114
  93. data/utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl +0 -90
  94. data/utils/enveomics/Scripts/BlastTab.topHits_sorted.rb +0 -101
  95. data/utils/enveomics/Scripts/Chao1.pl +0 -97
  96. data/utils/enveomics/Scripts/CharTable.classify.rb +0 -234
  97. data/utils/enveomics/Scripts/EBIseq2tax.rb +0 -83
  98. data/utils/enveomics/Scripts/FastA.N50.pl +0 -56
  99. data/utils/enveomics/Scripts/FastA.extract.rb +0 -152
  100. data/utils/enveomics/Scripts/FastA.filter.pl +0 -52
  101. data/utils/enveomics/Scripts/FastA.filterLen.pl +0 -28
  102. data/utils/enveomics/Scripts/FastA.filterN.pl +0 -60
  103. data/utils/enveomics/Scripts/FastA.fragment.rb +0 -92
  104. data/utils/enveomics/Scripts/FastA.gc.pl +0 -42
  105. data/utils/enveomics/Scripts/FastA.interpose.pl +0 -93
  106. data/utils/enveomics/Scripts/FastA.length.pl +0 -38
  107. data/utils/enveomics/Scripts/FastA.mask.rb +0 -89
  108. data/utils/enveomics/Scripts/FastA.per_file.pl +0 -36
  109. data/utils/enveomics/Scripts/FastA.qlen.pl +0 -57
  110. data/utils/enveomics/Scripts/FastA.rename.pl +0 -65
  111. data/utils/enveomics/Scripts/FastA.revcom.pl +0 -23
  112. data/utils/enveomics/Scripts/FastA.sample.rb +0 -83
  113. data/utils/enveomics/Scripts/FastA.slider.pl +0 -85
  114. data/utils/enveomics/Scripts/FastA.split.pl +0 -55
  115. data/utils/enveomics/Scripts/FastA.split.rb +0 -79
  116. data/utils/enveomics/Scripts/FastA.subsample.pl +0 -131
  117. data/utils/enveomics/Scripts/FastA.tag.rb +0 -65
  118. data/utils/enveomics/Scripts/FastA.wrap.rb +0 -48
  119. data/utils/enveomics/Scripts/FastQ.filter.pl +0 -54
  120. data/utils/enveomics/Scripts/FastQ.interpose.pl +0 -90
  121. data/utils/enveomics/Scripts/FastQ.offset.pl +0 -90
  122. data/utils/enveomics/Scripts/FastQ.split.pl +0 -53
  123. data/utils/enveomics/Scripts/FastQ.tag.rb +0 -63
  124. data/utils/enveomics/Scripts/FastQ.test-error.rb +0 -81
  125. data/utils/enveomics/Scripts/FastQ.toFastA.awk +0 -24
  126. data/utils/enveomics/Scripts/GFF.catsbj.pl +0 -127
  127. data/utils/enveomics/Scripts/GenBank.add_fields.rb +0 -84
  128. data/utils/enveomics/Scripts/HMM.essential.rb +0 -351
  129. data/utils/enveomics/Scripts/HMM.haai.rb +0 -168
  130. data/utils/enveomics/Scripts/HMMsearch.extractIds.rb +0 -83
  131. data/utils/enveomics/Scripts/JPlace.distances.rb +0 -88
  132. data/utils/enveomics/Scripts/JPlace.to_iToL.rb +0 -320
  133. data/utils/enveomics/Scripts/M5nr.getSequences.rb +0 -81
  134. data/utils/enveomics/Scripts/MeTaxa.distribution.pl +0 -198
  135. data/utils/enveomics/Scripts/MyTaxa.fragsByTax.pl +0 -35
  136. data/utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb +0 -49
  137. data/utils/enveomics/Scripts/NCBIacc2tax.rb +0 -92
  138. data/utils/enveomics/Scripts/Newick.autoprune.R +0 -27
  139. data/utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl +0 -228
  140. data/utils/enveomics/Scripts/RecPlot2.compareIdentities.R +0 -32
  141. data/utils/enveomics/Scripts/RefSeq.download.bash +0 -48
  142. data/utils/enveomics/Scripts/SRA.download.bash +0 -57
  143. data/utils/enveomics/Scripts/TRIBS.plot-test.R +0 -36
  144. data/utils/enveomics/Scripts/TRIBS.test.R +0 -39
  145. data/utils/enveomics/Scripts/Table.barplot.R +0 -31
  146. data/utils/enveomics/Scripts/Table.df2dist.R +0 -30
  147. data/utils/enveomics/Scripts/Table.filter.pl +0 -61
  148. data/utils/enveomics/Scripts/Table.merge.pl +0 -77
  149. data/utils/enveomics/Scripts/Table.replace.rb +0 -69
  150. data/utils/enveomics/Scripts/Table.round.rb +0 -63
  151. data/utils/enveomics/Scripts/Table.split.pl +0 -57
  152. data/utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb +0 -227
  153. data/utils/enveomics/Scripts/VCF.KaKs.rb +0 -147
  154. data/utils/enveomics/Scripts/VCF.SNPs.rb +0 -88
  155. data/utils/enveomics/Scripts/aai.rb +0 -418
  156. data/utils/enveomics/Scripts/ani.rb +0 -362
  157. data/utils/enveomics/Scripts/clust.rand.rb +0 -102
  158. data/utils/enveomics/Scripts/gi2tax.rb +0 -103
  159. data/utils/enveomics/Scripts/in_silico_GA_GI.pl +0 -96
  160. data/utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz +0 -0
  161. data/utils/enveomics/Scripts/lib/data/lee_2019_essential.hmm.gz +0 -0
  162. data/utils/enveomics/Scripts/lib/enveomics.R +0 -1
  163. data/utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb +0 -24
  164. data/utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb +0 -253
  165. data/utils/enveomics/Scripts/lib/enveomics_rb/og.rb +0 -182
  166. data/utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb +0 -74
  167. data/utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb +0 -237
  168. data/utils/enveomics/Scripts/lib/enveomics_rb/stat.rb +0 -30
  169. data/utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb +0 -135
  170. data/utils/enveomics/Scripts/ogs.annotate.rb +0 -88
  171. data/utils/enveomics/Scripts/ogs.core-pan.rb +0 -160
  172. data/utils/enveomics/Scripts/ogs.extract.rb +0 -125
  173. data/utils/enveomics/Scripts/ogs.mcl.rb +0 -186
  174. data/utils/enveomics/Scripts/ogs.rb +0 -104
  175. data/utils/enveomics/Scripts/ogs.stats.rb +0 -131
  176. data/utils/enveomics/Scripts/rbm.rb +0 -146
  177. data/utils/enveomics/Tests/Makefile +0 -10
  178. data/utils/enveomics/Tests/Mgen_M2288.faa +0 -3189
  179. data/utils/enveomics/Tests/Mgen_M2288.fna +0 -8282
  180. data/utils/enveomics/Tests/Mgen_M2321.fna +0 -8288
  181. data/utils/enveomics/Tests/Nequ_Kin4M.faa +0 -2970
  182. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata +0 -0
  183. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt +0 -7
  184. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv +0 -17
  185. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv +0 -137
  186. data/utils/enveomics/Tests/a_mg.cds-go.blast.tsv +0 -123
  187. data/utils/enveomics/Tests/a_mg.reads-cds.blast.tsv +0 -200
  188. data/utils/enveomics/Tests/a_mg.reads-cds.counts.tsv +0 -55
  189. data/utils/enveomics/Tests/alkB.nwk +0 -1
  190. data/utils/enveomics/Tests/anthrax-cansnp-data.tsv +0 -13
  191. data/utils/enveomics/Tests/anthrax-cansnp-key.tsv +0 -17
  192. data/utils/enveomics/Tests/hiv1.faa +0 -59
  193. data/utils/enveomics/Tests/hiv1.fna +0 -134
  194. data/utils/enveomics/Tests/hiv2.faa +0 -70
  195. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv +0 -233
  196. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim +0 -1
  197. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec +0 -233
  198. data/utils/enveomics/Tests/phyla_counts.tsv +0 -10
  199. data/utils/enveomics/Tests/primate_lentivirus.ogs +0 -11
  200. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm +0 -9
  201. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm +0 -8
  202. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm +0 -6
  203. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm +0 -9
  204. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm +0 -6
  205. data/utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm +0 -6
  206. data/utils/enveomics/build_enveomics_r.bash +0 -45
  207. data/utils/enveomics/enveomics.R/DESCRIPTION +0 -31
  208. data/utils/enveomics/enveomics.R/NAMESPACE +0 -39
  209. data/utils/enveomics/enveomics.R/R/autoprune.R +0 -155
  210. data/utils/enveomics/enveomics.R/R/barplot.R +0 -184
  211. data/utils/enveomics/enveomics.R/R/cliopts.R +0 -135
  212. data/utils/enveomics/enveomics.R/R/df2dist.R +0 -154
  213. data/utils/enveomics/enveomics.R/R/growthcurve.R +0 -331
  214. data/utils/enveomics/enveomics.R/R/recplot.R +0 -354
  215. data/utils/enveomics/enveomics.R/R/recplot2.R +0 -1631
  216. data/utils/enveomics/enveomics.R/R/tribs.R +0 -583
  217. data/utils/enveomics/enveomics.R/R/utils.R +0 -50
  218. data/utils/enveomics/enveomics.R/README.md +0 -80
  219. data/utils/enveomics/enveomics.R/data/growth.curves.rda +0 -0
  220. data/utils/enveomics/enveomics.R/data/phyla.counts.rda +0 -0
  221. data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd +0 -17
  222. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd +0 -17
  223. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd +0 -17
  224. data/utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd +0 -25
  225. data/utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd +0 -46
  226. data/utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd +0 -23
  227. data/utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd +0 -47
  228. data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd +0 -23
  229. data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd +0 -23
  230. data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +0 -32
  231. data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +0 -91
  232. data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +0 -57
  233. data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd +0 -24
  234. data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd +0 -19
  235. data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +0 -39
  236. data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +0 -38
  237. data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +0 -40
  238. data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +0 -67
  239. data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +0 -37
  240. data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +0 -122
  241. data/utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd +0 -45
  242. data/utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd +0 -24
  243. data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +0 -68
  244. data/utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd +0 -25
  245. data/utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd +0 -21
  246. data/utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd +0 -19
  247. data/utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd +0 -19
  248. data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +0 -41
  249. data/utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd +0 -29
  250. data/utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd +0 -18
  251. data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +0 -40
  252. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd +0 -36
  253. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd +0 -19
  254. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd +0 -19
  255. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd +0 -27
  256. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +0 -41
  257. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd +0 -17
  258. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +0 -43
  259. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +0 -37
  260. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +0 -74
  261. data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd +0 -59
  262. data/utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd +0 -27
  263. data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +0 -32
  264. data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +0 -59
  265. data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd +0 -28
  266. data/utils/enveomics/enveomics.R/man/enve.truncate.Rd +0 -27
  267. data/utils/enveomics/enveomics.R/man/growth.curves.Rd +0 -14
  268. data/utils/enveomics/enveomics.R/man/phyla.counts.Rd +0 -13
  269. data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +0 -63
  270. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +0 -38
  271. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +0 -38
  272. data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +0 -111
  273. data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd +0 -19
  274. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd +0 -19
  275. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd +0 -19
  276. data/utils/enveomics/globals.mk +0 -8
  277. data/utils/enveomics/manifest.json +0 -9

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