miga-base 0.7.26.0 → 1.0.0.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (337) hide show
  1. checksums.yaml +4 -4
  2. data/lib/miga/_data/aai-intax.blast.tsv.gz +0 -0
  3. data/lib/miga/_data/aai-intax.diamond.tsv.gz +0 -0
  4. data/lib/miga/_data/aai-novel.blast.tsv.gz +0 -0
  5. data/lib/miga/_data/aai-novel.diamond.tsv.gz +0 -0
  6. data/lib/miga/cli/action/classify_wf.rb +2 -2
  7. data/lib/miga/cli/action/derep_wf.rb +1 -1
  8. data/lib/miga/cli/action/doctor.rb +57 -14
  9. data/lib/miga/cli/action/doctor/base.rb +47 -23
  10. data/lib/miga/cli/action/init.rb +11 -7
  11. data/lib/miga/cli/action/init/files_helper.rb +1 -0
  12. data/lib/miga/cli/action/ncbi_get.rb +3 -3
  13. data/lib/miga/cli/action/tax_dist.rb +2 -2
  14. data/lib/miga/cli/action/wf.rb +5 -4
  15. data/lib/miga/common.rb +1 -0
  16. data/lib/miga/daemon.rb +11 -4
  17. data/lib/miga/dataset/result.rb +10 -6
  18. data/lib/miga/json.rb +5 -4
  19. data/lib/miga/metadata.rb +5 -1
  20. data/lib/miga/parallel.rb +36 -0
  21. data/lib/miga/project.rb +8 -8
  22. data/lib/miga/project/base.rb +4 -4
  23. data/lib/miga/project/result.rb +2 -2
  24. data/lib/miga/sqlite.rb +10 -2
  25. data/lib/miga/version.rb +23 -9
  26. data/scripts/aai_distances.bash +16 -18
  27. data/scripts/ani_distances.bash +16 -17
  28. data/scripts/assembly.bash +31 -16
  29. data/scripts/haai_distances.bash +3 -27
  30. data/scripts/miga.bash +6 -4
  31. data/scripts/p.bash +1 -1
  32. data/scripts/read_quality.bash +9 -18
  33. data/scripts/trimmed_fasta.bash +14 -30
  34. data/scripts/trimmed_reads.bash +36 -36
  35. data/test/parallel_test.rb +31 -0
  36. data/test/project_test.rb +2 -1
  37. data/test/remote_dataset_test.rb +1 -1
  38. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Archaea_SCG.hmm +41964 -0
  39. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Bacteria_SCG.hmm +32439 -0
  40. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Complete_SCG_DB.hmm +62056 -0
  41. data/utils/FastAAI/FastAAI/FastAAI +1336 -0
  42. data/utils/FastAAI/README.md +84 -0
  43. data/utils/FastAAI/kAAI_v1.0_virus.py +1296 -0
  44. data/utils/distance/commands.rb +1 -0
  45. data/utils/distance/database.rb +0 -1
  46. data/utils/distance/runner.rb +2 -4
  47. data/utils/enveomics/Docs/recplot2.md +244 -0
  48. data/utils/enveomics/Examples/aai-matrix.bash +66 -0
  49. data/utils/enveomics/Examples/ani-matrix.bash +66 -0
  50. data/utils/enveomics/Examples/essential-phylogeny.bash +105 -0
  51. data/utils/enveomics/Examples/unus-genome-phylogeny.bash +100 -0
  52. data/utils/enveomics/LICENSE.txt +73 -0
  53. data/utils/enveomics/Makefile +52 -0
  54. data/utils/enveomics/Manifest/Tasks/aasubs.json +103 -0
  55. data/utils/enveomics/Manifest/Tasks/blasttab.json +786 -0
  56. data/utils/enveomics/Manifest/Tasks/distances.json +161 -0
  57. data/utils/enveomics/Manifest/Tasks/fasta.json +802 -0
  58. data/utils/enveomics/Manifest/Tasks/fastq.json +291 -0
  59. data/utils/enveomics/Manifest/Tasks/graphics.json +126 -0
  60. data/utils/enveomics/Manifest/Tasks/mapping.json +137 -0
  61. data/utils/enveomics/Manifest/Tasks/ogs.json +382 -0
  62. data/utils/enveomics/Manifest/Tasks/other.json +906 -0
  63. data/utils/enveomics/Manifest/Tasks/remote.json +355 -0
  64. data/utils/enveomics/Manifest/Tasks/sequence-identity.json +638 -0
  65. data/utils/enveomics/Manifest/Tasks/tables.json +308 -0
  66. data/utils/enveomics/Manifest/Tasks/trees.json +68 -0
  67. data/utils/enveomics/Manifest/Tasks/variants.json +111 -0
  68. data/utils/enveomics/Manifest/categories.json +165 -0
  69. data/utils/enveomics/Manifest/examples.json +154 -0
  70. data/utils/enveomics/Manifest/tasks.json +4 -0
  71. data/utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash +69 -0
  72. data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +1 -0
  73. data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +1 -0
  74. data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +1 -0
  75. data/utils/enveomics/Pipelines/assembly.pbs/README.md +189 -0
  76. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash +112 -0
  77. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash +23 -0
  78. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash +44 -0
  79. data/utils/enveomics/Pipelines/assembly.pbs/RUNME.bash +50 -0
  80. data/utils/enveomics/Pipelines/assembly.pbs/kSelector.R +37 -0
  81. data/utils/enveomics/Pipelines/assembly.pbs/newbler.pbs +68 -0
  82. data/utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl +49 -0
  83. data/utils/enveomics/Pipelines/assembly.pbs/soap.pbs +80 -0
  84. data/utils/enveomics/Pipelines/assembly.pbs/stats.pbs +57 -0
  85. data/utils/enveomics/Pipelines/assembly.pbs/velvet.pbs +63 -0
  86. data/utils/enveomics/Pipelines/blast.pbs/01.pbs.bash +38 -0
  87. data/utils/enveomics/Pipelines/blast.pbs/02.pbs.bash +73 -0
  88. data/utils/enveomics/Pipelines/blast.pbs/03.pbs.bash +21 -0
  89. data/utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl +72 -0
  90. data/utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash +98 -0
  91. data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +1 -0
  92. data/utils/enveomics/Pipelines/blast.pbs/README.md +127 -0
  93. data/utils/enveomics/Pipelines/blast.pbs/RUNME.bash +109 -0
  94. data/utils/enveomics/Pipelines/blast.pbs/TASK.check.bash +128 -0
  95. data/utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash +16 -0
  96. data/utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash +22 -0
  97. data/utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash +26 -0
  98. data/utils/enveomics/Pipelines/blast.pbs/TASK.run.bash +89 -0
  99. data/utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash +29 -0
  100. data/utils/enveomics/Pipelines/idba.pbs/README.md +49 -0
  101. data/utils/enveomics/Pipelines/idba.pbs/RUNME.bash +95 -0
  102. data/utils/enveomics/Pipelines/idba.pbs/run.pbs +56 -0
  103. data/utils/enveomics/Pipelines/trim.pbs/README.md +54 -0
  104. data/utils/enveomics/Pipelines/trim.pbs/RUNME.bash +70 -0
  105. data/utils/enveomics/Pipelines/trim.pbs/run.pbs +130 -0
  106. data/utils/enveomics/README.md +42 -0
  107. data/utils/enveomics/Scripts/AAsubs.log2ratio.rb +171 -0
  108. data/utils/enveomics/Scripts/Aln.cat.rb +221 -0
  109. data/utils/enveomics/Scripts/Aln.convert.pl +35 -0
  110. data/utils/enveomics/Scripts/AlphaDiversity.pl +152 -0
  111. data/utils/enveomics/Scripts/BedGraph.tad.rb +93 -0
  112. data/utils/enveomics/Scripts/BedGraph.window.rb +71 -0
  113. data/utils/enveomics/Scripts/BlastPairwise.AAsubs.pl +102 -0
  114. data/utils/enveomics/Scripts/BlastTab.addlen.rb +63 -0
  115. data/utils/enveomics/Scripts/BlastTab.advance.bash +48 -0
  116. data/utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl +55 -0
  117. data/utils/enveomics/Scripts/BlastTab.catsbj.pl +104 -0
  118. data/utils/enveomics/Scripts/BlastTab.cogCat.rb +76 -0
  119. data/utils/enveomics/Scripts/BlastTab.filter.pl +47 -0
  120. data/utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl +194 -0
  121. data/utils/enveomics/Scripts/BlastTab.metaxaPrep.pl +104 -0
  122. data/utils/enveomics/Scripts/BlastTab.pairedHits.rb +157 -0
  123. data/utils/enveomics/Scripts/BlastTab.recplot2.R +48 -0
  124. data/utils/enveomics/Scripts/BlastTab.seqdepth.pl +86 -0
  125. data/utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl +119 -0
  126. data/utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl +86 -0
  127. data/utils/enveomics/Scripts/BlastTab.subsample.pl +47 -0
  128. data/utils/enveomics/Scripts/BlastTab.sumPerHit.pl +114 -0
  129. data/utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl +90 -0
  130. data/utils/enveomics/Scripts/BlastTab.topHits_sorted.rb +101 -0
  131. data/utils/enveomics/Scripts/Chao1.pl +97 -0
  132. data/utils/enveomics/Scripts/CharTable.classify.rb +234 -0
  133. data/utils/enveomics/Scripts/EBIseq2tax.rb +83 -0
  134. data/utils/enveomics/Scripts/FastA.N50.pl +60 -0
  135. data/utils/enveomics/Scripts/FastA.extract.rb +152 -0
  136. data/utils/enveomics/Scripts/FastA.filter.pl +52 -0
  137. data/utils/enveomics/Scripts/FastA.filterLen.pl +28 -0
  138. data/utils/enveomics/Scripts/FastA.filterN.pl +60 -0
  139. data/utils/enveomics/Scripts/FastA.fragment.rb +100 -0
  140. data/utils/enveomics/Scripts/FastA.gc.pl +42 -0
  141. data/utils/enveomics/Scripts/FastA.interpose.pl +93 -0
  142. data/utils/enveomics/Scripts/FastA.length.pl +38 -0
  143. data/utils/enveomics/Scripts/FastA.mask.rb +89 -0
  144. data/utils/enveomics/Scripts/FastA.per_file.pl +36 -0
  145. data/utils/enveomics/Scripts/FastA.qlen.pl +57 -0
  146. data/utils/enveomics/Scripts/FastA.rename.pl +65 -0
  147. data/utils/enveomics/Scripts/FastA.revcom.pl +23 -0
  148. data/utils/enveomics/Scripts/FastA.sample.rb +98 -0
  149. data/utils/enveomics/Scripts/FastA.slider.pl +85 -0
  150. data/utils/enveomics/Scripts/FastA.split.pl +55 -0
  151. data/utils/enveomics/Scripts/FastA.split.rb +79 -0
  152. data/utils/enveomics/Scripts/FastA.subsample.pl +131 -0
  153. data/utils/enveomics/Scripts/FastA.tag.rb +65 -0
  154. data/utils/enveomics/Scripts/FastA.toFastQ.rb +69 -0
  155. data/utils/enveomics/Scripts/FastA.wrap.rb +48 -0
  156. data/utils/enveomics/Scripts/FastQ.filter.pl +54 -0
  157. data/utils/enveomics/Scripts/FastQ.interpose.pl +90 -0
  158. data/utils/enveomics/Scripts/FastQ.maskQual.rb +89 -0
  159. data/utils/enveomics/Scripts/FastQ.offset.pl +90 -0
  160. data/utils/enveomics/Scripts/FastQ.split.pl +53 -0
  161. data/utils/enveomics/Scripts/FastQ.tag.rb +70 -0
  162. data/utils/enveomics/Scripts/FastQ.test-error.rb +81 -0
  163. data/utils/enveomics/Scripts/FastQ.toFastA.awk +24 -0
  164. data/utils/enveomics/Scripts/GFF.catsbj.pl +127 -0
  165. data/utils/enveomics/Scripts/GenBank.add_fields.rb +84 -0
  166. data/utils/enveomics/Scripts/HMM.essential.rb +351 -0
  167. data/utils/enveomics/Scripts/HMM.haai.rb +168 -0
  168. data/utils/enveomics/Scripts/HMMsearch.extractIds.rb +83 -0
  169. data/utils/enveomics/Scripts/JPlace.distances.rb +88 -0
  170. data/utils/enveomics/Scripts/JPlace.to_iToL.rb +320 -0
  171. data/utils/enveomics/Scripts/M5nr.getSequences.rb +81 -0
  172. data/utils/enveomics/Scripts/MeTaxa.distribution.pl +198 -0
  173. data/utils/enveomics/Scripts/MyTaxa.fragsByTax.pl +35 -0
  174. data/utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb +49 -0
  175. data/utils/enveomics/Scripts/NCBIacc2tax.rb +92 -0
  176. data/utils/enveomics/Scripts/Newick.autoprune.R +27 -0
  177. data/utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl +228 -0
  178. data/utils/enveomics/Scripts/RecPlot2.compareIdentities.R +32 -0
  179. data/utils/enveomics/Scripts/RefSeq.download.bash +48 -0
  180. data/utils/enveomics/Scripts/SRA.download.bash +55 -0
  181. data/utils/enveomics/Scripts/TRIBS.plot-test.R +36 -0
  182. data/utils/enveomics/Scripts/TRIBS.test.R +39 -0
  183. data/utils/enveomics/Scripts/Table.barplot.R +31 -0
  184. data/utils/enveomics/Scripts/Table.df2dist.R +30 -0
  185. data/utils/enveomics/Scripts/Table.filter.pl +61 -0
  186. data/utils/enveomics/Scripts/Table.merge.pl +77 -0
  187. data/utils/enveomics/Scripts/Table.prefScore.R +60 -0
  188. data/utils/enveomics/Scripts/Table.replace.rb +69 -0
  189. data/utils/enveomics/Scripts/Table.round.rb +63 -0
  190. data/utils/enveomics/Scripts/Table.split.pl +57 -0
  191. data/utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb +227 -0
  192. data/utils/enveomics/Scripts/VCF.KaKs.rb +147 -0
  193. data/utils/enveomics/Scripts/VCF.SNPs.rb +88 -0
  194. data/utils/enveomics/Scripts/aai.rb +419 -0
  195. data/utils/enveomics/Scripts/ani.rb +362 -0
  196. data/utils/enveomics/Scripts/anir.rb +137 -0
  197. data/utils/enveomics/Scripts/clust.rand.rb +102 -0
  198. data/utils/enveomics/Scripts/gi2tax.rb +103 -0
  199. data/utils/enveomics/Scripts/in_silico_GA_GI.pl +96 -0
  200. data/utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz +0 -0
  201. data/utils/enveomics/Scripts/lib/data/lee_2019_essential.hmm.gz +0 -0
  202. data/utils/enveomics/Scripts/lib/enveomics.R +1 -0
  203. data/utils/enveomics/Scripts/lib/enveomics_rb/anir.rb +293 -0
  204. data/utils/enveomics/Scripts/lib/enveomics_rb/bm_set.rb +175 -0
  205. data/utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb +24 -0
  206. data/utils/enveomics/Scripts/lib/enveomics_rb/errors.rb +17 -0
  207. data/utils/enveomics/Scripts/lib/enveomics_rb/gmm_em.rb +30 -0
  208. data/utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb +253 -0
  209. data/utils/enveomics/Scripts/lib/enveomics_rb/match.rb +63 -0
  210. data/utils/enveomics/Scripts/lib/enveomics_rb/og.rb +182 -0
  211. data/utils/enveomics/Scripts/lib/enveomics_rb/rbm.rb +49 -0
  212. data/utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb +74 -0
  213. data/utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb +237 -0
  214. data/utils/enveomics/Scripts/lib/enveomics_rb/stats.rb +3 -0
  215. data/utils/enveomics/Scripts/lib/enveomics_rb/stats/rand.rb +31 -0
  216. data/utils/enveomics/Scripts/lib/enveomics_rb/stats/sample.rb +152 -0
  217. data/utils/enveomics/Scripts/lib/enveomics_rb/utils.rb +73 -0
  218. data/utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb +135 -0
  219. data/utils/enveomics/Scripts/ogs.annotate.rb +88 -0
  220. data/utils/enveomics/Scripts/ogs.core-pan.rb +160 -0
  221. data/utils/enveomics/Scripts/ogs.extract.rb +125 -0
  222. data/utils/enveomics/Scripts/ogs.mcl.rb +186 -0
  223. data/utils/enveomics/Scripts/ogs.rb +104 -0
  224. data/utils/enveomics/Scripts/ogs.stats.rb +131 -0
  225. data/utils/enveomics/Scripts/rbm-legacy.rb +172 -0
  226. data/utils/enveomics/Scripts/rbm.rb +100 -0
  227. data/utils/enveomics/Scripts/sam.filter.rb +148 -0
  228. data/utils/enveomics/Tests/Makefile +10 -0
  229. data/utils/enveomics/Tests/Mgen_M2288.faa +3189 -0
  230. data/utils/enveomics/Tests/Mgen_M2288.fna +8282 -0
  231. data/utils/enveomics/Tests/Mgen_M2321.fna +8288 -0
  232. data/utils/enveomics/Tests/Nequ_Kin4M.faa +2970 -0
  233. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata +0 -0
  234. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt +7 -0
  235. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv +17 -0
  236. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv +137 -0
  237. data/utils/enveomics/Tests/a_mg.cds-go.blast.tsv +123 -0
  238. data/utils/enveomics/Tests/a_mg.reads-cds.blast.tsv +200 -0
  239. data/utils/enveomics/Tests/a_mg.reads-cds.counts.tsv +55 -0
  240. data/utils/enveomics/Tests/alkB.nwk +1 -0
  241. data/utils/enveomics/Tests/anthrax-cansnp-data.tsv +13 -0
  242. data/utils/enveomics/Tests/anthrax-cansnp-key.tsv +17 -0
  243. data/utils/enveomics/Tests/hiv1.faa +59 -0
  244. data/utils/enveomics/Tests/hiv1.fna +134 -0
  245. data/utils/enveomics/Tests/hiv2.faa +70 -0
  246. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv +233 -0
  247. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim +1 -0
  248. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec +233 -0
  249. data/utils/enveomics/Tests/phyla_counts.tsv +10 -0
  250. data/utils/enveomics/Tests/primate_lentivirus.ogs +11 -0
  251. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm +9 -0
  252. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm +8 -0
  253. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm +6 -0
  254. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm +9 -0
  255. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm +6 -0
  256. data/utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm +6 -0
  257. data/utils/enveomics/build_enveomics_r.bash +45 -0
  258. data/utils/enveomics/enveomics.R/DESCRIPTION +31 -0
  259. data/utils/enveomics/enveomics.R/NAMESPACE +39 -0
  260. data/utils/enveomics/enveomics.R/R/autoprune.R +155 -0
  261. data/utils/enveomics/enveomics.R/R/barplot.R +184 -0
  262. data/utils/enveomics/enveomics.R/R/cliopts.R +135 -0
  263. data/utils/enveomics/enveomics.R/R/df2dist.R +154 -0
  264. data/utils/enveomics/enveomics.R/R/growthcurve.R +331 -0
  265. data/utils/enveomics/enveomics.R/R/prefscore.R +79 -0
  266. data/utils/enveomics/enveomics.R/R/recplot.R +354 -0
  267. data/utils/enveomics/enveomics.R/R/recplot2.R +1631 -0
  268. data/utils/enveomics/enveomics.R/R/tribs.R +583 -0
  269. data/utils/enveomics/enveomics.R/R/utils.R +80 -0
  270. data/utils/enveomics/enveomics.R/README.md +81 -0
  271. data/utils/enveomics/enveomics.R/data/growth.curves.rda +0 -0
  272. data/utils/enveomics/enveomics.R/data/phyla.counts.rda +0 -0
  273. data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd +16 -0
  274. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd +16 -0
  275. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd +16 -0
  276. data/utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd +25 -0
  277. data/utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd +46 -0
  278. data/utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd +23 -0
  279. data/utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd +47 -0
  280. data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd +23 -0
  281. data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd +23 -0
  282. data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +40 -0
  283. data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +103 -0
  284. data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +67 -0
  285. data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd +24 -0
  286. data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd +19 -0
  287. data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +45 -0
  288. data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +44 -0
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  295. data/utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd +24 -0
  296. data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +77 -0
  297. data/utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd +25 -0
  298. data/utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd +21 -0
  299. data/utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd +19 -0
  300. data/utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd +19 -0
  301. data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +47 -0
  302. data/utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd +29 -0
  303. data/utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd +18 -0
  304. data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +45 -0
  305. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd +36 -0
  306. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd +19 -0
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  308. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd +27 -0
  309. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +52 -0
  310. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd +17 -0
  311. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +51 -0
  312. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +43 -0
  313. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +82 -0
  314. data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd +59 -0
  315. data/utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd +27 -0
  316. data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +36 -0
  317. data/utils/enveomics/enveomics.R/man/enve.selvector.Rd +23 -0
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  319. data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd +28 -0
  320. data/utils/enveomics/enveomics.R/man/enve.truncate.Rd +27 -0
  321. data/utils/enveomics/enveomics.R/man/growth.curves.Rd +14 -0
  322. data/utils/enveomics/enveomics.R/man/phyla.counts.Rd +13 -0
  323. data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +78 -0
  324. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +46 -0
  325. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +45 -0
  326. data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +125 -0
  327. data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd +19 -0
  328. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd +19 -0
  329. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd +19 -0
  330. data/utils/enveomics/globals.mk +8 -0
  331. data/utils/enveomics/manifest.json +9 -0
  332. data/utils/multitrim/Multitrim How-To.pdf +0 -0
  333. data/utils/multitrim/README.md +67 -0
  334. data/utils/multitrim/multitrim.py +1555 -0
  335. data/utils/multitrim/multitrim.yml +13 -0
  336. data/utils/requirements.txt +4 -3
  337. metadata +304 -3
data/utils/multitrim/multitrim.yml ADDED
@@ -0,0 +1,13 @@
1
+ name: multitrim
2
+ dependencies:
3
+ - faqcs
4
+ - falco
5
+ - seqtk
6
+ - fastp
7
+ - pigz
8
+ - multitrim
9
+
10
+ channels:
11
+ - conda-forge
12
+ - bioconda
13
+ - kgerhardt
data/utils/requirements.txt CHANGED
@@ -13,9 +13,10 @@ Prodigal prodigal http://prodigal.ornl.gov
13
13
  MCL mcl http://micans.org/mcl/
14
14
  Barrnap barrnap http://www.vicbioinformatics.com/software.barrnap.shtml
15
15
  IDBA (reads) idba_ud http://i.cs.hku.hk/~alse/hkubrg/projects/idba
16
- Scythe (reads) scythe https://github.com/vsbuffalo/scythe Required version: 0.991+
17
- FastQC (reads) fastqc http://www.bioinformatics.babraham.ac.uk/projects/fastqc
18
- SolexaQA++ (reads) SolexaQA++ http://solexaqa.sourceforge.net Required version: v3.1.3+
16
+ FaQCs (reads) FaQCs https://github.com/LANL-Bioinformatics/FaQCs
17
+ Falco (reads) falco https://github.com/smithlabcode/falco
18
+ Seqtk (reads) seqtk https://github.com/lh3/seqtk
19
+ Fastp (reads) fastp https://github.com/OpenGene/fastp
19
20
  OpenJDK (rdp) java https://adoptopenjdk.net/ Any Java VM would work
20
21
  MyTaxa (mytaxa) MyTaxa http://enve-omics.ce.gatech.edu/mytaxa
21
22
  Krona (mytaxa) ktImportText https://github.com/marbl/Krona/wiki
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: miga-base
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.7.26.0
4
+ version: 1.0.0.1
5
5
  platform: ruby
6
6
  authors:
7
7
  - Luis M. Rodriguez-R
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2021-03-01 00:00:00.000000000 Z
11
+ date: 2021-04-13 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: daemons
@@ -110,8 +110,12 @@ files:
110
110
  - lib/miga.rb
111
111
  - lib/miga/_data/aai-intax-blast.tsv.gz
112
112
  - lib/miga/_data/aai-intax-diamond.tsv.gz
113
+ - lib/miga/_data/aai-intax.blast.tsv.gz
114
+ - lib/miga/_data/aai-intax.diamond.tsv.gz
113
115
  - lib/miga/_data/aai-novel-blast.tsv.gz
114
116
  - lib/miga/_data/aai-novel-diamond.tsv.gz
117
+ - lib/miga/_data/aai-novel.blast.tsv.gz
118
+ - lib/miga/_data/aai-novel.diamond.tsv.gz
115
119
  - lib/miga/cli.rb
116
120
  - lib/miga/cli/action.rb
117
121
  - lib/miga/cli/action/about.rb
@@ -187,6 +191,7 @@ files:
187
191
  - lib/miga/json.rb
188
192
  - lib/miga/lair.rb
189
193
  - lib/miga/metadata.rb
194
+ - lib/miga/parallel.rb
190
195
  - lib/miga/project.rb
191
196
  - lib/miga/project/base.rb
192
197
  - lib/miga/project/dataset.rb
@@ -240,6 +245,7 @@ files:
240
245
  - test/lair_test.rb
241
246
  - test/metadata_test.rb
242
247
  - test/net_test.rb
248
+ - test/parallel_test.rb
243
249
  - test/project_test.rb
244
250
  - test/remote_dataset_test.rb
245
251
  - test/result_stats_test.rb
@@ -250,6 +256,12 @@ files:
250
256
  - test/test_helper.rb
251
257
  - test/with_daemon_test.rb
252
258
  - test/with_option_test.rb
259
+ - utils/FastAAI/00.Libraries/01.SCG_HMMs/Archaea_SCG.hmm
260
+ - utils/FastAAI/00.Libraries/01.SCG_HMMs/Bacteria_SCG.hmm
261
+ - utils/FastAAI/00.Libraries/01.SCG_HMMs/Complete_SCG_DB.hmm
262
+ - utils/FastAAI/FastAAI/FastAAI
263
+ - utils/FastAAI/README.md
264
+ - utils/FastAAI/kAAI_v1.0_virus.py
253
265
  - utils/adapters.fa
254
266
  - utils/cleanup-databases.rb
255
267
  - utils/core-pan-plot.R
@@ -261,8 +273,297 @@ files:
261
273
  - utils/distance/temporal.rb
262
274
  - utils/distances.rb
263
275
  - utils/domain-ess-genes.rb
276
+ - utils/enveomics/Docs/recplot2.md
277
+ - utils/enveomics/Examples/aai-matrix.bash
278
+ - utils/enveomics/Examples/ani-matrix.bash
279
+ - utils/enveomics/Examples/essential-phylogeny.bash
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+ - utils/enveomics/Examples/unus-genome-phylogeny.bash
281
+ - utils/enveomics/LICENSE.txt
282
+ - utils/enveomics/Makefile
283
+ - utils/enveomics/Manifest/Tasks/aasubs.json
284
+ - utils/enveomics/Manifest/Tasks/blasttab.json
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+ - utils/enveomics/Manifest/Tasks/distances.json
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+ - utils/enveomics/Manifest/Tasks/fasta.json
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+ - utils/enveomics/Manifest/Tasks/fastq.json
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+ - utils/enveomics/Manifest/Tasks/graphics.json
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+ - utils/enveomics/Manifest/Tasks/mapping.json
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+ - utils/enveomics/Manifest/Tasks/ogs.json
291
+ - utils/enveomics/Manifest/Tasks/other.json
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+ - utils/enveomics/Manifest/Tasks/remote.json
293
+ - utils/enveomics/Manifest/Tasks/sequence-identity.json
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+ - utils/enveomics/Manifest/Tasks/tables.json
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+ - utils/enveomics/Manifest/Tasks/trees.json
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+ - utils/enveomics/Manifest/Tasks/variants.json
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+ - utils/enveomics/Manifest/categories.json
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+ - utils/enveomics/Manifest/examples.json
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+ - utils/enveomics/Manifest/tasks.json
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+ - utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash
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+ - utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl
302
+ - utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl
303
+ - utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl
304
+ - utils/enveomics/Pipelines/assembly.pbs/README.md
305
+ - utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash
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+ - utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash
307
+ - utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash
308
+ - utils/enveomics/Pipelines/assembly.pbs/RUNME.bash
309
+ - utils/enveomics/Pipelines/assembly.pbs/kSelector.R
310
+ - utils/enveomics/Pipelines/assembly.pbs/newbler.pbs
311
+ - utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl
312
+ - utils/enveomics/Pipelines/assembly.pbs/soap.pbs
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+ - utils/enveomics/Pipelines/assembly.pbs/stats.pbs
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+ - utils/enveomics/Pipelines/assembly.pbs/velvet.pbs
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+ - utils/enveomics/Pipelines/blast.pbs/01.pbs.bash
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+ - utils/enveomics/Pipelines/blast.pbs/02.pbs.bash
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+ - utils/enveomics/Pipelines/blast.pbs/03.pbs.bash
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+ - utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl
319
+ - utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash
320
+ - utils/enveomics/Pipelines/blast.pbs/FastA.split.pl
321
+ - utils/enveomics/Pipelines/blast.pbs/README.md
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+ - utils/enveomics/Pipelines/blast.pbs/RUNME.bash
323
+ - utils/enveomics/Pipelines/blast.pbs/TASK.check.bash
324
+ - utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash
325
+ - utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash
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+ - utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash
327
+ - utils/enveomics/Pipelines/blast.pbs/TASK.run.bash
328
+ - utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash
329
+ - utils/enveomics/Pipelines/idba.pbs/README.md
330
+ - utils/enveomics/Pipelines/idba.pbs/RUNME.bash
331
+ - utils/enveomics/Pipelines/idba.pbs/run.pbs
332
+ - utils/enveomics/Pipelines/trim.pbs/README.md
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+ - utils/enveomics/Pipelines/trim.pbs/RUNME.bash
334
+ - utils/enveomics/Pipelines/trim.pbs/run.pbs
335
+ - utils/enveomics/README.md
336
+ - utils/enveomics/Scripts/AAsubs.log2ratio.rb
337
+ - utils/enveomics/Scripts/Aln.cat.rb
338
+ - utils/enveomics/Scripts/Aln.convert.pl
339
+ - utils/enveomics/Scripts/AlphaDiversity.pl
340
+ - utils/enveomics/Scripts/BedGraph.tad.rb
341
+ - utils/enveomics/Scripts/BedGraph.window.rb
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+ - utils/enveomics/Scripts/BlastPairwise.AAsubs.pl
343
+ - utils/enveomics/Scripts/BlastTab.addlen.rb
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+ - utils/enveomics/Scripts/BlastTab.advance.bash
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+ - utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl
346
+ - utils/enveomics/Scripts/BlastTab.catsbj.pl
347
+ - utils/enveomics/Scripts/BlastTab.cogCat.rb
348
+ - utils/enveomics/Scripts/BlastTab.filter.pl
349
+ - utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl
350
+ - utils/enveomics/Scripts/BlastTab.metaxaPrep.pl
351
+ - utils/enveomics/Scripts/BlastTab.pairedHits.rb
352
+ - utils/enveomics/Scripts/BlastTab.recplot2.R
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+ - utils/enveomics/Scripts/BlastTab.seqdepth.pl
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+ - utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl
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+ - utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl
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+ - utils/enveomics/Scripts/BlastTab.subsample.pl
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+ - utils/enveomics/Scripts/BlastTab.sumPerHit.pl
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+ - utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl
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+ - utils/enveomics/Scripts/BlastTab.topHits_sorted.rb
360
+ - utils/enveomics/Scripts/Chao1.pl
361
+ - utils/enveomics/Scripts/CharTable.classify.rb
362
+ - utils/enveomics/Scripts/EBIseq2tax.rb
363
+ - utils/enveomics/Scripts/FastA.N50.pl
364
+ - utils/enveomics/Scripts/FastA.extract.rb
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+ - utils/enveomics/Scripts/FastA.filter.pl
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+ - utils/enveomics/Scripts/FastA.filterLen.pl
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+ - utils/enveomics/Scripts/FastA.filterN.pl
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+ - utils/enveomics/Scripts/FastA.fragment.rb
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+ - utils/enveomics/Scripts/FastA.gc.pl
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+ - utils/enveomics/Scripts/FastA.interpose.pl
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+ - utils/enveomics/Scripts/FastA.length.pl
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+ - utils/enveomics/Scripts/FastA.mask.rb
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+ - utils/enveomics/Scripts/FastA.per_file.pl
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+ - utils/enveomics/Scripts/FastA.qlen.pl
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+ - utils/enveomics/Scripts/FastA.rename.pl
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+ - utils/enveomics/Scripts/FastA.revcom.pl
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+ - utils/enveomics/Scripts/FastA.sample.rb
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+ - utils/enveomics/Scripts/FastA.slider.pl
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+ - utils/enveomics/Scripts/FastA.split.pl
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+ - utils/enveomics/Scripts/FastA.split.rb
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+ - utils/enveomics/Scripts/FastA.subsample.pl
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+ - utils/enveomics/Scripts/FastA.tag.rb
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+ - utils/enveomics/Scripts/FastA.toFastQ.rb
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+ - utils/enveomics/Scripts/FastA.wrap.rb
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+ - utils/enveomics/Scripts/FastQ.filter.pl
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+ - utils/enveomics/Scripts/FastQ.interpose.pl
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+ - utils/enveomics/Scripts/FastQ.maskQual.rb
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+ - utils/enveomics/Scripts/FastQ.offset.pl
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+ - utils/enveomics/Scripts/FastQ.split.pl
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+ - utils/enveomics/Scripts/FastQ.tag.rb
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+ - utils/enveomics/Scripts/FastQ.test-error.rb
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+ - utils/enveomics/Scripts/FastQ.toFastA.awk
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+ - utils/enveomics/Scripts/GFF.catsbj.pl
394
+ - utils/enveomics/Scripts/GenBank.add_fields.rb
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+ - utils/enveomics/Scripts/HMM.essential.rb
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+ - utils/enveomics/Scripts/HMM.haai.rb
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+ - utils/enveomics/Scripts/HMMsearch.extractIds.rb
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+ - utils/enveomics/Scripts/JPlace.distances.rb
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+ - utils/enveomics/Scripts/JPlace.to_iToL.rb
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+ - utils/enveomics/Scripts/M5nr.getSequences.rb
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+ - utils/enveomics/Scripts/MeTaxa.distribution.pl
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+ - utils/enveomics/Scripts/MyTaxa.fragsByTax.pl
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+ - utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb
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+ - utils/enveomics/Scripts/NCBIacc2tax.rb
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+ - utils/enveomics/Scripts/Newick.autoprune.R
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+ - utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl
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+ - utils/enveomics/Scripts/RecPlot2.compareIdentities.R
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+ - utils/enveomics/Scripts/RefSeq.download.bash
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+ - utils/enveomics/Scripts/SRA.download.bash
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+ - utils/enveomics/Scripts/TRIBS.plot-test.R
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+ - utils/enveomics/Scripts/Table.barplot.R
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+ - utils/enveomics/Scripts/Table.df2dist.R
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+ - utils/enveomics/Scripts/Table.filter.pl
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+ - utils/enveomics/Scripts/Table.merge.pl
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+ - utils/enveomics/Scripts/Table.prefScore.R
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+ - utils/enveomics/Scripts/Table.round.rb
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+ - utils/enveomics/Scripts/Table.split.pl
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+ - utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb
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+ - utils/enveomics/Scripts/VCF.KaKs.rb
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+ - utils/enveomics/Scripts/VCF.SNPs.rb
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+ - utils/enveomics/Scripts/aai.rb
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+ - utils/enveomics/Scripts/ani.rb
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+ - utils/enveomics/Scripts/anir.rb
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+ - utils/enveomics/Scripts/clust.rand.rb
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+ - utils/enveomics/Scripts/gi2tax.rb
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+ - utils/enveomics/Scripts/in_silico_GA_GI.pl
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+ - utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz
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+ - utils/enveomics/Scripts/lib/enveomics.R
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+ - utils/enveomics/Scripts/lib/enveomics_rb/anir.rb
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+ - utils/enveomics/Scripts/lib/enveomics_rb/bm_set.rb
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+ - utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb
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+ - utils/enveomics/Scripts/lib/enveomics_rb/errors.rb
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+ - utils/enveomics/Scripts/lib/enveomics_rb/gmm_em.rb
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+ - utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb
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+ - utils/enveomics/Scripts/lib/enveomics_rb/match.rb
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+ - utils/enveomics/Scripts/lib/enveomics_rb/og.rb
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+ - utils/enveomics/Scripts/lib/enveomics_rb/rbm.rb
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+ - utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb
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+ - utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb
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+ - utils/enveomics/Scripts/lib/enveomics_rb/stats.rb
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+ - utils/enveomics/Scripts/lib/enveomics_rb/stats/rand.rb
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+ - utils/enveomics/Scripts/lib/enveomics_rb/stats/sample.rb
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+ - utils/enveomics/Scripts/lib/enveomics_rb/utils.rb
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+ - utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb
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+ - utils/enveomics/Scripts/ogs.annotate.rb
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+ - utils/enveomics/Scripts/ogs.core-pan.rb
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+ - utils/enveomics/Scripts/ogs.extract.rb
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+ - utils/enveomics/Scripts/ogs.mcl.rb
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+ - utils/enveomics/Scripts/ogs.rb
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+ - utils/enveomics/Scripts/ogs.stats.rb
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+ - utils/enveomics/Scripts/rbm-legacy.rb
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+ - utils/enveomics/Scripts/rbm.rb
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+ - utils/enveomics/Tests/Mgen_M2288.faa
459
+ - utils/enveomics/Tests/Mgen_M2288.fna
460
+ - utils/enveomics/Tests/Mgen_M2321.fna
461
+ - utils/enveomics/Tests/Nequ_Kin4M.faa
462
+ - utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata
463
+ - utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt
464
+ - utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv
465
+ - utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv
466
+ - utils/enveomics/Tests/a_mg.cds-go.blast.tsv
467
+ - utils/enveomics/Tests/a_mg.reads-cds.blast.tsv
468
+ - utils/enveomics/Tests/a_mg.reads-cds.counts.tsv
469
+ - utils/enveomics/Tests/alkB.nwk
470
+ - utils/enveomics/Tests/anthrax-cansnp-data.tsv
471
+ - utils/enveomics/Tests/anthrax-cansnp-key.tsv
472
+ - utils/enveomics/Tests/hiv1.faa
473
+ - utils/enveomics/Tests/hiv1.fna
474
+ - utils/enveomics/Tests/hiv2.faa
475
+ - utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv
476
+ - utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim
477
+ - utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec
478
+ - utils/enveomics/Tests/phyla_counts.tsv
479
+ - utils/enveomics/Tests/primate_lentivirus.ogs
480
+ - utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm
481
+ - utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm
482
+ - utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm
483
+ - utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm
484
+ - utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm
485
+ - utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm
486
+ - utils/enveomics/build_enveomics_r.bash
487
+ - utils/enveomics/enveomics.R/DESCRIPTION
488
+ - utils/enveomics/enveomics.R/NAMESPACE
489
+ - utils/enveomics/enveomics.R/R/autoprune.R
490
+ - utils/enveomics/enveomics.R/R/barplot.R
491
+ - utils/enveomics/enveomics.R/R/cliopts.R
492
+ - utils/enveomics/enveomics.R/R/df2dist.R
493
+ - utils/enveomics/enveomics.R/R/growthcurve.R
494
+ - utils/enveomics/enveomics.R/R/prefscore.R
495
+ - utils/enveomics/enveomics.R/R/recplot.R
496
+ - utils/enveomics/enveomics.R/R/recplot2.R
497
+ - utils/enveomics/enveomics.R/R/tribs.R
498
+ - utils/enveomics/enveomics.R/R/utils.R
499
+ - utils/enveomics/enveomics.R/README.md
500
+ - utils/enveomics/enveomics.R/data/growth.curves.rda
501
+ - utils/enveomics/enveomics.R/data/phyla.counts.rda
502
+ - utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd
503
+ - utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd
504
+ - utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd
505
+ - utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd
506
+ - utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd
507
+ - utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd
508
+ - utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd
509
+ - utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd
510
+ - utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd
511
+ - utils/enveomics/enveomics.R/man/enve.__tribs.Rd
512
+ - utils/enveomics/enveomics.R/man/enve.barplot.Rd
513
+ - utils/enveomics/enveomics.R/man/enve.cliopts.Rd
514
+ - utils/enveomics/enveomics.R/man/enve.col.alpha.Rd
515
+ - utils/enveomics/enveomics.R/man/enve.col2alpha.Rd
516
+ - utils/enveomics/enveomics.R/man/enve.df2dist.Rd
517
+ - utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd
518
+ - utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd
519
+ - utils/enveomics/enveomics.R/man/enve.growthcurve.Rd
520
+ - utils/enveomics/enveomics.R/man/enve.prefscore.Rd
521
+ - utils/enveomics/enveomics.R/man/enve.prune.dist.Rd
522
+ - utils/enveomics/enveomics.R/man/enve.recplot.Rd
523
+ - utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd
524
+ - utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd
525
+ - utils/enveomics/enveomics.R/man/enve.recplot2.Rd
526
+ - utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd
527
+ - utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd
528
+ - utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd
529
+ - utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd
530
+ - utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd
531
+ - utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd
532
+ - utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd
533
+ - utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd
534
+ - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd
535
+ - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd
536
+ - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd
537
+ - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd
538
+ - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd
539
+ - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd
540
+ - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd
541
+ - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd
542
+ - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd
543
+ - utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd
544
+ - utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd
545
+ - utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd
546
+ - utils/enveomics/enveomics.R/man/enve.selvector.Rd
547
+ - utils/enveomics/enveomics.R/man/enve.tribs.Rd
548
+ - utils/enveomics/enveomics.R/man/enve.tribs.test.Rd
549
+ - utils/enveomics/enveomics.R/man/enve.truncate.Rd
550
+ - utils/enveomics/enveomics.R/man/growth.curves.Rd
551
+ - utils/enveomics/enveomics.R/man/phyla.counts.Rd
552
+ - utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd
553
+ - utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd
554
+ - utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd
555
+ - utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd
556
+ - utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd
557
+ - utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd
558
+ - utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd
559
+ - utils/enveomics/globals.mk
560
+ - utils/enveomics/manifest.json
264
561
  - utils/find-medoid.R
265
562
  - utils/index_metadata.rb
563
+ - utils/multitrim/Multitrim How-To.pdf
564
+ - utils/multitrim/README.md
565
+ - utils/multitrim/multitrim.py
566
+ - utils/multitrim/multitrim.yml
266
567
  - utils/mytaxa_scan.R
267
568
  - utils/mytaxa_scan.rb
268
569
  - utils/plot-taxdist.R
@@ -302,7 +603,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
302
603
  - !ruby/object:Gem::Version
303
604
  version: '0'
304
605
  requirements: []
305
- rubygems_version: 3.1.4
606
+ rubygems_version: 3.1.6
306
607
  signing_key:
307
608
  specification_version: 4
308
609
  summary: MiGA