miga-base 0.3.0.0 → 0.3.0.1

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Files changed (260) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +21 -4
  3. data/actions/init.rb +258 -0
  4. data/actions/run_local.rb +1 -2
  5. data/actions/test_taxonomy.rb +4 -1
  6. data/bin/miga +8 -1
  7. data/lib/miga/dataset.rb +4 -4
  8. data/lib/miga/dataset_result.rb +7 -4
  9. data/lib/miga/version.rb +2 -2
  10. data/scripts/_distances_noref_nomulti.bash +3 -1
  11. data/scripts/clade_finding.bash +1 -1
  12. data/scripts/init.bash +1 -1
  13. data/scripts/miga.bash +1 -1
  14. data/scripts/mytaxa.bash +78 -72
  15. data/scripts/mytaxa_scan.bash +67 -62
  16. data/scripts/ogs.bash +1 -1
  17. data/scripts/trimmed_fasta.bash +4 -3
  18. data/utils/enveomics/Examples/aai-matrix.bash +66 -0
  19. data/utils/enveomics/Examples/ani-matrix.bash +66 -0
  20. data/utils/enveomics/Examples/essential-phylogeny.bash +105 -0
  21. data/utils/enveomics/Examples/unus-genome-phylogeny.bash +100 -0
  22. data/utils/enveomics/LICENSE.txt +73 -0
  23. data/utils/enveomics/Makefile +52 -0
  24. data/utils/enveomics/Manifest/Tasks/aasubs.json +103 -0
  25. data/utils/enveomics/Manifest/Tasks/blasttab.json +703 -0
  26. data/utils/enveomics/Manifest/Tasks/distances.json +161 -0
  27. data/utils/enveomics/Manifest/Tasks/fasta.json +571 -0
  28. data/utils/enveomics/Manifest/Tasks/fastq.json +208 -0
  29. data/utils/enveomics/Manifest/Tasks/graphics.json +126 -0
  30. data/utils/enveomics/Manifest/Tasks/ogs.json +339 -0
  31. data/utils/enveomics/Manifest/Tasks/other.json +746 -0
  32. data/utils/enveomics/Manifest/Tasks/remote.json +355 -0
  33. data/utils/enveomics/Manifest/Tasks/sequence-identity.json +454 -0
  34. data/utils/enveomics/Manifest/Tasks/tables.json +308 -0
  35. data/utils/enveomics/Manifest/Tasks/trees.json +68 -0
  36. data/utils/enveomics/Manifest/Tasks/variants.json +111 -0
  37. data/utils/enveomics/Manifest/categories.json +132 -0
  38. data/utils/enveomics/Manifest/examples.json +154 -0
  39. data/utils/enveomics/Manifest/tasks.json +4 -0
  40. data/utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash +69 -0
  41. data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +56 -0
  42. data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +60 -0
  43. data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +38 -0
  44. data/utils/enveomics/Pipelines/assembly.pbs/README.md +189 -0
  45. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash +112 -0
  46. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash +23 -0
  47. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash +44 -0
  48. data/utils/enveomics/Pipelines/assembly.pbs/RUNME.bash +50 -0
  49. data/utils/enveomics/Pipelines/assembly.pbs/kSelector.R +37 -0
  50. data/utils/enveomics/Pipelines/assembly.pbs/newbler.pbs +68 -0
  51. data/utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl +49 -0
  52. data/utils/enveomics/Pipelines/assembly.pbs/soap.pbs +80 -0
  53. data/utils/enveomics/Pipelines/assembly.pbs/stats.pbs +57 -0
  54. data/utils/enveomics/Pipelines/assembly.pbs/velvet.pbs +63 -0
  55. data/utils/enveomics/Pipelines/blast.pbs/01.pbs.bash +38 -0
  56. data/utils/enveomics/Pipelines/blast.pbs/02.pbs.bash +73 -0
  57. data/utils/enveomics/Pipelines/blast.pbs/03.pbs.bash +21 -0
  58. data/utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl +72 -0
  59. data/utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash +98 -0
  60. data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +55 -0
  61. data/utils/enveomics/Pipelines/blast.pbs/README.md +127 -0
  62. data/utils/enveomics/Pipelines/blast.pbs/RUNME.bash +109 -0
  63. data/utils/enveomics/Pipelines/blast.pbs/TASK.check.bash +128 -0
  64. data/utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash +16 -0
  65. data/utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash +22 -0
  66. data/utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash +26 -0
  67. data/utils/enveomics/Pipelines/blast.pbs/TASK.run.bash +89 -0
  68. data/utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash +29 -0
  69. data/utils/enveomics/Pipelines/idba.pbs/README.md +49 -0
  70. data/utils/enveomics/Pipelines/idba.pbs/RUNME.bash +95 -0
  71. data/utils/enveomics/Pipelines/idba.pbs/run.pbs +56 -0
  72. data/utils/enveomics/Pipelines/trim.pbs/README.md +54 -0
  73. data/utils/enveomics/Pipelines/trim.pbs/RUNME.bash +70 -0
  74. data/utils/enveomics/Pipelines/trim.pbs/run.pbs +130 -0
  75. data/utils/enveomics/README.md +40 -0
  76. data/utils/enveomics/Scripts/AAsubs.log2ratio.rb +171 -0
  77. data/utils/enveomics/Scripts/Aln.cat.rb +162 -0
  78. data/utils/enveomics/Scripts/Aln.convert.pl +35 -0
  79. data/utils/enveomics/Scripts/AlphaDiversity.pl +152 -0
  80. data/utils/enveomics/Scripts/BlastPairwise.AAsubs.pl +102 -0
  81. data/utils/enveomics/Scripts/BlastTab.addlen.rb +61 -0
  82. data/utils/enveomics/Scripts/BlastTab.advance.bash +48 -0
  83. data/utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl +55 -0
  84. data/utils/enveomics/Scripts/BlastTab.catsbj.pl +106 -0
  85. data/utils/enveomics/Scripts/BlastTab.cogCat.rb +76 -0
  86. data/utils/enveomics/Scripts/BlastTab.filter.pl +47 -0
  87. data/utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl +194 -0
  88. data/utils/enveomics/Scripts/BlastTab.metaxaPrep.pl +104 -0
  89. data/utils/enveomics/Scripts/BlastTab.pairedHits.rb +157 -0
  90. data/utils/enveomics/Scripts/BlastTab.recplot2.R +40 -0
  91. data/utils/enveomics/Scripts/BlastTab.seqdepth.pl +86 -0
  92. data/utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl +119 -0
  93. data/utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl +86 -0
  94. data/utils/enveomics/Scripts/BlastTab.subsample.pl +47 -0
  95. data/utils/enveomics/Scripts/BlastTab.sumPerHit.pl +114 -0
  96. data/utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl +90 -0
  97. data/utils/enveomics/Scripts/BlastTab.topHits_sorted.rb +101 -0
  98. data/utils/enveomics/Scripts/Chao1.pl +97 -0
  99. data/utils/enveomics/Scripts/CharTable.classify.rb +234 -0
  100. data/utils/enveomics/Scripts/EBIseq2tax.rb +83 -0
  101. data/utils/enveomics/Scripts/FastA.N50.pl +56 -0
  102. data/utils/enveomics/Scripts/FastA.filter.pl +52 -0
  103. data/utils/enveomics/Scripts/FastA.filterLen.pl +28 -0
  104. data/utils/enveomics/Scripts/FastA.filterN.pl +60 -0
  105. data/utils/enveomics/Scripts/FastA.fragment.rb +92 -0
  106. data/utils/enveomics/Scripts/FastA.gc.pl +42 -0
  107. data/utils/enveomics/Scripts/FastA.interpose.pl +87 -0
  108. data/utils/enveomics/Scripts/FastA.length.pl +38 -0
  109. data/utils/enveomics/Scripts/FastA.per_file.pl +36 -0
  110. data/utils/enveomics/Scripts/FastA.qlen.pl +57 -0
  111. data/utils/enveomics/Scripts/FastA.rename.pl +65 -0
  112. data/utils/enveomics/Scripts/FastA.revcom.pl +23 -0
  113. data/utils/enveomics/Scripts/FastA.slider.pl +85 -0
  114. data/utils/enveomics/Scripts/FastA.split.pl +55 -0
  115. data/utils/enveomics/Scripts/FastA.subsample.pl +131 -0
  116. data/utils/enveomics/Scripts/FastA.tag.rb +64 -0
  117. data/utils/enveomics/Scripts/FastA.wrap.rb +48 -0
  118. data/utils/enveomics/Scripts/FastQ.filter.pl +54 -0
  119. data/utils/enveomics/Scripts/FastQ.interpose.pl +90 -0
  120. data/utils/enveomics/Scripts/FastQ.offset.pl +90 -0
  121. data/utils/enveomics/Scripts/FastQ.split.pl +53 -0
  122. data/utils/enveomics/Scripts/FastQ.tag.rb +63 -0
  123. data/utils/enveomics/Scripts/FastQ.toFastA.awk +24 -0
  124. data/utils/enveomics/Scripts/GenBank.add_fields.rb +84 -0
  125. data/utils/enveomics/Scripts/HMM.essential.rb +254 -0
  126. data/utils/enveomics/Scripts/HMMsearch.extractIds.rb +83 -0
  127. data/utils/enveomics/Scripts/JPlace.distances.rb +88 -0
  128. data/utils/enveomics/Scripts/JPlace.to_iToL.rb +306 -0
  129. data/utils/enveomics/Scripts/M5nr.getSequences.rb +81 -0
  130. data/utils/enveomics/Scripts/MeTaxa.distribution.pl +198 -0
  131. data/utils/enveomics/Scripts/MyTaxa.fragsByTax.pl +35 -0
  132. data/utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb +49 -0
  133. data/utils/enveomics/Scripts/NCBIacc2tax.rb +92 -0
  134. data/utils/enveomics/Scripts/Newick.autoprune.R +27 -0
  135. data/utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl +228 -0
  136. data/utils/enveomics/Scripts/RefSeq.download.bash +48 -0
  137. data/utils/enveomics/Scripts/SRA.download.bash +50 -0
  138. data/utils/enveomics/Scripts/TRIBS.plot-test.R +36 -0
  139. data/utils/enveomics/Scripts/TRIBS.test.R +39 -0
  140. data/utils/enveomics/Scripts/Table.barplot.R +30 -0
  141. data/utils/enveomics/Scripts/Table.df2dist.R +30 -0
  142. data/utils/enveomics/Scripts/Table.filter.pl +61 -0
  143. data/utils/enveomics/Scripts/Table.merge.pl +77 -0
  144. data/utils/enveomics/Scripts/Table.replace.rb +69 -0
  145. data/utils/enveomics/Scripts/Table.round.rb +63 -0
  146. data/utils/enveomics/Scripts/Table.split.pl +57 -0
  147. data/utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb +227 -0
  148. data/utils/enveomics/Scripts/VCF.KaKs.rb +147 -0
  149. data/utils/enveomics/Scripts/VCF.SNPs.rb +88 -0
  150. data/utils/enveomics/Scripts/aai.rb +373 -0
  151. data/utils/enveomics/Scripts/ani.rb +362 -0
  152. data/utils/enveomics/Scripts/gi2tax.rb +103 -0
  153. data/utils/enveomics/Scripts/in_silico_GA_GI.pl +96 -0
  154. data/utils/enveomics/Scripts/lib/data/essential.hmm.gz +0 -0
  155. data/utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb +26 -0
  156. data/utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb +253 -0
  157. data/utils/enveomics/Scripts/lib/enveomics_rb/og.rb +182 -0
  158. data/utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb +74 -0
  159. data/utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb +237 -0
  160. data/utils/enveomics/Scripts/lib/enveomics_rb/stat.rb +30 -0
  161. data/utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb +135 -0
  162. data/utils/enveomics/Scripts/ogs.annotate.rb +88 -0
  163. data/utils/enveomics/Scripts/ogs.core-pan.rb +160 -0
  164. data/utils/enveomics/Scripts/ogs.extract.rb +125 -0
  165. data/utils/enveomics/Scripts/ogs.mcl.rb +186 -0
  166. data/utils/enveomics/Scripts/ogs.rb +104 -0
  167. data/utils/enveomics/Scripts/ogs.stats.rb +131 -0
  168. data/utils/enveomics/Scripts/rbm.rb +137 -0
  169. data/utils/enveomics/Tests/Makefile +10 -0
  170. data/utils/enveomics/Tests/Mgen_M2288.faa +3189 -0
  171. data/utils/enveomics/Tests/Mgen_M2288.fna +8282 -0
  172. data/utils/enveomics/Tests/Mgen_M2321.fna +8288 -0
  173. data/utils/enveomics/Tests/Nequ_Kin4M.faa +2970 -0
  174. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata +0 -0
  175. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt +7 -0
  176. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv +17 -0
  177. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv +137 -0
  178. data/utils/enveomics/Tests/a_mg.cds-go.blast.tsv +123 -0
  179. data/utils/enveomics/Tests/a_mg.reads-cds.blast.tsv +200 -0
  180. data/utils/enveomics/Tests/a_mg.reads-cds.counts.tsv +55 -0
  181. data/utils/enveomics/Tests/alkB.nwk +1 -0
  182. data/utils/enveomics/Tests/anthrax-cansnp-data.tsv +13 -0
  183. data/utils/enveomics/Tests/anthrax-cansnp-key.tsv +17 -0
  184. data/utils/enveomics/Tests/hiv1.faa +59 -0
  185. data/utils/enveomics/Tests/hiv1.fna +134 -0
  186. data/utils/enveomics/Tests/hiv2.faa +70 -0
  187. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv +233 -0
  188. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim +1 -0
  189. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec +233 -0
  190. data/utils/enveomics/Tests/phyla_counts.tsv +10 -0
  191. data/utils/enveomics/Tests/primate_lentivirus.ogs +11 -0
  192. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm +9 -0
  193. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm +8 -0
  194. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm +6 -0
  195. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm +9 -0
  196. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm +6 -0
  197. data/utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm +6 -0
  198. data/utils/enveomics/build_enveomics_r.bash +44 -0
  199. data/utils/enveomics/enveomics.R/DESCRIPTION +31 -0
  200. data/utils/enveomics/enveomics.R/NAMESPACE +35 -0
  201. data/utils/enveomics/enveomics.R/R/autoprune.R +121 -0
  202. data/utils/enveomics/enveomics.R/R/barplot.R +165 -0
  203. data/utils/enveomics/enveomics.R/R/cliopts.R +119 -0
  204. data/utils/enveomics/enveomics.R/R/df2dist.R +117 -0
  205. data/utils/enveomics/enveomics.R/R/growthcurve.R +263 -0
  206. data/utils/enveomics/enveomics.R/R/recplot.R +320 -0
  207. data/utils/enveomics/enveomics.R/R/recplot2.R +745 -0
  208. data/utils/enveomics/enveomics.R/R/tribs.R +423 -0
  209. data/utils/enveomics/enveomics.R/R/utils.R +16 -0
  210. data/utils/enveomics/enveomics.R/README.md +52 -0
  211. data/utils/enveomics/enveomics.R/data/growth.curves.rda +0 -0
  212. data/utils/enveomics/enveomics.R/data/phyla.counts.rda +0 -0
  213. data/utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd +30 -0
  214. data/utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd +43 -0
  215. data/utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd +19 -0
  216. data/utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd +37 -0
  217. data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd +24 -0
  218. data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd +24 -0
  219. data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +33 -0
  220. data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +64 -0
  221. data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +37 -0
  222. data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd +19 -0
  223. data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd +18 -0
  224. data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +26 -0
  225. data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +25 -0
  226. data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +26 -0
  227. data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +49 -0
  228. data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +28 -0
  229. data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +97 -0
  230. data/utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd +40 -0
  231. data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +40 -0
  232. data/utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd +24 -0
  233. data/utils/enveomics/enveomics.R/man/enve.recplot2.__findPeak.Rd +40 -0
  234. data/utils/enveomics/enveomics.R/man/enve.recplot2.__findPeaks.Rd +18 -0
  235. data/utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd +22 -0
  236. data/utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd +20 -0
  237. data/utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd +18 -0
  238. data/utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd +18 -0
  239. data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +27 -0
  240. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd +53 -0
  241. data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd +44 -0
  242. data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +44 -0
  243. data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd +21 -0
  244. data/utils/enveomics/enveomics.R/man/enveomics.R-package.Rd +15 -0
  245. data/utils/enveomics/enveomics.R/man/growth.curves.Rd +14 -0
  246. data/utils/enveomics/enveomics.R/man/phyla.counts.Rd +13 -0
  247. data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +43 -0
  248. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +29 -0
  249. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +30 -0
  250. data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +71 -0
  251. data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd +18 -0
  252. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd +18 -0
  253. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd +18 -0
  254. data/utils/enveomics/enveomics.R/man/z$-methods.Rd +27 -0
  255. data/utils/enveomics/globals.mk +8 -0
  256. data/utils/enveomics/manifest.json +9 -0
  257. data/utils/index_metadata.rb +0 -0
  258. data/utils/plot-taxdist.R +0 -0
  259. data/utils/requirements.txt +19 -19
  260. metadata +242 -2
data/utils/enveomics/enveomics.R/man/z$-methods.Rd ADDED
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+ \name{$-methods}
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+ \docType{methods}
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+ \alias{$-methods}
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+ \alias{$,enve.GrowthCurve-method}
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+ \alias{$,enve.RecPlot2-method}
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+ \alias{$,enve.RecPlot2.Peak-method}
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+ \title{ ~~ Methods for Function \code{$} ~~}
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+ \description{
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+ ~~ Methods for function \code{$} ~~
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+ }
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+ \section{Methods}{
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+ \describe{
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+
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+ \item{\code{signature(x = "enve.GrowthCurve")}}{
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+ %% ~~describe this method here~~
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+ }
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+
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+ \item{\code{signature(x = "enve.RecPlot2")}}{
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+ %% ~~describe this method here~~
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+ }
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+
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+ \item{\code{signature(x = "enve.RecPlot2.Peak")}}{
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+ %% ~~describe this method here~~
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+ }
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+ }}
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+ \keyword{methods}
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+ \keyword{ ~~ other possible keyword(s) ~~ }
data/utils/enveomics/globals.mk ADDED
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+ # Global variables for the Enve-omics collection
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+
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+ R=R
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+ prefix=/usr/local
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+ bindir=$(prefix)/bin
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+ mandir=$(prefix)/man/man1
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+ SCRIPTS := $(wildcard Scripts/*.*)
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+
data/utils/enveomics/manifest.json ADDED
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+ {
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+ "_": ["This is not standard JSON, to parse use EnveJSON, available at:",
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+ "https://github.com/lmrodriguezr/enveomics-gui/."],
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+ "_include": [
5
+ "Manifest/categories.json",
6
+ "Manifest/examples.json",
7
+ "Manifest/tasks.json"
8
+ ]
9
+ }
data/utils/index_metadata.rb CHANGED
File without changes
data/utils/plot-taxdist.R CHANGED
File without changes
data/utils/requirements.txt CHANGED
@@ -1,19 +1,19 @@
1
- Software Test executable Website Notes
2
- -------- --------------- ------- -----
3
- Enve-omics scripts FastQ.tag.rb http://github.com/lmrodriguezr/enveomics All the collection must be present
4
- SolexaQA++ SolexaQA++ http://solexaqa.sourceforge.net Required version: v3.1.3+
5
- Scythe scythe https://github.com/vsbuffalo/scythe Required version: 0.991+
6
- FastQC fastqc http://www.bioinformatics.babraham.ac.uk/projects/fastqc
7
- IDBA idba_ud http://i.cs.hku.hk/~alse/hkubrg/projects/idba
8
- Prodigal prodigal http://prodigal.ornl.gov
9
- HMMer 3.0+ hmmsearch http://hmmer.janelia.org/software
10
- NCBI BLAST+ blastp ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST
11
- R R http://www.r-project.org/
12
- SQLite3 sqlite3 https://www.sqlite.org/
13
- RAxML (pthreads) raxmlHPC-PTHREADS http://sco.h-its.org/exelixis/web/software/raxml/index.html
14
- MCL mcl http://micans.org/mcl/
15
- DIAMOND diamond http://ab.inf.uni-tuebingen.de/software/diamond Required version: v0.7.9+
16
- MyTaxa MyTaxa http://enve-omics.ce.gatech.edu/mytaxa The folder must contain the db and utils dirs, and the AllGenomes.faa BLAST database
17
- Krona ktImportText https://github.com/marbl/Krona/wiki
18
- Barrnap barrnap http://www.vicbioinformatics.com/software.barrnap.shtml
19
- bedtools bedtools http://bedtools.readthedocs.org/en/latest/
1
+ Software Test exec Website Notes
2
+ -------- --------- ------- -----
3
+ Ruby ruby https://www.ruby-lang.org/ Required version: 1.9+
4
+ Python python https://www.python.org/
5
+ R R http://www.r-project.org/
6
+ SQLite3 sqlite3 https://www.sqlite.org/
7
+ NCBI BLAST+ blastp ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST
8
+ HMMer 3.0+ hmmsearch http://hmmer.janelia.org/software
9
+ Bedtools bedtools http://bedtools.readthedocs.org/en/latest/
10
+ Prodigal prodigal http://prodigal.ornl.gov
11
+ IDBA idba_ud http://i.cs.hku.hk/~alse/hkubrg/projects/idba
12
+ MCL mcl http://micans.org/mcl/
13
+ Barrnap barrnap http://www.vicbioinformatics.com/software.barrnap.shtml
14
+ Scythe scythe https://github.com/vsbuffalo/scythe Required version: 0.991+
15
+ FastQC fastqc http://www.bioinformatics.babraham.ac.uk/projects/fastqc
16
+ SolexaQA++ SolexaQA++ http://solexaqa.sourceforge.net Required version: v3.1.3+
17
+ DIAMOND (opt) diamond http://ab.inf.uni-tuebingen.de/software/diamond Required version: v0.7.9+
18
+ MyTaxa (opt) MyTaxa http://enve-omics.ce.gatech.edu/mytaxa The folder must contain the db and utils dirs, and the AllGenomes.faa.dmnd database
19
+ Krona (opt) 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: 0.3.0.0
4
+ version: 0.3.0.1
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: 2017-05-29 00:00:00.000000000 Z
11
+ date: 2017-06-06 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: rest-client
@@ -158,6 +158,245 @@ files:
158
158
  - scripts/trimmed_reads.bash
159
159
  - utils/adapters.fa
160
160
  - utils/core-pan-plot.R
161
+ - utils/enveomics/build_enveomics_r.bash
162
+ - utils/enveomics/enveomics.R/data/growth.curves.rda
163
+ - utils/enveomics/enveomics.R/data/phyla.counts.rda
164
+ - utils/enveomics/enveomics.R/DESCRIPTION
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+ - utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd
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+ - utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd
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+ - utils/enveomics/enveomics.R/man/enve.__tribs.Rd
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+ - utils/enveomics/enveomics.R/man/enve.barplot.Rd
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+ - utils/enveomics/enveomics.R/man/enve.cliopts.Rd
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+ - utils/enveomics/enveomics.R/man/enve.col.alpha.Rd
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+ - utils/enveomics/enveomics.R/man/enve.col2alpha.Rd
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+ - utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd
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+ - utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd
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+ - utils/enveomics/enveomics.R/man/enve.df2dist.Rd
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+ - utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd
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+ - utils/enveomics/enveomics.R/man/enve.growthcurve.Rd
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+ - utils/enveomics/enveomics.R/man/enve.prune.dist.Rd
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+ - utils/enveomics/enveomics.R/man/enve.recplot.Rd
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+ - utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd
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+ - utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd
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+ - utils/enveomics/enveomics.R/man/enve.recplot2.__findPeak.Rd
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+ - utils/enveomics/enveomics.R/man/enve.recplot2.__findPeaks.Rd
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+ - utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd
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+ - utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd
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+ - utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd
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+ - utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd
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+ - utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd
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+ - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd
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+ - utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd
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+ - utils/enveomics/enveomics.R/man/enve.recplot2.Rd
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+ - utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd
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+ - utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd
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+ - utils/enveomics/enveomics.R/man/enve.tribs.Rd
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+ - utils/enveomics/enveomics.R/man/enve.tribs.test.Rd
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+ - utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd
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+ - utils/enveomics/enveomics.R/man/enveomics.R-package.Rd
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+ - utils/enveomics/enveomics.R/man/growth.curves.Rd
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+ - utils/enveomics/enveomics.R/man/phyla.counts.Rd
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+ - utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd
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+ - utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd
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+ - utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd
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+ - utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd
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+ - utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd
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+ - utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd
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+ - utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd
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+ - utils/enveomics/enveomics.R/man/z$-methods.Rd
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+ - utils/enveomics/enveomics.R/NAMESPACE
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+ - utils/enveomics/enveomics.R/R/autoprune.R
209
+ - utils/enveomics/enveomics.R/R/barplot.R
210
+ - utils/enveomics/enveomics.R/R/cliopts.R
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+ - utils/enveomics/enveomics.R/R/df2dist.R
212
+ - utils/enveomics/enveomics.R/R/growthcurve.R
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+ - utils/enveomics/enveomics.R/R/recplot.R
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+ - utils/enveomics/enveomics.R/R/recplot2.R
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+ - utils/enveomics/enveomics.R/R/tribs.R
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+ - utils/enveomics/enveomics.R/R/utils.R
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+ - utils/enveomics/enveomics.R/README.md
218
+ - utils/enveomics/Examples/aai-matrix.bash
219
+ - utils/enveomics/Examples/ani-matrix.bash
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+ - utils/enveomics/Examples/essential-phylogeny.bash
221
+ - utils/enveomics/Examples/unus-genome-phylogeny.bash
222
+ - utils/enveomics/globals.mk
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+ - utils/enveomics/LICENSE.txt
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+ - utils/enveomics/Makefile
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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/aasubs.json
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+ - 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/ogs.json
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+ - utils/enveomics/Manifest/Tasks/other.json
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+ - utils/enveomics/Manifest/Tasks/remote.json
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+ - 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/tasks.json
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+ - utils/enveomics/manifest.json
242
+ - utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash
243
+ - utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl
244
+ - utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl
245
+ - utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl
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+ - utils/enveomics/Pipelines/assembly.pbs/kSelector.R
247
+ - utils/enveomics/Pipelines/assembly.pbs/newbler.pbs
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+ - utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl
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+ - utils/enveomics/Pipelines/assembly.pbs/README.md
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+ - utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash
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+ - utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash
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+ - utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash
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+ - utils/enveomics/Pipelines/assembly.pbs/RUNME.bash
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+ - 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
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+ - utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash
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+ - utils/enveomics/Pipelines/blast.pbs/FastA.split.pl
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+ - utils/enveomics/Pipelines/blast.pbs/README.md
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+ - utils/enveomics/Pipelines/blast.pbs/RUNME.bash
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+ - utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash
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+ - utils/enveomics/Pipelines/blast.pbs/TASK.check.bash
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+ - utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash
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+ - utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash
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+ - utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash
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+ - utils/enveomics/Pipelines/blast.pbs/TASK.run.bash
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+ - utils/enveomics/Pipelines/idba.pbs/README.md
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+ - utils/enveomics/Pipelines/idba.pbs/run.pbs
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+ - utils/enveomics/Pipelines/idba.pbs/RUNME.bash
274
+ - utils/enveomics/Pipelines/trim.pbs/README.md
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+ - utils/enveomics/Pipelines/trim.pbs/run.pbs
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+ - utils/enveomics/Pipelines/trim.pbs/RUNME.bash
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+ - utils/enveomics/README.md
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+ - utils/enveomics/Scripts/aai.rb
279
+ - utils/enveomics/Scripts/AAsubs.log2ratio.rb
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+ - utils/enveomics/Scripts/Aln.cat.rb
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+ - utils/enveomics/Scripts/Aln.convert.pl
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+ - utils/enveomics/Scripts/AlphaDiversity.pl
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+ - utils/enveomics/Scripts/ani.rb
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+ - utils/enveomics/Scripts/BlastPairwise.AAsubs.pl
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+ - 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
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+ - utils/enveomics/Scripts/BlastTab.catsbj.pl
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+ - utils/enveomics/Scripts/BlastTab.cogCat.rb
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+ - utils/enveomics/Scripts/BlastTab.filter.pl
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+ - utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl
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+ - utils/enveomics/Scripts/BlastTab.metaxaPrep.pl
293
+ - utils/enveomics/Scripts/BlastTab.pairedHits.rb
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+ - utils/enveomics/Scripts/BlastTab.recplot2.R
295
+ - utils/enveomics/Scripts/BlastTab.seqdepth.pl
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+ - utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl
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+ - utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.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
301
+ - utils/enveomics/Scripts/BlastTab.topHits_sorted.rb
302
+ - utils/enveomics/Scripts/Chao1.pl
303
+ - utils/enveomics/Scripts/CharTable.classify.rb
304
+ - utils/enveomics/Scripts/EBIseq2tax.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.N50.pl
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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.slider.pl
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+ - utils/enveomics/Scripts/FastA.split.pl
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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.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.offset.pl
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+ - utils/enveomics/Scripts/FastQ.split.pl
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+ - utils/enveomics/Scripts/FastQ.tag.rb
327
+ - utils/enveomics/Scripts/FastQ.toFastA.awk
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+ - utils/enveomics/Scripts/GenBank.add_fields.rb
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+ - utils/enveomics/Scripts/gi2tax.rb
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+ - utils/enveomics/Scripts/HMM.essential.rb
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+ - utils/enveomics/Scripts/HMMsearch.extractIds.rb
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+ - utils/enveomics/Scripts/in_silico_GA_GI.pl
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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/lib/data/essential.hmm.gz
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+ - utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb
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+ - utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb
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+ - utils/enveomics/Scripts/lib/enveomics_rb/og.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/stat.rb
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+ - utils/enveomics/Scripts/lib/enveomics_rb/vcf.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
349
+ - 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/RAxML-EPA.to_iToL.pl
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+ - utils/enveomics/Scripts/rbm.rb
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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/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.replace.rb
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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/TRIBS.plot-test.R
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+ - utils/enveomics/Scripts/TRIBS.test.R
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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/Tests/a_mg.cds-go.blast.tsv
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+ - utils/enveomics/Tests/a_mg.reads-cds.blast.tsv
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+ - utils/enveomics/Tests/a_mg.reads-cds.counts.tsv
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+ - utils/enveomics/Tests/alkB.nwk
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+ - utils/enveomics/Tests/anthrax-cansnp-data.tsv
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+ - utils/enveomics/Tests/anthrax-cansnp-key.tsv
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+ - utils/enveomics/Tests/hiv1.faa
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+ - utils/enveomics/Tests/hiv1.fna
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+ - utils/enveomics/Tests/hiv2.faa
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+ - utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv
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+ - utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim
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+ - utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec
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+ - utils/enveomics/Tests/Makefile
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+ - utils/enveomics/Tests/Mgen_M2288.faa
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+ - utils/enveomics/Tests/Mgen_M2288.fna
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+ - utils/enveomics/Tests/Mgen_M2321.fna
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+ - utils/enveomics/Tests/Nequ_Kin4M.faa
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+ - utils/enveomics/Tests/phyla_counts.tsv
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+ - utils/enveomics/Tests/primate_lentivirus.ogs
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+ - utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm
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+ - utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm
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+ - utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm
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+ - utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm
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+ - utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm
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+ - utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm
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+ - utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata
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  - utils/mytaxa_scan.rb
@@ -178,6 +417,7 @@ files:
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  - actions/find_datasets.rb
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  - actions/import_datasets.rb
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  - actions/index_taxonomy.rb
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  - actions/list_datasets.rb
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  - actions/list_files.rb
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  - actions/plugins.rb