miga-base 0.7.26.0 → 0.7.26.1

data/utils/enveomics/enveomics.R/man/enve.truncate.Rd

@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{enve.truncate}
+\alias{enve.truncate}
+\title{Enveomics: Truncate}
+\usage{
+enve.truncate(x, f = 0.95, FUN = mean)
+}
+\arguments{
+\item{x}{A vector of numbers.}
+
+\item{f}{The fraction of values to retain.}
+
+\item{FUN}{Summary function to apply to the vectors. To obtain the 
+truncated vector itself, use \code{c}.}
+}
+\value{
+Returns the summary \code{(FUN)} of the truncated vector.
+}
+\description{
+Removes the \code{n} highest and lowest values from a vector, and applies
+summary function. The value of \code{n} is determined such that the central
+range is used, corresponding to the \code{f} fraction of values.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/growth.curves.Rd

@@ -0,0 +1,14 @@
+
+\name{growth.curves}
+\docType{data}
+\alias{growth.curves}
+\title{Bacterial growth curves for three Escherichia coli mutants}
+\description{
+  This data set provides time (first column) and three triplicated growth
+  curves as optical density at 600nm (OD_600nm) for different mutants of E.
+  coli.
+}
+\usage{growth.curves}
+\format{A data frame with 16 rows (times) and 10 rows (times and OD_600nm).}
+\keyword{datasets}
+

data/utils/enveomics/enveomics.R/man/phyla.counts.Rd

@@ -0,0 +1,13 @@
+
+\name{phyla.counts}
+\docType{data}
+\alias{phyla.counts}
+\title{Counts of microbial phyla in four sites}
+\description{
+  This data set gives the counts of phyla in three different
+  sites.
+}
+\usage{phyla.counts}
+\format{A data frame with 9 rows (phyla) and 4 rows (sites).}
+\keyword{datasets}
+

data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd

@@ -0,0 +1,63 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/growthcurve.R
+\name{plot.enve.GrowthCurve}
+\alias{plot.enve.GrowthCurve}
+\title{Enveomics: Plot of Growth Curve}
+\usage{
+\method{plot}{enve.GrowthCurve}(x, col, pt.alpha = 0.9, ln.alpha = 1,
+  ln.lwd = 1, ln.lty = 1, band.alpha = 0.4, band.density = NULL,
+  band.angle = 45, xp.alpha = 0.5, xp.lwd = 1, xp.lty = 1,
+  pch = 19, new = TRUE, legend = new, add.params = FALSE, ...)
+}
+\arguments{
+\item{x}{An \code{\link{enve.GrowthCurve}} object to plot.}
+
+\item{col}{Base colors to use for the different samples. Can be recycled.
+By default, grey for one sample or rainbow colors for more than one.}
+
+\item{pt.alpha}{Color alpha for the observed data points, using \code{col}
+as a base.}
+
+\item{ln.alpha}{Color alpha for the fitted growth curve, using \code{col}
+as a base.}
+
+\item{ln.lwd}{Line width for the fitted curve.}
+
+\item{ln.lty}{Line type for the fitted curve.}
+
+\item{band.alpha}{Color alpha for the confidence interval band of the 
+fitted growth curve, using \code{col} as a base.}
+
+\item{band.density}{Density of the filling pattern in the interval band.
+If \code{NULL}, a solid color is used.}
+
+\item{band.angle}{Angle of the density filling pattern in the interval 
+band. Ignored if \code{band.density} is \code{NULL}.}
+
+\item{xp.alpha}{Color alpha for the line connecting individual experiments,
+using \code{col} as a base.}
+
+\item{xp.lwd}{Width of line for the experiments.}
+
+\item{xp.lty}{Type of line for the experiments.}
+
+\item{pch}{Point character for observed data points.}
+
+\item{new}{Should a new plot be generated? If \code{FALSE}, the existing
+canvas is used.}
+
+\item{legend}{Should the plot include a legend? If \code{FALSE}, no legend
+is added. If \code{TRUE}, a legend is added in the bottom-right corner.
+Otherwise, a legend is added in the position specified as \code{xy.coords}.}
+
+\item{add.params}{Should the legend include the parameters of the fitted 
+model?}
+
+\item{...}{Any other graphic parameters.}
+}
+\description{
+Plots an \code{\link{enve.GrowthCurve}} object.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd

@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tribs.R
+\name{plot.enve.TRIBS}
+\alias{plot.enve.TRIBS}
+\title{Enveomics: TRIBS Plot}
+\usage{
+\method{plot}{enve.TRIBS}(x, new = TRUE, type = c("boxplot", "points"),
+  col = "#00000044", pt.cex = 1/2, pt.pch = 19, pt.col = col,
+  ln.col = col, ...)
+}
+\arguments{
+\item{x}{\code{\link{enve.TRIBS}} object to plot.}
+
+\item{new}{Should a new canvas be drawn?}
+
+\item{type}{Type of plot. The \strong{points} plot shows all the replicates, the 
+\strong{boxplot} plot represents the values found by
+\code{\link[grDevices]{boxplot.stats}}.
+as areas, and plots the outliers as points.}
+
+\item{col}{Color of the areas and/or the points.}
+
+\item{pt.cex}{Size of the points.}
+
+\item{pt.pch}{Points character.}
+
+\item{pt.col}{Color of the points.}
+
+\item{ln.col}{Color of the lines.}
+
+\item{...}{Any additional parameters supported by \code{plot}.}
+}
+\description{
+Plot an \code{\link{enve.TRIBS}} object.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd

@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tribs.R
+\name{plot.enve.TRIBStest}
+\alias{plot.enve.TRIBStest}
+\title{Enveomics: TRIBS Plot Test}
+\usage{
+\method{plot}{enve.TRIBStest}(x, type = c("overlap", "difference"),
+  col = "#00000044", col1 = col, col2 = "#44001144",
+  ylab = "Probability", xlim = range(attr(x, "dist.mids")),
+  ylim = c(0, max(c(attr(x, "all.dist"), attr(x, "sel.dist")))), ...)
+}
+\arguments{
+\item{x}{\code{\link{enve.TRIBStest}} object to plot.}
+
+\item{type}{What to plot. \code{overlap} generates a plot of the two contrasting empirical
+PDFs (to compare against each other), \code{difference} produces a plot of the
+differences between the empirical PDFs (to compare against zero).}
+
+\item{col}{Main color of the plot if type=\code{difference}.}
+
+\item{col1}{First color of the plot if type=\code{overlap}.}
+
+\item{col2}{Second color of the plot if type=\code{overlap}.}
+
+\item{ylab}{Y-axis label.}
+
+\item{xlim}{X-axis limits.}
+
+\item{ylim}{Y-axis limits.}
+
+\item{...}{Any other graphical arguments.}
+}
+\description{
+Plots an \code{\link{enve.TRIBStest}} object.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd

@@ -0,0 +1,111 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{plot.enve.RecPlot2}
+\alias{plot.enve.RecPlot2}
+\title{Enveomics: Recruitment Plot (2)}
+\usage{
+\method{plot}{enve.RecPlot2}(x, layout = matrix(c(5, 5, 2, 1, 4, 3), nrow
+  = 2), panel.fun = list(), widths = c(1, 7, 2), heights = c(1, 2),
+  palette = grey((100:0)/100), underlay.group = TRUE,
+  peaks.col = "darkred", use.peaks, id.lim = range(x$id.breaks),
+  pos.lim = range(x$pos.breaks), pos.units = c("Mbp", "Kbp", "bp"),
+  mar = list(`1` = c(5, 4, 1, 1) + 0.1, `2` = c(ifelse(any(layout == 1),
+  1, 5), 4, 4, 1) + 0.1, `3` = c(5, ifelse(any(layout == 1), 1, 4), 1, 2) +
+  0.1, `4` = c(ifelse(any(layout == 1), 1, 5), ifelse(any(layout == 2), 1,
+  4), 4, 2) + 0.1, `5` = c(5, 3, 4, 1) + 0.1, `6` = c(5, 4, 4, 2) + 0.1),
+  pos.splines = 0, id.splines = 1/2,
+  in.lwd = ifelse(is.null(pos.splines) || pos.splines > 0, 1/2, 2),
+  out.lwd = ifelse(is.null(pos.splines) || pos.splines > 0, 1/2, 2),
+  id.lwd = ifelse(is.null(id.splines) || id.splines > 0, 1/2, 2),
+  in.col = "darkblue", out.col = "lightblue", id.col = "black",
+  breaks.col = "#AAAAAA40", peaks.opts = list(), ...)
+}
+\arguments{
+\item{x}{\code{\link{enve.RecPlot2}} object to plot.}
+
+\item{layout}{Matrix indicating the position of the different panels in the layout,
+where:
+\itemize{
+  \item 0: Empty space
+  \item 1: Counts matrix
+  \item 2: position histogram (sequencing depth)
+  \item 3: identity histogram
+  \item 4: Populations histogram (histogram of sequencing depths)
+  \item 5: Color scale for the counts matrix (vertical)
+  \item 6: Color scale of the counts matrix (horizontal)
+}
+Only panels indicated here will be plotted. To plot only one panel
+simply set this to the number of the panel you want to plot.}
+
+\item{panel.fun}{List of functions to be executed after drawing each panel. Use the
+indices in \code{layout} (as characters) as keys. Functions for indices
+missing in \code{layout} are ignored. For example, to add a vertical line
+at the 3Mbp mark in both the position histogram and the counts matrix:
+\code{list('1'=function() abline(v=3), '2'=function() abline(v=3))}.
+Note that the X-axis in both panels is in Mbp by default. To change
+this behavior, set \code{pos.units} accordingly.}
+
+\item{widths}{Relative widths of the columns of \code{layout}.}
+
+\item{heights}{Relative heights of the rows of \code{layout}.}
+
+\item{palette}{Colors to be used to represent the counts matrix, sorted from no hits
+to the maximum sequencing depth.}
+
+\item{underlay.group}{If TRUE, it indicates the in-group and out-group areas couloured based
+on \code{in.col} and \code{out.col}. Requires support for semi-transparency.}
+
+\item{peaks.col}{If not \code{NA}, it attempts to represent peaks in the population histogram
+in the specified color. Set to \code{NA} to avoid peak-finding.}
+
+\item{use.peaks}{A list of \code{\link{enve.RecPlot2.Peak}} objects, as returned by
+\code{\link{enve.recplot2.findPeaks}}. If passed, \code{peaks.opts} is ignored.}
+
+\item{id.lim}{Limits of identities to represent.}
+
+\item{pos.lim}{Limits of positions to represent (in bp, regardless of \code{pos.units}).}
+
+\item{pos.units}{Units in which the positions should be represented (powers of 1,000
+base pairs).}
+
+\item{mar}{Margins of the panels as a list, with the character representation of
+the number of the panel as index (see \code{layout}).}
+
+\item{pos.splines}{Smoothing parameter for the splines in the position histogram. Zero
+(0) for no splines. Use \code{NULL} to automatically detect by leave-one-out
+cross-validation.}
+
+\item{id.splines}{Smoothing parameter for the splines in the identity histogram. Zero
+(0) for no splines. Use \code{NULL} to automatically detect by leave-one-out
+cross-validation.}
+
+\item{in.lwd}{Line width for the sequencing depth of in-group matches.}
+
+\item{out.lwd}{Line width for the sequencing depth of out-group matches.}
+
+\item{id.lwd}{Line width for the identity histogram.}
+
+\item{in.col}{Color associated to in-group matches.}
+
+\item{out.col}{Color associated to out-group matches.}
+
+\item{id.col}{Color for the identity histogram.}
+
+\item{breaks.col}{Color of the vertical lines indicating sequence breaks.}
+
+\item{peaks.opts}{Options passed to \code{\link{enve.recplot2.findPeaks}},
+if \code{peaks.col} is not \code{NA}.}
+
+\item{...}{Any other graphic parameters (currently ignored).}
+}
+\value{
+Returns a list of \code{\link{enve.RecPlot2.Peak}} objects (see
+\code{\link{enve.recplot2.findPeaks}}). If \code{peaks.col=NA} or
+\code{layout} doesn't include 4, returns \code{NA}.
+}
+\description{
+Plots an \code{\link{enve.RecPlot2}} object.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/growthcurve.R
+\name{summary.enve.GrowthCurve}
+\alias{summary.enve.GrowthCurve}
+\title{Enveomics: Summary of Growth Curve}
+\usage{
+\method{summary}{enve.GrowthCurve}(object, ...)
+}
+\arguments{
+\item{object}{An \code{\link{enve.GrowthCurve}} object.}
+
+\item{...}{No additional parameters are currently supported.}
+}
+\description{
+Summary of an \code{\link{enve.GrowthCurve}} object.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tribs.R
+\name{summary.enve.TRIBS}
+\alias{summary.enve.TRIBS}
+\title{Enveomics: TRIBS Summary}
+\usage{
+\method{summary}{enve.TRIBS}(object, ...)
+}
+\arguments{
+\item{object}{\code{\link{enve.TRIBS}} object.}
+
+\item{...}{No additional parameters are currently supported.}
+}
+\description{
+Summary of an \code{\link{enve.TRIBS}} object.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tribs.R
+\name{summary.enve.TRIBStest}
+\alias{summary.enve.TRIBStest}
+\title{Enveomics: TRIBS Summary Test}
+\usage{
+\method{summary}{enve.TRIBStest}(object, ...)
+}
+\arguments{
+\item{object}{\code{\link{enve.TRIBStest}} object.}
+
+\item{...}{No additional parameters are currently supported.}
+}
+\description{
+Summary of an \code{\link{enve.TRIBStest}} object.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/globals.mk

@@ -0,0 +1,8 @@
+# Global variables for the Enve-omics collection
+
+R=R
+prefix=/usr/local
+bindir=$(prefix)/bin
+mandir=$(prefix)/man/man1
+SCRIPTS := $(wildcard Scripts/*.*)
+

data/utils/enveomics/manifest.json

@@ -0,0 +1,9 @@
+{
+  "_": ["This is not standard JSON, to parse use EnveJSON, available at:",
+    "https://github.com/lmrodriguezr/enveomics-gui/."],
+  "_include": [
+    "Manifest/categories.json",
+    "Manifest/examples.json",
+    "Manifest/tasks.json"
+  ]
+}

metadata

@@ -1,11 +1,11 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.26.0
+  version: 0.7.26.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
 date: 2021-03-01 00:00:00.000000000 Z
@@ -250,6 +250,12 @@ files:
 - test/test_helper.rb
 - test/with_daemon_test.rb
 - test/with_option_test.rb
+- utils/FastAAI/00.Libraries/01.SCG_HMMs/Archaea_SCG.hmm
+- utils/FastAAI/00.Libraries/01.SCG_HMMs/Bacteria_SCG.hmm
+- utils/FastAAI/00.Libraries/01.SCG_HMMs/Complete_SCG_DB.hmm
+- utils/FastAAI/FastAAI/FastAAI
+- utils/FastAAI/README.md
+- utils/FastAAI/kAAI_v1.0_virus.py
 - utils/adapters.fa
 - utils/cleanup-databases.rb
 - utils/core-pan-plot.R
@@ -261,6 +267,273 @@ files:
 - utils/distance/temporal.rb
 - utils/distances.rb
 - utils/domain-ess-genes.rb
+- utils/enveomics/Docs/recplot2.md
+- utils/enveomics/Examples/aai-matrix.bash
+- utils/enveomics/Examples/ani-matrix.bash
+- utils/enveomics/Examples/essential-phylogeny.bash
+- utils/enveomics/Examples/unus-genome-phylogeny.bash
+- utils/enveomics/LICENSE.txt
+- utils/enveomics/Makefile
+- utils/enveomics/Manifest/Tasks/aasubs.json
+- utils/enveomics/Manifest/Tasks/blasttab.json
+- utils/enveomics/Manifest/Tasks/distances.json
+- utils/enveomics/Manifest/Tasks/fasta.json
+- utils/enveomics/Manifest/Tasks/fastq.json
+- utils/enveomics/Manifest/Tasks/graphics.json
+- utils/enveomics/Manifest/Tasks/mapping.json
+- utils/enveomics/Manifest/Tasks/ogs.json
+- utils/enveomics/Manifest/Tasks/other.json
+- utils/enveomics/Manifest/Tasks/remote.json
+- utils/enveomics/Manifest/Tasks/sequence-identity.json
+- utils/enveomics/Manifest/Tasks/tables.json
+- utils/enveomics/Manifest/Tasks/trees.json
+- utils/enveomics/Manifest/Tasks/variants.json
+- utils/enveomics/Manifest/categories.json
+- utils/enveomics/Manifest/examples.json
+- utils/enveomics/Manifest/tasks.json
+- utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash
+- utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl
+- utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl
+- utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl
+- utils/enveomics/Pipelines/assembly.pbs/README.md
+- utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash
+- utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash
+- utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash
+- utils/enveomics/Pipelines/assembly.pbs/RUNME.bash
+- utils/enveomics/Pipelines/assembly.pbs/kSelector.R
+- utils/enveomics/Pipelines/assembly.pbs/newbler.pbs
+- utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl
+- utils/enveomics/Pipelines/assembly.pbs/soap.pbs
+- utils/enveomics/Pipelines/assembly.pbs/stats.pbs
+- utils/enveomics/Pipelines/assembly.pbs/velvet.pbs
+- utils/enveomics/Pipelines/blast.pbs/01.pbs.bash
+- utils/enveomics/Pipelines/blast.pbs/02.pbs.bash
+- utils/enveomics/Pipelines/blast.pbs/03.pbs.bash
+- utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl
+- utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash
+- utils/enveomics/Pipelines/blast.pbs/FastA.split.pl
+- utils/enveomics/Pipelines/blast.pbs/README.md
+- utils/enveomics/Pipelines/blast.pbs/RUNME.bash
+- utils/enveomics/Pipelines/blast.pbs/TASK.check.bash
+- utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash
+- utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash
+- utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash
+- utils/enveomics/Pipelines/blast.pbs/TASK.run.bash
+- utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash
+- utils/enveomics/Pipelines/idba.pbs/README.md
+- utils/enveomics/Pipelines/idba.pbs/RUNME.bash
+- utils/enveomics/Pipelines/idba.pbs/run.pbs
+- utils/enveomics/Pipelines/trim.pbs/README.md
+- utils/enveomics/Pipelines/trim.pbs/RUNME.bash
+- utils/enveomics/Pipelines/trim.pbs/run.pbs
+- utils/enveomics/README.md
+- utils/enveomics/Scripts/AAsubs.log2ratio.rb
+- utils/enveomics/Scripts/Aln.cat.rb
+- utils/enveomics/Scripts/Aln.convert.pl
+- utils/enveomics/Scripts/AlphaDiversity.pl
+- utils/enveomics/Scripts/BedGraph.tad.rb
+- utils/enveomics/Scripts/BedGraph.window.rb
+- utils/enveomics/Scripts/BlastPairwise.AAsubs.pl
+- utils/enveomics/Scripts/BlastTab.addlen.rb
+- utils/enveomics/Scripts/BlastTab.advance.bash
+- utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl
+- utils/enveomics/Scripts/BlastTab.catsbj.pl
+- utils/enveomics/Scripts/BlastTab.cogCat.rb
+- utils/enveomics/Scripts/BlastTab.filter.pl
+- utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl
+- utils/enveomics/Scripts/BlastTab.metaxaPrep.pl
+- utils/enveomics/Scripts/BlastTab.pairedHits.rb
+- utils/enveomics/Scripts/BlastTab.recplot2.R
+- utils/enveomics/Scripts/BlastTab.seqdepth.pl
+- utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl
+- utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl
+- utils/enveomics/Scripts/BlastTab.subsample.pl
+- utils/enveomics/Scripts/BlastTab.sumPerHit.pl
+- utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl
+- utils/enveomics/Scripts/BlastTab.topHits_sorted.rb
+- utils/enveomics/Scripts/Chao1.pl
+- utils/enveomics/Scripts/CharTable.classify.rb
+- utils/enveomics/Scripts/EBIseq2tax.rb
+- utils/enveomics/Scripts/FastA.N50.pl
+- utils/enveomics/Scripts/FastA.extract.rb
+- utils/enveomics/Scripts/FastA.filter.pl
+- utils/enveomics/Scripts/FastA.filterLen.pl
+- utils/enveomics/Scripts/FastA.filterN.pl
+- utils/enveomics/Scripts/FastA.fragment.rb
+- utils/enveomics/Scripts/FastA.gc.pl
+- utils/enveomics/Scripts/FastA.interpose.pl
+- utils/enveomics/Scripts/FastA.length.pl
+- utils/enveomics/Scripts/FastA.mask.rb
+- utils/enveomics/Scripts/FastA.per_file.pl
+- utils/enveomics/Scripts/FastA.qlen.pl
+- utils/enveomics/Scripts/FastA.rename.pl
+- utils/enveomics/Scripts/FastA.revcom.pl
+- utils/enveomics/Scripts/FastA.sample.rb
+- utils/enveomics/Scripts/FastA.slider.pl
+- utils/enveomics/Scripts/FastA.split.pl
+- utils/enveomics/Scripts/FastA.split.rb
+- utils/enveomics/Scripts/FastA.subsample.pl
+- utils/enveomics/Scripts/FastA.tag.rb
+- utils/enveomics/Scripts/FastA.wrap.rb
+- utils/enveomics/Scripts/FastQ.filter.pl
+- utils/enveomics/Scripts/FastQ.interpose.pl
+- utils/enveomics/Scripts/FastQ.offset.pl
+- utils/enveomics/Scripts/FastQ.split.pl
+- utils/enveomics/Scripts/FastQ.tag.rb
+- utils/enveomics/Scripts/FastQ.test-error.rb
+- utils/enveomics/Scripts/FastQ.toFastA.awk
+- utils/enveomics/Scripts/GFF.catsbj.pl
+- utils/enveomics/Scripts/GenBank.add_fields.rb
+- utils/enveomics/Scripts/HMM.essential.rb
+- utils/enveomics/Scripts/HMM.haai.rb
+- utils/enveomics/Scripts/HMMsearch.extractIds.rb
+- utils/enveomics/Scripts/JPlace.distances.rb
+- utils/enveomics/Scripts/JPlace.to_iToL.rb
+- utils/enveomics/Scripts/M5nr.getSequences.rb
+- utils/enveomics/Scripts/MeTaxa.distribution.pl
+- utils/enveomics/Scripts/MyTaxa.fragsByTax.pl
+- utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb
+- utils/enveomics/Scripts/NCBIacc2tax.rb
+- utils/enveomics/Scripts/Newick.autoprune.R
+- utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl
+- utils/enveomics/Scripts/RecPlot2.compareIdentities.R
+- utils/enveomics/Scripts/RefSeq.download.bash
+- utils/enveomics/Scripts/SRA.download.bash
+- utils/enveomics/Scripts/TRIBS.plot-test.R
+- utils/enveomics/Scripts/TRIBS.test.R
+- utils/enveomics/Scripts/Table.barplot.R
+- utils/enveomics/Scripts/Table.df2dist.R
+- utils/enveomics/Scripts/Table.filter.pl
+- utils/enveomics/Scripts/Table.merge.pl
+- utils/enveomics/Scripts/Table.replace.rb
+- utils/enveomics/Scripts/Table.round.rb
+- utils/enveomics/Scripts/Table.split.pl
+- utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb
+- utils/enveomics/Scripts/VCF.KaKs.rb
+- utils/enveomics/Scripts/VCF.SNPs.rb
+- utils/enveomics/Scripts/aai.rb
+- utils/enveomics/Scripts/ani.rb
+- utils/enveomics/Scripts/clust.rand.rb
+- utils/enveomics/Scripts/gi2tax.rb
+- utils/enveomics/Scripts/in_silico_GA_GI.pl
+- utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz
+- utils/enveomics/Scripts/lib/data/lee_2019_essential.hmm.gz
+- utils/enveomics/Scripts/lib/enveomics.R
+- utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb
+- utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb
+- utils/enveomics/Scripts/lib/enveomics_rb/og.rb
+- utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb
+- utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb
+- utils/enveomics/Scripts/lib/enveomics_rb/stat.rb
+- utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb
+- utils/enveomics/Scripts/ogs.annotate.rb
+- utils/enveomics/Scripts/ogs.core-pan.rb
+- utils/enveomics/Scripts/ogs.extract.rb
+- utils/enveomics/Scripts/ogs.mcl.rb
+- utils/enveomics/Scripts/ogs.rb
+- utils/enveomics/Scripts/ogs.stats.rb
+- utils/enveomics/Scripts/rbm.rb
+- utils/enveomics/Tests/Makefile
+- utils/enveomics/Tests/Mgen_M2288.faa
+- utils/enveomics/Tests/Mgen_M2288.fna
+- utils/enveomics/Tests/Mgen_M2321.fna
+- utils/enveomics/Tests/Nequ_Kin4M.faa
+- utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata
+- utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt
+- utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv
+- utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv
+- utils/enveomics/Tests/a_mg.cds-go.blast.tsv
+- utils/enveomics/Tests/a_mg.reads-cds.blast.tsv
+- utils/enveomics/Tests/a_mg.reads-cds.counts.tsv
+- utils/enveomics/Tests/alkB.nwk
+- utils/enveomics/Tests/anthrax-cansnp-data.tsv
+- utils/enveomics/Tests/anthrax-cansnp-key.tsv
+- utils/enveomics/Tests/hiv1.faa
+- utils/enveomics/Tests/hiv1.fna
+- utils/enveomics/Tests/hiv2.faa
+- utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv
+- utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim
+- utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec
+- utils/enveomics/Tests/phyla_counts.tsv
+- utils/enveomics/Tests/primate_lentivirus.ogs
+- utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm
+- utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm
+- utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm
+- utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm
+- utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm
+- utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm
+- utils/enveomics/build_enveomics_r.bash
+- utils/enveomics/enveomics.R/DESCRIPTION
+- utils/enveomics/enveomics.R/NAMESPACE
+- utils/enveomics/enveomics.R/R/autoprune.R
+- utils/enveomics/enveomics.R/R/barplot.R
+- utils/enveomics/enveomics.R/R/cliopts.R
+- utils/enveomics/enveomics.R/R/df2dist.R
+- utils/enveomics/enveomics.R/R/growthcurve.R
+- utils/enveomics/enveomics.R/R/recplot.R
+- utils/enveomics/enveomics.R/R/recplot2.R
+- utils/enveomics/enveomics.R/R/tribs.R
+- utils/enveomics/enveomics.R/R/utils.R
+- utils/enveomics/enveomics.R/README.md
+- utils/enveomics/enveomics.R/data/growth.curves.rda
+- utils/enveomics/enveomics.R/data/phyla.counts.rda
+- utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd
+- utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd
+- utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd
+- utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd
+- utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd
+- utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd
+- utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd
+- utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd
+- utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd
+- utils/enveomics/enveomics.R/man/enve.__tribs.Rd
+- utils/enveomics/enveomics.R/man/enve.barplot.Rd
+- utils/enveomics/enveomics.R/man/enve.cliopts.Rd
+- utils/enveomics/enveomics.R/man/enve.col.alpha.Rd
+- utils/enveomics/enveomics.R/man/enve.col2alpha.Rd
+- utils/enveomics/enveomics.R/man/enve.df2dist.Rd
+- utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd
+- utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd
+- utils/enveomics/enveomics.R/man/enve.growthcurve.Rd
+- utils/enveomics/enveomics.R/man/enve.prune.dist.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd
+- utils/enveomics/enveomics.R/man/enve.tribs.Rd
+- utils/enveomics/enveomics.R/man/enve.tribs.test.Rd
+- utils/enveomics/enveomics.R/man/enve.truncate.Rd
+- utils/enveomics/enveomics.R/man/growth.curves.Rd
+- utils/enveomics/enveomics.R/man/phyla.counts.Rd
+- utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd
+- utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd
+- utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd
+- utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd
+- utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd
+- utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd
+- utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd
+- utils/enveomics/globals.mk
+- utils/enveomics/manifest.json
 - utils/find-medoid.R
 - utils/index_metadata.rb
 - utils/mytaxa_scan.R
@@ -281,7 +554,7 @@ homepage: http://enve-omics.ce.gatech.edu/miga
 licenses:
 - Artistic-2.0
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options:
 - lib
 - README.md
@@ -303,7 +576,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubygems_version: 3.1.4
-signing_key: 
+signing_key:
 specification_version: 4
 summary: MiGA
 test_files: []