miga-base 0.3.6.3 → 0.3.7.0

data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl

@@ -0,0 +1,38 @@
+#!/usr/bin/env perl
+#
+# @author  Luis M Rodriguez-R
+# @update  Oct-07-2015
+# @license artistic license 2.0
+#
+
+use warnings;
+use strict;
+
+$#ARGV>=0 or die "
+Usage:
+   $0 seqs.fa... > length.txt
+
+   seqs.fa	One or more FastA files.
+   length.txt	A table with the lengths of the sequences.
+
+";
+
+for my $fa (@ARGV){
+   open FA, "<", $fa or die "Cannot open file: $fa: $!\n";
+   my $def = '';
+   my $len = 0;
+   while(<FA>){
+      next if /^;/;
+      if(m/^>(\S+)\s?/){
+         print "$def\t$len\n" if $def;
+	 $def = $1;
+	 $len = 0;
+      }else{
+         s/[^A-Za-z]//g;
+	 $len+= length $_;
+      }
+   }
+   print "$def\t$len\n" if $def;
+   close FA;
+}
+

data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl

@@ -0,0 +1,55 @@
+#!/usr/bin/env perl
+#
+# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @update Oct-13-2015
+# @license artistic license 2.0
+#
+
+use warnings;
+use strict;
+use Symbol;
+
+my ($file, $base, $outN) = @ARGV;
+
+$outN ||= 12;
+($file and $base) or die "
+Usage
+   $0 in_file.fa out_base[ no_files]
+   
+   in_file.fa	Input file in FastA format.
+   out_base	Prefix for the name of the output files.  It will
+   		be appended with .<i>.fa, where <i> is a consecutive
+		number starting in 1.
+   no_files	Number of files to generate.  By default: 12.
+
+";
+
+
+my @outSym = ();
+for my $i (1 .. $outN){
+   $outSym[$i-1] = gensym;
+   open $outSym[$i-1], ">", "$base.$i.fa" or
+      die "I can not create the file: $base.$i.fa: $!\n";
+}
+
+
+my($i, $seq) = (-1, '');
+open FILE, "<", $file or die "I can not read the file: $file: $!\n";
+while(my $ln=<FILE>){
+   next if $ln=~/^;/;
+   if($ln =~ m/^>/){
+      print { $outSym[$i % $outN] } $seq if $seq;
+      $i++;
+      $seq = '';
+   }
+   $seq.=$ln;
+}
+print { $outSym[$i % $outN] } $seq if $seq;
+close FILE;
+
+for(my $j=0; $j<$outN; $j++){
+   close $outSym[$j];
+}
+
+print STDERR "Sequences: ".($i+1)."\nFiles: $outN\n";
+

data/utils/plot-taxdist.R

@@ -7,8 +7,7 @@
 # To update the AAI data files, use:
 # 
 # ```bash
-# miga tax_distributions -P /Path/To/RefSeq --ref | cut -f 1-5 \
-#   > aai-tax-index.tsv
+# miga tax_dist -P /Path/To/TypeMat --ref > aai-tax-index.tsv
 # ```
 # 
 # Next, in R:
@@ -16,12 +15,12 @@
 # ```R
 # source("utils/plot-taxdist.R")
 # p.val <- plot.miga.taxdist("aai-tax-index.tsv",
-#   exclude=c("g:Mycoplasma", "ssp:Prochlorococcus_marinus_subsp__marinus",
+#   exclude = c("g:Mycoplasma", "ssp:Prochlorococcus_marinus_subsp__marinus",
 #   "f:Rhizobiaceae", "s:Buchnera_aphidicola", "s:Prochlorococcus_marinus"))
-# write.table(p.val[[1]], file="lib/miga/_data/aai-intax.tsv",
-#   sep="\t", row.names=TRUE, col.names=NA, quote=FALSE)
-# write.table(p.val[[2]], file="lib/miga/_data/aai-novel.tsv",
-#   sep="\t", row.names=TRUE, col.names=NA, quote=FALSE)
+# write.table(p.val[[1]], file = "lib/miga/_data/aai-intax.tsv",
+#   sep = "\t", row.names = TRUE, col.names = NA, quote = FALSE)
+# write.table(p.val[[2]], file = "lib/miga/_data/aai-novel.tsv",
+#   sep = "\t", row.names = TRUE, col.names = NA, quote = FALSE)
 # ```
 #
 # And finally, back in bash:
@@ -37,55 +36,64 @@
 #argv <- commandArgs(trailingOnly=T)
 
 #= Functions
-plot.miga.taxdist <- function(file, exclude=c()){
-  pdf(paste(file, ".pdf", sep=""), 6, 7)
+plot.miga.taxdist <- function(file, exclude = c(), format = 'pdf'){
+  if(format == 'pdf'){
+    pdf(paste(file, '.pdf', sep = ''), 6, 7)
+  }else if(format == 'png'){
+    png(paste(file, '.png', sep = ''), 960, 1024, pointsize = 32)
+  }else{
+    stop('Supported formats: "pdf" and "png".')
+  }
   layout(1:3, heights=c(2,1,1.5))
-  d <- read.table(file, sep="\t", header=FALSE,
-    col.names=c("a","b","aai","rank","taxon"), as.is=TRUE)
+  d <- read.table(file, sep = "\t", header = FALSE, as.is = TRUE,
+    col.names=c('a', 'b', 'aai', 'n', 'omega', 'rank', 'taxon', 'taxonomy'))
   a <- d[!(d$taxon %in% exclude),]
-  col <- rainbow(max(a$rank)+1, s=3/4, v=3/4, alpha=1/3)
-  col2 <- rainbow(max(a$rank)+1, s=3/4, v=3/4)
+  col  <- rainbow(max(a$rank)+1, s = 3/4, v = 3/4, alpha = 1/3)
+  col2 <- rainbow(max(a$rank)+1, s = 3/4, v = 3/4)
 
   cat("o Plot pairs.\n")
   par(mar=c(0,4,1,1)+0.1)
-  plot(d$aai, d$rank+runif(nrow(d), -0.3, 0.3), cex=1/2, pch=16, las=1, bty="l",
-    col=ifelse(d$taxon %in% exclude, rgb(.8,.8,.8,1/4), col[d$rank+1]),
-    xlab="", ylab="Lowest common taxon", xaxt="n", ylim=rev(range(a$rank)))
+  plot(d$aai, d$rank+runif(nrow(d), -0.3, 0.3),
+    cex = 1/2, pch = 16, las = 1, bty = "l",
+    col = ifelse(d$taxon %in% exclude, rgb(.8,.8,.8,1/4), col[d$rank+1]),
+    xlab = "", ylab = "Lowest common taxon",
+    xaxt = "n", ylim = rev(range(a$rank)))
   for(i in c(0.1, 0.05, 0.01)){
     min_q <- tapply(a$aai, a$rank, quantile, probs=i)
     max_q <- tapply(a$aai, a$rank, quantile, probs=1-i)
-    arrows(x0=min_q, length=0, col=grey(1+log10(i)/2),
-      y0=as.numeric(names(min_q))-0.45, y1=as.numeric(names(min_q))+0.45)
-    arrows(x0=max_q, length=0, col=grey(1+log10(i)/2),
-      y0=as.numeric(names(max_q))-0.45, y1=as.numeric(names(max_q))+0.45)
+    arrows(x0 = min_q, length = 0, col = grey(1+log10(i)/2),
+      y0 = as.numeric(names(min_q))-0.45, y1 = as.numeric(names(min_q))+0.45)
+    arrows(x0 = max_q, length = 0, col = grey(1+log10(i)/2),
+      y0 = as.numeric(names(max_q))-0.45, y1 = as.numeric(names(max_q))+0.45)
   }
   
   cat("o Plot taxa.\n")
-  par(mar=c(0,4,0,1)+0.1)
-  plot(1, type="n", xlim=range(a$aai), ylim=rev(range(a$rank)),
-    xlab="", ylab="Lowest common taxon", xaxt="n", las=1, bty="l")
+  par(mar = c(0,4,0,1)+0.1)
+  plot(1, type = "n", xlim = range(a$aai), ylim = rev(range(a$rank)),
+    xlab = "", ylab = "Lowest common taxon", xaxt = "n", las = 1, bty = "l")
   for(i in unique(a$rank)){
     t.aai <- tapply(d$aai[d$rank==i], d$taxon[d$rank==i], mean)
     t.size <- tapply(d$aai[d$rank==i], d$taxon[d$rank==i], length)
-    points(t.aai, i+runif(length(t.aai), -0.15, 0.15), pch=16,
-      cex=2*log2(1+t.size)/log2(1+max(t.size)),
-      col=ifelse(names(t.aai) %in% exclude, rgb(.8,.8,.8,1/4), col[i+1]))
+    points(t.aai, i+runif(length(t.aai), -0.15, 0.15), pch = 16,
+      cex = 2*log2(1+t.size)/log2(1+max(t.size)),
+      col = ifelse(names(t.aai) %in% exclude, rgb(.8,.8,.8,1/4), col[i+1]))
   }
   
   cat("o Plot p-values.\n")
-  par(mar=c(4,4,0,1)+0.1)
-  plot(1, type="n", xlim=range(a$aai), ylim=c(0,0.5),
-    xlab="AAI (%)", ylab="P-value (--- intax; - - novel)", las=1, bty="l")
+  par(mar = c(4,4,0,1)+0.1)
+  plot(1, type = "n", xlim = range(a$aai), ylim = c(0,0.5),
+    xlab = "AAI (%)", ylab = "P-value (--- intax; - - novel)",
+    las = 1, bty = "l")
   x <- seq(30, 100, 0.1)
-  intax <- data.frame(row.names=x)
-  novel <- data.frame(row.names=x)
+  intax <- data.frame(row.names = x)
+  novel <- data.frame(row.names = x)
   for(i in sort(unique(a$rank))){
     if(i==12) next
     k <- as.character(i)
     intax[,k] <- miga.taxprob.intax(x, i, a)
     novel[,k] <- miga.taxprob.novel(x, i, a)
-    lines(x, intax[,k], col=col2[i+1], lwd=2)
-    lines(x, novel[,k], col=col2[i+1], lwd=2, lty=2)
+    lines(x, intax[,k], col = col2[i+1], lwd = 2)
+    lines(x, novel[,k], col = col2[i+1], lwd = 2, lty = 2)
   }
   dev.off()
   return(list(intax, novel))
@@ -106,3 +114,4 @@ miga.taxprob.intax <- function(max.aai, rank, data){
   }
   return(o)
 }
+

data/utils/requirements.txt

@@ -17,3 +17,4 @@ SolexaQA++	SolexaQA++	http://solexaqa.sourceforge.net					Required version: v3.1
 DIAMOND (opt)	diamond		http://ab.inf.uni-tuebingen.de/software/diamond			Required version: v0.9.20+
 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
 Krona (opt)	ktImportText	https://github.com/marbl/Krona/wiki
+FastANI (opt)	fastANI		https://github.com/ParBLiSS/FastANI				Required version: 1.1+

metadata

@@ -1,95 +1,95 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.3.6.3
+  version: 0.3.7.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-12-10 00:00:00.000000000 Z
+date: 2019-02-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.2'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.2.4
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.2'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.2.4
 - !ruby/object:Gem::Dependency
   name: json
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">"
+    - - '>'
       - !ruby/object:Gem::Version
         version: '1.8'
-    - - "<"
+    - - <
       - !ruby/object:Gem::Version
         version: '3'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">"
+    - - '>'
       - !ruby/object:Gem::Version
         version: '1.8'
-    - - "<"
+    - - <
       - !ruby/object:Gem::Version
         version: '3'
 - !ruby/object:Gem::Dependency
   name: sqlite3
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.3'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.3'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '11'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '11'
 - !ruby/object:Gem::Dependency
   name: test-unit
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '3'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '3'
 description: Microbial Genomes Atlas
@@ -100,62 +100,43 @@ extensions: []
 extra_rdoc_files:
 - README.md
 files:
-- Gemfile
-- LICENSE
-- README.md
-- Rakefile
-- actions/about.rb
-- actions/add.rb
-- actions/add_result.rb
-- actions/daemon.rb
-- actions/date.rb
-- actions/doctor.rb
-- actions/files.rb
-- actions/find.rb
-- actions/get.rb
-- actions/init.rb
-- actions/ln.rb
-- actions/ls.rb
-- actions/ncbi_get.rb
-- actions/new.rb
-- actions/plugins.rb
-- actions/rm.rb
-- actions/run.rb
-- actions/stats.rb
-- actions/summary.rb
-- actions/tax_dist.rb
-- actions/tax_index.rb
-- actions/tax_set.rb
-- actions/tax_test.rb
-- bin/miga
-- lib/miga.rb
-- lib/miga/_data/aai-intax.tsv.gz
-- lib/miga/_data/aai-novel.tsv.gz
-- lib/miga/common.rb
 - lib/miga/common/base.rb
 - lib/miga/common/format.rb
 - lib/miga/common/path.rb
-- lib/miga/daemon.rb
+- lib/miga/common.rb
 - lib/miga/daemon/base.rb
-- lib/miga/dataset.rb
+- lib/miga/daemon.rb
 - lib/miga/dataset/base.rb
 - lib/miga/dataset/result.rb
+- lib/miga/dataset.rb
 - lib/miga/metadata.rb
-- lib/miga/project.rb
 - lib/miga/project/base.rb
 - lib/miga/project/dataset.rb
 - lib/miga/project/plugins.rb
 - lib/miga/project/result.rb
-- lib/miga/remote_dataset.rb
+- lib/miga/project.rb
 - lib/miga/remote_dataset/base.rb
 - lib/miga/remote_dataset/download.rb
-- lib/miga/result.rb
+- lib/miga/remote_dataset.rb
 - lib/miga/result/base.rb
 - lib/miga/result/dates.rb
+- lib/miga/result.rb
 - lib/miga/tax_dist.rb
 - lib/miga/tax_index.rb
 - lib/miga/taxonomy.rb
 - lib/miga/version.rb
+- lib/miga.rb
+- test/common_test.rb
+- test/daemon_test.rb
+- test/dataset_test.rb
+- test/metadata_test.rb
+- test/project_test.rb
+- test/remote_dataset_test.rb
+- test/tax_index_test.rb
+- test/taxonomy_test.rb
+- test/test_helper.rb
+- lib/miga/_data/aai-intax.tsv.gz
+- lib/miga/_data/aai-novel.tsv.gz
 - scripts/aai_distances.bash
 - scripts/ani_distances.bash
 - scripts/assembly.bash
@@ -177,15 +158,6 @@ files:
 - scripts/taxonomy.bash
 - scripts/trimmed_fasta.bash
 - scripts/trimmed_reads.bash
-- test/common_test.rb
-- test/daemon_test.rb
-- test/dataset_test.rb
-- test/metadata_test.rb
-- test/project_test.rb
-- test/remote_dataset_test.rb
-- test/tax_index_test.rb
-- test/taxonomy_test.rb
-- test/test_helper.rb
 - utils/adapters.fa
 - utils/arch-ess-genes.rb
 - utils/cleanup-databases.rb
@@ -197,13 +169,83 @@ files:
 - utils/distance/runner.rb
 - utils/distance/temporal.rb
 - utils/distances.rb
+- utils/enveomics/build_enveomics_r.bash
 - utils/enveomics/Docs/recplot2.md
+- utils/enveomics/enveomics.R/data/growth.curves.rda
+- utils/enveomics/enveomics.R/data/phyla.counts.rda
+- utils/enveomics/enveomics.R/DESCRIPTION
+- 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.group.Rd
+- utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd
+- utils/enveomics/enveomics.R/man/enve.df2dist.Rd
+- utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.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.__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.ANIr.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.__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.findPeaks.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.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.tribs.Rd
+- utils/enveomics/enveomics.R/man/enve.tribs.test.Rd
+- utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd
+- utils/enveomics/enveomics.R/man/enveomics.R-package.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.recplot2.Rd
+- utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd
+- utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.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/enveomics.R/man/z$-methods.Rd
+- 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/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/globals.mk
 - utils/enveomics/LICENSE.txt
 - utils/enveomics/Makefile
+- utils/enveomics/Manifest/categories.json
+- utils/enveomics/Manifest/examples.json
 - utils/enveomics/Manifest/Tasks/aasubs.json
 - utils/enveomics/Manifest/Tasks/blasttab.json
 - utils/enveomics/Manifest/Tasks/distances.json
@@ -218,21 +260,20 @@ files:
 - 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/manifest.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/FastA.N50.pl
+- 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/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
@@ -244,23 +285,25 @@ files:
 - 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/sentinel.pbs.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/idba.pbs/RUNME.bash
 - utils/enveomics/Pipelines/trim.pbs/README.md
-- utils/enveomics/Pipelines/trim.pbs/RUNME.bash
 - utils/enveomics/Pipelines/trim.pbs/run.pbs
+- utils/enveomics/Pipelines/trim.pbs/RUNME.bash
 - utils/enveomics/README.md
+- utils/enveomics/Scripts/aai.rb
 - 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/ani.rb
 - utils/enveomics/Scripts/BedGraph.tad.rb
 - utils/enveomics/Scripts/BedGraph.window.rb
 - utils/enveomics/Scripts/BlastPairwise.AAsubs.pl
@@ -275,16 +318,16 @@ files:
 - 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.seqdepth_ZIP.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/clust.rand.rb
 - utils/enveomics/Scripts/EBIseq2tax.rb
-- utils/enveomics/Scripts/FastA.N50.pl
 - utils/enveomics/Scripts/FastA.filter.pl
 - utils/enveomics/Scripts/FastA.filterLen.pl
 - utils/enveomics/Scripts/FastA.filterN.pl
@@ -292,6 +335,7 @@ files:
 - utils/enveomics/Scripts/FastA.gc.pl
 - utils/enveomics/Scripts/FastA.interpose.pl
 - utils/enveomics/Scripts/FastA.length.pl
+- utils/enveomics/Scripts/FastA.N50.pl
 - utils/enveomics/Scripts/FastA.per_file.pl
 - utils/enveomics/Scripts/FastA.qlen.pl
 - utils/enveomics/Scripts/FastA.rename.pl
@@ -310,22 +354,37 @@ files:
 - utils/enveomics/Scripts/FastQ.test-error.rb
 - utils/enveomics/Scripts/FastQ.toFastA.awk
 - utils/enveomics/Scripts/GenBank.add_fields.rb
+- utils/enveomics/Scripts/gi2tax.rb
 - utils/enveomics/Scripts/HMM.essential.rb
 - utils/enveomics/Scripts/HMMsearch.extractIds.rb
+- utils/enveomics/Scripts/in_silico_GA_GI.pl
 - utils/enveomics/Scripts/JPlace.distances.rb
 - utils/enveomics/Scripts/JPlace.to_iToL.rb
+- utils/enveomics/Scripts/lib/data/essential.hmm.gz
+- 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/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/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/RAxML-EPA.to_iToL.pl
+- utils/enveomics/Scripts/rbm.rb
 - 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
@@ -334,38 +393,10 @@ files:
 - utils/enveomics/Scripts/Table.round.rb
 - utils/enveomics/Scripts/Table.split.pl
 - utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb
+- utils/enveomics/Scripts/TRIBS.plot-test.R
+- utils/enveomics/Scripts/TRIBS.test.R
 - 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/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
@@ -378,6 +409,11 @@ files:
 - 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/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/phyla_counts.tsv
 - utils/enveomics/Tests/primate_lentivirus.ogs
 - utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm
@@ -386,75 +422,10 @@ files:
 - 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/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.tribs.Rd
-- utils/enveomics/enveomics.R/man/enve.tribs.test.Rd
-- utils/enveomics/enveomics.R/man/enveomics.R-package.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/enveomics.R/man/z$-methods.Rd
-- utils/enveomics/globals.mk
-- utils/enveomics/manifest.json
+- 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/find-medoid.R
 - utils/index_metadata.rb
 - utils/mytaxa_scan.R
@@ -471,6 +442,34 @@ files:
 - utils/subclades-nj.R
 - utils/subclades.R
 - utils/subclades.rb
+- bin/miga
+- actions/about.rb
+- actions/add.rb
+- actions/add_result.rb
+- actions/daemon.rb
+- actions/date.rb
+- actions/doctor.rb
+- actions/files.rb
+- actions/find.rb
+- actions/get.rb
+- actions/init.rb
+- actions/ln.rb
+- actions/ls.rb
+- actions/ncbi_get.rb
+- actions/new.rb
+- actions/plugins.rb
+- actions/rm.rb
+- actions/run.rb
+- actions/stats.rb
+- actions/summary.rb
+- actions/tax_dist.rb
+- actions/tax_index.rb
+- actions/tax_set.rb
+- actions/tax_test.rb
+- Gemfile
+- Rakefile
+- README.md
+- LICENSE
 homepage: http://enve-omics.ce.gatech.edu/miga
 licenses:
 - Artistic-2.0
@@ -479,26 +478,27 @@ post_install_message:
 rdoc_options:
 - lib
 - README.md
-- "--main"
+- --main
 - README.md
-- "--title"
+- --title
 - MiGA
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - '>='
     - !ruby/object:Gem::Version
       version: '1.9'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.7.7
+rubygems_version: 2.0.14.1
 signing_key: 
 specification_version: 4
 summary: MiGA
 test_files: []
+has_rdoc: