miga-base 0.3.6.3 → 0.3.7.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (21) hide show
  1. checksums.yaml +5 -5
  2. data/actions/init.rb +1 -1
  3. data/actions/tax_dist.rb +32 -26
  4. data/bin/miga +38 -38
  5. data/lib/miga/daemon.rb +11 -5
  6. data/lib/miga/version.rb +1 -1
  7. data/scripts/ogs.bash +4 -2
  8. data/utils/cleanup-databases.rb +6 -5
  9. data/utils/distance/commands.rb +1 -0
  10. data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +56 -0
  11. data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +60 -0
  12. data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +38 -0
  13. data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +55 -0
  14. data/utils/plot-taxdist.R +42 -33
  15. data/utils/requirements.txt +1 -0
  16. metadata +179 -179
  17. data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +0 -1
  18. data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +0 -1
  19. data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +0 -1
  20. data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +0 -1
  21. data/utils/enveomics/Scripts/lib/enveomics.R +0 -1
data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl ADDED
@@ -0,0 +1,38 @@
1
+ #!/usr/bin/env perl
2
+ #
3
+ # @author Luis M Rodriguez-R
4
+ # @update Oct-07-2015
5
+ # @license artistic license 2.0
6
+ #
7
+
8
+ use warnings;
9
+ use strict;
10
+
11
+ $#ARGV>=0 or die "
12
+ Usage:
13
+ $0 seqs.fa... > length.txt
14
+
15
+ seqs.fa One or more FastA files.
16
+ length.txt A table with the lengths of the sequences.
17
+
18
+ ";
19
+
20
+ for my $fa (@ARGV){
21
+ open FA, "<", $fa or die "Cannot open file: $fa: $!\n";
22
+ my $def = '';
23
+ my $len = 0;
24
+ while(<FA>){
25
+ next if /^;/;
26
+ if(m/^>(\S+)\s?/){
27
+ print "$def\t$len\n" if $def;
28
+ $def = $1;
29
+ $len = 0;
30
+ }else{
31
+ s/[^A-Za-z]//g;
32
+ $len+= length $_;
33
+ }
34
+ }
35
+ print "$def\t$len\n" if $def;
36
+ close FA;
37
+ }
38
+
data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl ADDED
@@ -0,0 +1,55 @@
1
+ #!/usr/bin/env perl
2
+ #
3
+ # @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
4
+ # @update Oct-13-2015
5
+ # @license artistic license 2.0
6
+ #
7
+
8
+ use warnings;
9
+ use strict;
10
+ use Symbol;
11
+
12
+ my ($file, $base, $outN) = @ARGV;
13
+
14
+ $outN ||= 12;
15
+ ($file and $base) or die "
16
+ Usage
17
+ $0 in_file.fa out_base[ no_files]
18
+
19
+ in_file.fa Input file in FastA format.
20
+ out_base Prefix for the name of the output files. It will
21
+ be appended with .<i>.fa, where <i> is a consecutive
22
+ number starting in 1.
23
+ no_files Number of files to generate. By default: 12.
24
+
25
+ ";
26
+
27
+
28
+ my @outSym = ();
29
+ for my $i (1 .. $outN){
30
+ $outSym[$i-1] = gensym;
31
+ open $outSym[$i-1], ">", "$base.$i.fa" or
32
+ die "I can not create the file: $base.$i.fa: $!\n";
33
+ }
34
+
35
+
36
+ my($i, $seq) = (-1, '');
37
+ open FILE, "<", $file or die "I can not read the file: $file: $!\n";
38
+ while(my $ln=<FILE>){
39
+ next if $ln=~/^;/;
40
+ if($ln =~ m/^>/){
41
+ print { $outSym[$i % $outN] } $seq if $seq;
42
+ $i++;
43
+ $seq = '';
44
+ }
45
+ $seq.=$ln;
46
+ }
47
+ print { $outSym[$i % $outN] } $seq if $seq;
48
+ close FILE;
49
+
50
+ for(my $j=0; $j<$outN; $j++){
51
+ close $outSym[$j];
52
+ }
53
+
54
+ print STDERR "Sequences: ".($i+1)."\nFiles: $outN\n";
55
+
data/utils/plot-taxdist.R CHANGED
@@ -7,8 +7,7 @@
7
7
  # To update the AAI data files, use:
8
8
  #
9
9
  # ```bash
10
- # miga tax_distributions -P /Path/To/RefSeq --ref | cut -f 1-5 \
11
- # > aai-tax-index.tsv
10
+ # miga tax_dist -P /Path/To/TypeMat --ref > aai-tax-index.tsv
12
11
  # ```
13
12
  #
14
13
  # Next, in R:
@@ -16,12 +15,12 @@
16
15
  # ```R
17
16
  # source("utils/plot-taxdist.R")
18
17
  # p.val <- plot.miga.taxdist("aai-tax-index.tsv",
19
- # exclude=c("g:Mycoplasma", "ssp:Prochlorococcus_marinus_subsp__marinus",
18
+ # exclude = c("g:Mycoplasma", "ssp:Prochlorococcus_marinus_subsp__marinus",
20
19
  # "f:Rhizobiaceae", "s:Buchnera_aphidicola", "s:Prochlorococcus_marinus"))
21
- # write.table(p.val[[1]], file="lib/miga/_data/aai-intax.tsv",
22
- # sep="\t", row.names=TRUE, col.names=NA, quote=FALSE)
23
- # write.table(p.val[[2]], file="lib/miga/_data/aai-novel.tsv",
24
- # sep="\t", row.names=TRUE, col.names=NA, quote=FALSE)
20
+ # write.table(p.val[[1]], file = "lib/miga/_data/aai-intax.tsv",
21
+ # sep = "\t", row.names = TRUE, col.names = NA, quote = FALSE)
22
+ # write.table(p.val[[2]], file = "lib/miga/_data/aai-novel.tsv",
23
+ # sep = "\t", row.names = TRUE, col.names = NA, quote = FALSE)
25
24
  # ```
26
25
  #
27
26
  # And finally, back in bash:
@@ -37,55 +36,64 @@
37
36
  #argv <- commandArgs(trailingOnly=T)
38
37
 
39
38
  #= Functions
40
- plot.miga.taxdist <- function(file, exclude=c()){
41
- pdf(paste(file, ".pdf", sep=""), 6, 7)
39
+ plot.miga.taxdist <- function(file, exclude = c(), format = 'pdf'){
40
+ if(format == 'pdf'){
41
+ pdf(paste(file, '.pdf', sep = ''), 6, 7)
42
+ }else if(format == 'png'){
43
+ png(paste(file, '.png', sep = ''), 960, 1024, pointsize = 32)
44
+ }else{
45
+ stop('Supported formats: "pdf" and "png".')
46
+ }
42
47
  layout(1:3, heights=c(2,1,1.5))
43
- d <- read.table(file, sep="\t", header=FALSE,
44
- col.names=c("a","b","aai","rank","taxon"), as.is=TRUE)
48
+ d <- read.table(file, sep = "\t", header = FALSE, as.is = TRUE,
49
+ col.names=c('a', 'b', 'aai', 'n', 'omega', 'rank', 'taxon', 'taxonomy'))
45
50
  a <- d[!(d$taxon %in% exclude),]
46
- col <- rainbow(max(a$rank)+1, s=3/4, v=3/4, alpha=1/3)
47
- col2 <- rainbow(max(a$rank)+1, s=3/4, v=3/4)
51
+ col <- rainbow(max(a$rank)+1, s = 3/4, v = 3/4, alpha = 1/3)
52
+ col2 <- rainbow(max(a$rank)+1, s = 3/4, v = 3/4)
48
53
 
49
54
  cat("o Plot pairs.\n")
50
55
  par(mar=c(0,4,1,1)+0.1)
51
- plot(d$aai, d$rank+runif(nrow(d), -0.3, 0.3), cex=1/2, pch=16, las=1, bty="l",
52
- col=ifelse(d$taxon %in% exclude, rgb(.8,.8,.8,1/4), col[d$rank+1]),
53
- xlab="", ylab="Lowest common taxon", xaxt="n", ylim=rev(range(a$rank)))
56
+ plot(d$aai, d$rank+runif(nrow(d), -0.3, 0.3),
57
+ cex = 1/2, pch = 16, las = 1, bty = "l",
58
+ col = ifelse(d$taxon %in% exclude, rgb(.8,.8,.8,1/4), col[d$rank+1]),
59
+ xlab = "", ylab = "Lowest common taxon",
60
+ xaxt = "n", ylim = rev(range(a$rank)))
54
61
  for(i in c(0.1, 0.05, 0.01)){
55
62
  min_q <- tapply(a$aai, a$rank, quantile, probs=i)
56
63
  max_q <- tapply(a$aai, a$rank, quantile, probs=1-i)
57
- arrows(x0=min_q, length=0, col=grey(1+log10(i)/2),
58
- y0=as.numeric(names(min_q))-0.45, y1=as.numeric(names(min_q))+0.45)
59
- arrows(x0=max_q, length=0, col=grey(1+log10(i)/2),
60
- y0=as.numeric(names(max_q))-0.45, y1=as.numeric(names(max_q))+0.45)
64
+ arrows(x0 = min_q, length = 0, col = grey(1+log10(i)/2),
65
+ y0 = as.numeric(names(min_q))-0.45, y1 = as.numeric(names(min_q))+0.45)
66
+ arrows(x0 = max_q, length = 0, col = grey(1+log10(i)/2),
67
+ y0 = as.numeric(names(max_q))-0.45, y1 = as.numeric(names(max_q))+0.45)
61
68
  }
62
69
 
63
70
  cat("o Plot taxa.\n")
64
- par(mar=c(0,4,0,1)+0.1)
65
- plot(1, type="n", xlim=range(a$aai), ylim=rev(range(a$rank)),
66
- xlab="", ylab="Lowest common taxon", xaxt="n", las=1, bty="l")
71
+ par(mar = c(0,4,0,1)+0.1)
72
+ plot(1, type = "n", xlim = range(a$aai), ylim = rev(range(a$rank)),
73
+ xlab = "", ylab = "Lowest common taxon", xaxt = "n", las = 1, bty = "l")
67
74
  for(i in unique(a$rank)){
68
75
  t.aai <- tapply(d$aai[d$rank==i], d$taxon[d$rank==i], mean)
69
76
  t.size <- tapply(d$aai[d$rank==i], d$taxon[d$rank==i], length)
70
- points(t.aai, i+runif(length(t.aai), -0.15, 0.15), pch=16,
71
- cex=2*log2(1+t.size)/log2(1+max(t.size)),
72
- col=ifelse(names(t.aai) %in% exclude, rgb(.8,.8,.8,1/4), col[i+1]))
77
+ points(t.aai, i+runif(length(t.aai), -0.15, 0.15), pch = 16,
78
+ cex = 2*log2(1+t.size)/log2(1+max(t.size)),
79
+ col = ifelse(names(t.aai) %in% exclude, rgb(.8,.8,.8,1/4), col[i+1]))
73
80
  }
74
81
 
75
82
  cat("o Plot p-values.\n")
76
- par(mar=c(4,4,0,1)+0.1)
77
- plot(1, type="n", xlim=range(a$aai), ylim=c(0,0.5),
78
- xlab="AAI (%)", ylab="P-value (--- intax; - - novel)", las=1, bty="l")
83
+ par(mar = c(4,4,0,1)+0.1)
84
+ plot(1, type = "n", xlim = range(a$aai), ylim = c(0,0.5),
85
+ xlab = "AAI (%)", ylab = "P-value (--- intax; - - novel)",
86
+ las = 1, bty = "l")
79
87
  x <- seq(30, 100, 0.1)
80
- intax <- data.frame(row.names=x)
81
- novel <- data.frame(row.names=x)
88
+ intax <- data.frame(row.names = x)
89
+ novel <- data.frame(row.names = x)
82
90
  for(i in sort(unique(a$rank))){
83
91
  if(i==12) next
84
92
  k <- as.character(i)
85
93
  intax[,k] <- miga.taxprob.intax(x, i, a)
86
94
  novel[,k] <- miga.taxprob.novel(x, i, a)
87
- lines(x, intax[,k], col=col2[i+1], lwd=2)
88
- lines(x, novel[,k], col=col2[i+1], lwd=2, lty=2)
95
+ lines(x, intax[,k], col = col2[i+1], lwd = 2)
96
+ lines(x, novel[,k], col = col2[i+1], lwd = 2, lty = 2)
89
97
  }
90
98
  dev.off()
91
99
  return(list(intax, novel))
@@ -106,3 +114,4 @@ miga.taxprob.intax <- function(max.aai, rank, data){
106
114
  }
107
115
  return(o)
108
116
  }
117
+
data/utils/requirements.txt CHANGED
@@ -17,3 +17,4 @@ SolexaQA++ SolexaQA++ http://solexaqa.sourceforge.net Required version: v3.1
17
17
  DIAMOND (opt) diamond http://ab.inf.uni-tuebingen.de/software/diamond Required version: v0.9.20+
18
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
19
  Krona (opt) ktImportText https://github.com/marbl/Krona/wiki
20
+ FastANI (opt) fastANI https://github.com/ParBLiSS/FastANI Required version: 1.1+
metadata CHANGED
@@ -1,95 +1,95 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: miga-base
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.3.6.3
4
+ version: 0.3.7.0
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: 2018-12-10 00:00:00.000000000 Z
11
+ date: 2019-02-05 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: daemons
15
15
  requirement: !ruby/object:Gem::Requirement
16
16
  requirements:
17
- - - "~>"
17
+ - - ~>
18
18
  - !ruby/object:Gem::Version
19
19
  version: '1.2'
20
- - - ">="
20
+ - - '>='
21
21
  - !ruby/object:Gem::Version
22
22
  version: 1.2.4
23
23
  type: :runtime
24
24
  prerelease: false
25
25
  version_requirements: !ruby/object:Gem::Requirement
26
26
  requirements:
27
- - - "~>"
27
+ - - ~>
28
28
  - !ruby/object:Gem::Version
29
29
  version: '1.2'
30
- - - ">="
30
+ - - '>='
31
31
  - !ruby/object:Gem::Version
32
32
  version: 1.2.4
33
33
  - !ruby/object:Gem::Dependency
34
34
  name: json
35
35
  requirement: !ruby/object:Gem::Requirement
36
36
  requirements:
37
- - - ">"
37
+ - - '>'
38
38
  - !ruby/object:Gem::Version
39
39
  version: '1.8'
40
- - - "<"
40
+ - - <
41
41
  - !ruby/object:Gem::Version
42
42
  version: '3'
43
43
  type: :runtime
44
44
  prerelease: false
45
45
  version_requirements: !ruby/object:Gem::Requirement
46
46
  requirements:
47
- - - ">"
47
+ - - '>'
48
48
  - !ruby/object:Gem::Version
49
49
  version: '1.8'
50
- - - "<"
50
+ - - <
51
51
  - !ruby/object:Gem::Version
52
52
  version: '3'
53
53
  - !ruby/object:Gem::Dependency
54
54
  name: sqlite3
55
55
  requirement: !ruby/object:Gem::Requirement
56
56
  requirements:
57
- - - "~>"
57
+ - - ~>
58
58
  - !ruby/object:Gem::Version
59
59
  version: '1.3'
60
60
  type: :runtime
61
61
  prerelease: false
62
62
  version_requirements: !ruby/object:Gem::Requirement
63
63
  requirements:
64
- - - "~>"
64
+ - - ~>
65
65
  - !ruby/object:Gem::Version
66
66
  version: '1.3'
67
67
  - !ruby/object:Gem::Dependency
68
68
  name: rake
69
69
  requirement: !ruby/object:Gem::Requirement
70
70
  requirements:
71
- - - "~>"
71
+ - - ~>
72
72
  - !ruby/object:Gem::Version
73
73
  version: '11'
74
74
  type: :development
75
75
  prerelease: false
76
76
  version_requirements: !ruby/object:Gem::Requirement
77
77
  requirements:
78
- - - "~>"
78
+ - - ~>
79
79
  - !ruby/object:Gem::Version
80
80
  version: '11'
81
81
  - !ruby/object:Gem::Dependency
82
82
  name: test-unit
83
83
  requirement: !ruby/object:Gem::Requirement
84
84
  requirements:
85
- - - "~>"
85
+ - - ~>
86
86
  - !ruby/object:Gem::Version
87
87
  version: '3'
88
88
  type: :development
89
89
  prerelease: false
90
90
  version_requirements: !ruby/object:Gem::Requirement
91
91
  requirements:
92
- - - "~>"
92
+ - - ~>
93
93
  - !ruby/object:Gem::Version
94
94
  version: '3'
95
95
  description: Microbial Genomes Atlas
@@ -100,62 +100,43 @@ extensions: []
100
100
  extra_rdoc_files:
101
101
  - README.md
102
102
  files:
103
- - Gemfile
104
- - LICENSE
105
- - README.md
106
- - Rakefile
107
- - actions/about.rb
108
- - actions/add.rb
109
- - actions/add_result.rb
110
- - actions/daemon.rb
111
- - actions/date.rb
112
- - actions/doctor.rb
113
- - actions/files.rb
114
- - actions/find.rb
115
- - actions/get.rb
116
- - actions/init.rb
117
- - actions/ln.rb
118
- - actions/ls.rb
119
- - actions/ncbi_get.rb
120
- - actions/new.rb
121
- - actions/plugins.rb
122
- - actions/rm.rb
123
- - actions/run.rb
124
- - actions/stats.rb
125
- - actions/summary.rb
126
- - actions/tax_dist.rb
127
- - actions/tax_index.rb
128
- - actions/tax_set.rb
129
- - actions/tax_test.rb
130
- - bin/miga
131
- - lib/miga.rb
132
- - lib/miga/_data/aai-intax.tsv.gz
133
- - lib/miga/_data/aai-novel.tsv.gz
134
- - lib/miga/common.rb
135
103
  - lib/miga/common/base.rb
136
104
  - lib/miga/common/format.rb
137
105
  - lib/miga/common/path.rb
138
- - lib/miga/daemon.rb
106
+ - lib/miga/common.rb
139
107
  - lib/miga/daemon/base.rb
140
- - lib/miga/dataset.rb
108
+ - lib/miga/daemon.rb
141
109
  - lib/miga/dataset/base.rb
142
110
  - lib/miga/dataset/result.rb
111
+ - lib/miga/dataset.rb
143
112
  - lib/miga/metadata.rb
144
- - lib/miga/project.rb
145
113
  - lib/miga/project/base.rb
146
114
  - lib/miga/project/dataset.rb
147
115
  - lib/miga/project/plugins.rb
148
116
  - lib/miga/project/result.rb
149
- - lib/miga/remote_dataset.rb
117
+ - lib/miga/project.rb
150
118
  - lib/miga/remote_dataset/base.rb
151
119
  - lib/miga/remote_dataset/download.rb
152
- - lib/miga/result.rb
120
+ - lib/miga/remote_dataset.rb
153
121
  - lib/miga/result/base.rb
154
122
  - lib/miga/result/dates.rb
123
+ - lib/miga/result.rb
155
124
  - lib/miga/tax_dist.rb
156
125
  - lib/miga/tax_index.rb
157
126
  - lib/miga/taxonomy.rb
158
127
  - lib/miga/version.rb
128
+ - lib/miga.rb
129
+ - test/common_test.rb
130
+ - test/daemon_test.rb
131
+ - test/dataset_test.rb
132
+ - test/metadata_test.rb
133
+ - test/project_test.rb
134
+ - test/remote_dataset_test.rb
135
+ - test/tax_index_test.rb
136
+ - test/taxonomy_test.rb
137
+ - test/test_helper.rb
138
+ - lib/miga/_data/aai-intax.tsv.gz
139
+ - lib/miga/_data/aai-novel.tsv.gz
159
140
  - scripts/aai_distances.bash
160
141
  - scripts/ani_distances.bash
161
142
  - scripts/assembly.bash
@@ -177,15 +158,6 @@ files:
177
158
  - scripts/taxonomy.bash
178
159
  - scripts/trimmed_fasta.bash
179
160
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- - utils/enveomics/enveomics.R/man/enve.col2alpha.Rd
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- - utils/enveomics/enveomics.R/man/enve.df2dist.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.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.ANIr.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.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.__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.compareIdentities.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.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.findPeaks.__em_e.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.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.seqdepth.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/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/summary.enve.GrowthCurve.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/globals.mk
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- - utils/enveomics/manifest.json
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+ - utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata
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+ - utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt
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+ - utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv
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+ - utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv
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  - utils/find-medoid.R
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  - utils/index_metadata.rb
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  - utils/mytaxa_scan.R
@@ -471,6 +442,34 @@ files:
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  - utils/subclades-nj.R
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  - utils/subclades.R
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  - utils/subclades.rb
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+ - bin/miga
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+ - actions/about.rb
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+ - actions/add.rb
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+ - actions/add_result.rb
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+ - actions/daemon.rb
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+ - actions/date.rb
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+ - actions/doctor.rb
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+ - actions/files.rb
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+ - actions/find.rb
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+ - actions/get.rb
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+ - actions/init.rb
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+ - actions/ln.rb
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+ - actions/ls.rb
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+ - actions/ncbi_get.rb
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+ - actions/new.rb
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+ - actions/plugins.rb
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+ - actions/rm.rb
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+ - actions/run.rb
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+ - actions/stats.rb
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+ - actions/summary.rb
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+ - actions/tax_dist.rb
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+ - actions/tax_index.rb
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+ - actions/tax_set.rb
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+ - actions/tax_test.rb
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+ - Gemfile
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+ - Rakefile
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+ - README.md
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+ - LICENSE
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  homepage: http://enve-omics.ce.gatech.edu/miga
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  licenses:
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  - Artistic-2.0
@@ -479,26 +478,27 @@ post_install_message:
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  rdoc_options:
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  - lib
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  - README.md
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- - "--main"
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+ - --main
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  - README.md
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- - "--title"
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+ - --title
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  - MiGA
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  require_paths:
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  - lib
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  required_ruby_version: !ruby/object:Gem::Requirement
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  requirements:
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- - - ">="
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+ - - '>='
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  - !ruby/object:Gem::Version
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  version: '1.9'
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  required_rubygems_version: !ruby/object:Gem::Requirement
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  requirements:
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- - - ">="
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+ - - '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  requirements: []
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  rubyforge_project:
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- rubygems_version: 2.7.7
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+ rubygems_version: 2.0.14.1
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  signing_key:
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  specification_version: 4
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  summary: MiGA
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  test_files: []
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+ has_rdoc: