miga-base 0.3.0.6 → 0.3.0.7

Sign up to get free protection for your applications and to get access to all the features.
Files changed (13) hide show
  1. checksums.yaml +4 -4
  2. data/lib/miga/project.rb +4 -3
  3. data/lib/miga/version.rb +2 -2
  4. data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +56 -0
  5. data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +60 -0
  6. data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +38 -0
  7. data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +55 -0
  8. metadata +160 -161
  9. data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +0 -1
  10. data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +0 -1
  11. data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +0 -1
  12. data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +0 -1
  13. data/utils/enveomics/Scripts/lib/enveomics.R +0 -1
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
1
1
  ---
2
2
  SHA1:
3
- metadata.gz: e86b0a3fd7e0ef5b3d2ac6c82e0d6e44b595dfa7
4
- data.tar.gz: d0c718124aaee78e75f52db4679a29958e7df193
3
+ metadata.gz: 4132f066f463f3967517e7e278b765087a22bb89
4
+ data.tar.gz: 78fcfd7accea31d041991f26944d701cc6b31fef
5
5
  SHA512:
6
- metadata.gz: a1ff8aee53f8d3c2c10124cb6de6d363b6c8d15e842b1454b025ffc7a90580c4b06db573b0fc0290b802d4d0ba1344d952f41aa266141303f4dbb4502d20368e
7
- data.tar.gz: d84243fe1316b9d475fa43fe7559a712a5533b012d69268b1e92e4e47e6f75ed0c603dd07b3e2350fa9040c8188c1524250a92677a2bf534b2425602d9d6b6ba
6
+ metadata.gz: b7446a3f81368c04f4e8cdec66abe28eb7eeb0c9f00d046dee1b4882007c8f4f2325052f466069407a17a0d65b1e6b1cc274fa10f2a3c5dabf7684a3f34e6852
7
+ data.tar.gz: 1c47807eb8e3a97b2cd464495a0fd022f6c8f1aa86bfd8ed6dc018d376f63994dded3616467df4528b9286a057f0ac4e219313f76fa03542ad143925403c877d
data/lib/miga/project.rb CHANGED
@@ -273,9 +273,10 @@ class MiGA::Project < MiGA::MiGA
273
273
  def add_result(name, save=true)
274
274
  return nil if @@RESULT_DIRS[name].nil?
275
275
  base = "#{path}/data/#{@@RESULT_DIRS[name]}/miga-project"
276
- return MiGA::Result.load("#{base}.json") unless save
277
- return nil unless result_files_exist?(base, ".done")
278
- r = send("add_result_#{name}", base)
276
+ r_pre = MiGA::Result.load("#{base}.json")
277
+ return r_pre if (r_pre.nil? and not save) or not r_pre.nil?
278
+ r = result_files_exist?(base, ".done") ?
279
+ send("add_result_#{name}", base) : nil
279
280
  r.save unless r.nil?
280
281
  r
281
282
  end
data/lib/miga/version.rb CHANGED
@@ -10,7 +10,7 @@ module MiGA
10
10
  # - Float representing the major.minor version.
11
11
  # - Integer representing gem releases of the current version.
12
12
  # - Integer representing minor changes that require new version number.
13
- VERSION = [0.3, 0, 6]
13
+ VERSION = [0.3, 0, 7]
14
14
 
15
15
  ##
16
16
  # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
18
18
 
19
19
  ##
20
20
  # Date of the current gem release.
21
- VERSION_DATE = Date.new(2017, 8, 24)
21
+ VERSION_DATE = Date.new(2017, 8, 25)
22
22
 
23
23
  ##
24
24
  # Reference of MiGA.
data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl ADDED
@@ -0,0 +1,56 @@
1
+ #!/usr/bin/env perl
2
+ #
3
+ # @author: Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
4
+ # @update: Oct 07 2015
5
+ # @license: artistic license 2.0
6
+ #
7
+ use strict;
8
+ use warnings;
9
+ use List::Util qw/sum min max/;
10
+
11
+ my ($seqs, $minlen, $n__) = @ARGV;
12
+ $seqs or die "
13
+ Description:
14
+ Calculates the N50 value of a set of sequences. Alternatively, it
15
+ can calculate other N** values. It also calculates the total number
16
+ of sequences and the total added length.
17
+
18
+ Usage:
19
+ $0 seqs.fa[ minlen[ **]]
20
+
21
+ seqs.fa A FastA file containing the sequences.
22
+ minlen (optional) The minimum length to take into consideration.
23
+ By default: 0.
24
+ ** Value N** to calculate. By default: 50 (N50).
25
+ ";
26
+ $minlen ||= 0;
27
+ $n__ ||= 50;
28
+
29
+ my @len = ();
30
+ open SEQ, "<", $seqs or die "Cannot open file: $seqs: $!\n";
31
+ while(<SEQ>){
32
+ if(/^>/){
33
+ push @len, 0;
34
+ }else{
35
+ next if /^;/;
36
+ chomp;
37
+ s/\W//g;
38
+ $len[-1]+=length $_;
39
+ }
40
+ }
41
+ close SEQ;
42
+ @len = sort { $a <=> $b } map { $_>=$minlen?$_:() } @len;
43
+ my $tot = (sum(@len) || 0);
44
+
45
+ my $thr = $n__*$tot/100;
46
+ my $pos = 0;
47
+ for(@len){
48
+ $pos+= $_;
49
+ if($pos>=$thr){
50
+ print "N$n__: $_\n";
51
+ last;
52
+ }
53
+ }
54
+ print "Sequences: ".scalar(@len)."\n";
55
+ print "Total length: $tot\n";
56
+
data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl ADDED
@@ -0,0 +1,60 @@
1
+ #!/usr/bin/env perl
2
+ #
3
+ # @author Luis M. Rodriguez-R
4
+ # @update Oct-07-2015
5
+ # @license artistic license 2.0
6
+ #
7
+
8
+ use warnings;
9
+ use strict;
10
+
11
+ my($file, $content, $stretch) = @ARGV;
12
+ $file or die <<HELP
13
+
14
+ Description:
15
+ Filter sequences by N-content and presence of long homopolymers.
16
+ Usage:
17
+ $0 sequences.fa [content [stretch]] > filtered.fa
18
+ Where:
19
+ sequences.fa Input file in FastA format
20
+ content A number between 0 and 1 indicating the maximum proportion of Ns
21
+ (1 to turn off, 0.5 by default)
22
+ stretch A number indicating the maximum number of consecutive identical
23
+ nucleotides allowed (0 to turn off, 100 by default)
24
+ filtered.fa Filtered set of sequences.
25
+
26
+ HELP
27
+ ;
28
+ ($content ||= 0.5)+=0;
29
+ ($stretch ||= 100)+=0;
30
+
31
+ my $good = 0;
32
+ my $N = 0;
33
+
34
+ FASTA: {
35
+ local $/ = "\n>";
36
+ open FILE, "<", $file or die "I can not open the file: $file: $!\n";
37
+ SEQ: while(<FILE>){
38
+ $N++;
39
+ s/^;.*//gm;
40
+ s/>//g;
41
+ my($n,$s) = split /\n/, $_, 2;
42
+ (my $clean = $s) =~ s/[^ACTGN]//g;
43
+ if($content < 1){
44
+ (my $Ns = $clean) =~ s/[^N]//g;
45
+ next SEQ if length($Ns)>length($clean)*$content;
46
+ }
47
+ if($stretch > 0){
48
+ for my $nuc (qw(A C T G N)){
49
+ next SEQ if $clean =~ m/[$nuc]{$stretch}/;
50
+ }
51
+ }
52
+ print ">$n\n$s\n";
53
+ $good++;
54
+ }
55
+ close FILE;
56
+ print STDERR "Total sequences: $N\nAfter filtering: $good\n";
57
+ }
58
+
59
+
60
+
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
+
metadata CHANGED
@@ -1,109 +1,109 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: miga-base
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.3.0.6
4
+ version: 0.3.0.7
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: 2017-08-24 00:00:00.000000000 Z
11
+ date: 2017-08-25 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: rest-client
15
15
  requirement: !ruby/object:Gem::Requirement
16
16
  requirements:
17
- - - "~>"
17
+ - - ~>
18
18
  - !ruby/object:Gem::Version
19
19
  version: '1.7'
20
20
  type: :runtime
21
21
  prerelease: false
22
22
  version_requirements: !ruby/object:Gem::Requirement
23
23
  requirements:
24
- - - "~>"
24
+ - - ~>
25
25
  - !ruby/object:Gem::Version
26
26
  version: '1.7'
27
27
  - !ruby/object:Gem::Dependency
28
28
  name: daemons
29
29
  requirement: !ruby/object:Gem::Requirement
30
30
  requirements:
31
- - - "~>"
31
+ - - ~>
32
32
  - !ruby/object:Gem::Version
33
33
  version: '1.2'
34
- - - ">="
34
+ - - '>='
35
35
  - !ruby/object:Gem::Version
36
36
  version: 1.2.4
37
37
  type: :runtime
38
38
  prerelease: false
39
39
  version_requirements: !ruby/object:Gem::Requirement
40
40
  requirements:
41
- - - "~>"
41
+ - - ~>
42
42
  - !ruby/object:Gem::Version
43
43
  version: '1.2'
44
- - - ">="
44
+ - - '>='
45
45
  - !ruby/object:Gem::Version
46
46
  version: 1.2.4
47
47
  - !ruby/object:Gem::Dependency
48
48
  name: json
49
49
  requirement: !ruby/object:Gem::Requirement
50
50
  requirements:
51
- - - ">"
51
+ - - '>'
52
52
  - !ruby/object:Gem::Version
53
53
  version: '1.8'
54
- - - "<"
54
+ - - <
55
55
  - !ruby/object:Gem::Version
56
56
  version: '3'
57
57
  type: :runtime
58
58
  prerelease: false
59
59
  version_requirements: !ruby/object:Gem::Requirement
60
60
  requirements:
61
- - - ">"
61
+ - - '>'
62
62
  - !ruby/object:Gem::Version
63
63
  version: '1.8'
64
- - - "<"
64
+ - - <
65
65
  - !ruby/object:Gem::Version
66
66
  version: '3'
67
67
  - !ruby/object:Gem::Dependency
68
68
  name: sqlite3
69
69
  requirement: !ruby/object:Gem::Requirement
70
70
  requirements:
71
- - - "~>"
71
+ - - ~>
72
72
  - !ruby/object:Gem::Version
73
73
  version: '1.3'
74
74
  type: :runtime
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: '1.3'
81
81
  - !ruby/object:Gem::Dependency
82
82
  name: rake
83
83
  requirement: !ruby/object:Gem::Requirement
84
84
  requirements:
85
- - - "~>"
85
+ - - ~>
86
86
  - !ruby/object:Gem::Version
87
87
  version: '11'
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: '11'
95
95
  - !ruby/object:Gem::Dependency
96
96
  name: test-unit
97
97
  requirement: !ruby/object:Gem::Requirement
98
98
  requirements:
99
- - - "~>"
99
+ - - ~>
100
100
  - !ruby/object:Gem::Version
101
101
  version: '3'
102
102
  type: :development
103
103
  prerelease: false
104
104
  version_requirements: !ruby/object:Gem::Requirement
105
105
  requirements:
106
- - - "~>"
106
+ - - ~>
107
107
  - !ruby/object:Gem::Version
108
108
  version: '3'
109
109
  description: Microbial Genomes Atlas
@@ -114,34 +114,6 @@ extensions: []
114
114
  extra_rdoc_files:
115
115
  - README.md
116
116
  files:
117
- - Gemfile
118
- - LICENSE
119
- - README.md
120
- - Rakefile
121
- - actions/about.rb
122
- - actions/add.rb
123
- - actions/add_result.rb
124
- - actions/daemon.rb
125
- - actions/date.rb
126
- - actions/files.rb
127
- - actions/find.rb
128
- - actions/get.rb
129
- - actions/init.rb
130
- - actions/ln.rb
131
- - actions/ls.rb
132
- - actions/new.rb
133
- - actions/plugins.rb
134
- - actions/rm.rb
135
- - actions/run.rb
136
- - actions/stats.rb
137
- - actions/tax_dist.rb
138
- - actions/tax_index.rb
139
- - actions/tax_set.rb
140
- - actions/tax_test.rb
141
- - bin/miga
142
- - lib/miga.rb
143
- - lib/miga/_data/aai-intax.tsv.gz
144
- - lib/miga/_data/aai-novel.tsv.gz
145
117
  - lib/miga/common.rb
146
118
  - lib/miga/daemon.rb
147
119
  - lib/miga/dataset.rb
@@ -155,6 +127,18 @@ files:
155
127
  - lib/miga/tax_index.rb
156
128
  - lib/miga/taxonomy.rb
157
129
  - lib/miga/version.rb
130
+ - lib/miga.rb
131
+ - test/common_test.rb
132
+ - test/daemon_test.rb
133
+ - test/dataset_test.rb
134
+ - test/metadata_test.rb
135
+ - test/project_test.rb
136
+ - test/remote_dataset_test.rb
137
+ - test/tax_index_test.rb
138
+ - test/taxonomy_test.rb
139
+ - test/test_helper.rb
140
+ - lib/miga/_data/aai-intax.tsv.gz
141
+ - lib/miga/_data/aai-novel.tsv.gz
158
142
  - scripts/_distances_functions.bash
159
143
  - scripts/_distances_noref_nomulti.bash
160
144
  - scripts/_distances_ref_nomulti.bash
@@ -178,23 +162,74 @@ files:
178
162
  - scripts/subclades.bash
179
163
  - scripts/trimmed_fasta.bash
180
164
  - scripts/trimmed_reads.bash
181
- - test/common_test.rb
182
- - test/daemon_test.rb
183
- - test/dataset_test.rb
184
- - test/metadata_test.rb
185
- - test/project_test.rb
186
- - test/remote_dataset_test.rb
187
- - test/tax_index_test.rb
188
- - test/taxonomy_test.rb
189
- - test/test_helper.rb
190
165
  - utils/adapters.fa
191
166
  - utils/core-pan-plot.R
167
+ - utils/enveomics/build_enveomics_r.bash
168
+ - utils/enveomics/enveomics.R/data/growth.curves.rda
169
+ - utils/enveomics/enveomics.R/data/phyla.counts.rda
170
+ - utils/enveomics/enveomics.R/DESCRIPTION
171
+ - utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd
172
+ - utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd
173
+ - utils/enveomics/enveomics.R/man/enve.__tribs.Rd
174
+ - utils/enveomics/enveomics.R/man/enve.barplot.Rd
175
+ - utils/enveomics/enveomics.R/man/enve.cliopts.Rd
176
+ - utils/enveomics/enveomics.R/man/enve.col.alpha.Rd
177
+ - utils/enveomics/enveomics.R/man/enve.col2alpha.Rd
178
+ - utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd
179
+ - utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd
180
+ - utils/enveomics/enveomics.R/man/enve.df2dist.Rd
181
+ - utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd
182
+ - utils/enveomics/enveomics.R/man/enve.growthcurve.Rd
183
+ - utils/enveomics/enveomics.R/man/enve.prune.dist.Rd
184
+ - utils/enveomics/enveomics.R/man/enve.recplot.Rd
185
+ - utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd
186
+ - utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd
187
+ - utils/enveomics/enveomics.R/man/enve.recplot2.__findPeak.Rd
188
+ - utils/enveomics/enveomics.R/man/enve.recplot2.__findPeaks.Rd
189
+ - utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd
190
+ - utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd
191
+ - utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd
192
+ - utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd
193
+ - utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd
194
+ - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd
195
+ - utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd
196
+ - utils/enveomics/enveomics.R/man/enve.recplot2.Rd
197
+ - utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd
198
+ - utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd
199
+ - utils/enveomics/enveomics.R/man/enve.tribs.Rd
200
+ - utils/enveomics/enveomics.R/man/enve.tribs.test.Rd
201
+ - utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd
202
+ - utils/enveomics/enveomics.R/man/enveomics.R-package.Rd
203
+ - utils/enveomics/enveomics.R/man/growth.curves.Rd
204
+ - utils/enveomics/enveomics.R/man/phyla.counts.Rd
205
+ - utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd
206
+ - utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd
207
+ - utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd
208
+ - utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd
209
+ - utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd
210
+ - utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd
211
+ - utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd
212
+ - utils/enveomics/enveomics.R/man/z$-methods.Rd
213
+ - utils/enveomics/enveomics.R/NAMESPACE
214
+ - utils/enveomics/enveomics.R/R/autoprune.R
215
+ - utils/enveomics/enveomics.R/R/barplot.R
216
+ - utils/enveomics/enveomics.R/R/cliopts.R
217
+ - utils/enveomics/enveomics.R/R/df2dist.R
218
+ - utils/enveomics/enveomics.R/R/growthcurve.R
219
+ - utils/enveomics/enveomics.R/R/recplot.R
220
+ - utils/enveomics/enveomics.R/R/recplot2.R
221
+ - utils/enveomics/enveomics.R/R/tribs.R
222
+ - utils/enveomics/enveomics.R/R/utils.R
223
+ - utils/enveomics/enveomics.R/README.md
192
224
  - utils/enveomics/Examples/aai-matrix.bash
193
225
  - utils/enveomics/Examples/ani-matrix.bash
194
226
  - utils/enveomics/Examples/essential-phylogeny.bash
195
227
  - utils/enveomics/Examples/unus-genome-phylogeny.bash
228
+ - utils/enveomics/globals.mk
196
229
  - utils/enveomics/LICENSE.txt
197
230
  - utils/enveomics/Makefile
231
+ - utils/enveomics/Manifest/categories.json
232
+ - utils/enveomics/Manifest/examples.json
198
233
  - utils/enveomics/Manifest/Tasks/aasubs.json
199
234
  - utils/enveomics/Manifest/Tasks/blasttab.json
200
235
  - utils/enveomics/Manifest/Tasks/distances.json
@@ -208,21 +243,20 @@ files:
208
243
  - utils/enveomics/Manifest/Tasks/tables.json
209
244
  - utils/enveomics/Manifest/Tasks/trees.json
210
245
  - utils/enveomics/Manifest/Tasks/variants.json
211
- - utils/enveomics/Manifest/categories.json
212
- - utils/enveomics/Manifest/examples.json
213
246
  - utils/enveomics/Manifest/tasks.json
247
+ - utils/enveomics/manifest.json
214
248
  - utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash
215
- - utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl
216
249
  - utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl
217
250
  - utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl
251
+ - utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl
252
+ - utils/enveomics/Pipelines/assembly.pbs/kSelector.R
253
+ - utils/enveomics/Pipelines/assembly.pbs/newbler.pbs
254
+ - utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl
218
255
  - utils/enveomics/Pipelines/assembly.pbs/README.md
219
256
  - utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash
220
257
  - utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash
221
258
  - utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash
222
259
  - utils/enveomics/Pipelines/assembly.pbs/RUNME.bash
223
- - utils/enveomics/Pipelines/assembly.pbs/kSelector.R
224
- - utils/enveomics/Pipelines/assembly.pbs/newbler.pbs
225
- - utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl
226
260
  - utils/enveomics/Pipelines/assembly.pbs/soap.pbs
227
261
  - utils/enveomics/Pipelines/assembly.pbs/stats.pbs
228
262
  - utils/enveomics/Pipelines/assembly.pbs/velvet.pbs
@@ -234,23 +268,25 @@ files:
234
268
  - utils/enveomics/Pipelines/blast.pbs/FastA.split.pl
235
269
  - utils/enveomics/Pipelines/blast.pbs/README.md
236
270
  - utils/enveomics/Pipelines/blast.pbs/RUNME.bash
271
+ - utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash
237
272
  - utils/enveomics/Pipelines/blast.pbs/TASK.check.bash
238
273
  - utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash
239
274
  - utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash
240
275
  - utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash
241
276
  - utils/enveomics/Pipelines/blast.pbs/TASK.run.bash
242
- - utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash
243
277
  - utils/enveomics/Pipelines/idba.pbs/README.md
244
- - utils/enveomics/Pipelines/idba.pbs/RUNME.bash
245
278
  - utils/enveomics/Pipelines/idba.pbs/run.pbs
279
+ - utils/enveomics/Pipelines/idba.pbs/RUNME.bash
246
280
  - utils/enveomics/Pipelines/trim.pbs/README.md
247
- - utils/enveomics/Pipelines/trim.pbs/RUNME.bash
248
281
  - utils/enveomics/Pipelines/trim.pbs/run.pbs
282
+ - utils/enveomics/Pipelines/trim.pbs/RUNME.bash
249
283
  - utils/enveomics/README.md
284
+ - utils/enveomics/Scripts/aai.rb
250
285
  - utils/enveomics/Scripts/AAsubs.log2ratio.rb
251
286
  - utils/enveomics/Scripts/Aln.cat.rb
252
287
  - utils/enveomics/Scripts/Aln.convert.pl
253
288
  - utils/enveomics/Scripts/AlphaDiversity.pl
289
+ - utils/enveomics/Scripts/ani.rb
254
290
  - utils/enveomics/Scripts/BlastPairwise.AAsubs.pl
255
291
  - utils/enveomics/Scripts/BlastTab.addlen.rb
256
292
  - utils/enveomics/Scripts/BlastTab.advance.bash
@@ -263,8 +299,8 @@ files:
263
299
  - utils/enveomics/Scripts/BlastTab.pairedHits.rb
264
300
  - utils/enveomics/Scripts/BlastTab.recplot2.R
265
301
  - utils/enveomics/Scripts/BlastTab.seqdepth.pl
266
- - utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl
267
302
  - utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl
303
+ - utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl
268
304
  - utils/enveomics/Scripts/BlastTab.subsample.pl
269
305
  - utils/enveomics/Scripts/BlastTab.sumPerHit.pl
270
306
  - utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl
@@ -272,7 +308,6 @@ files:
272
308
  - utils/enveomics/Scripts/Chao1.pl
273
309
  - utils/enveomics/Scripts/CharTable.classify.rb
274
310
  - utils/enveomics/Scripts/EBIseq2tax.rb
275
- - utils/enveomics/Scripts/FastA.N50.pl
276
311
  - utils/enveomics/Scripts/FastA.filter.pl
277
312
  - utils/enveomics/Scripts/FastA.filterLen.pl
278
313
  - utils/enveomics/Scripts/FastA.filterN.pl
@@ -280,6 +315,7 @@ files:
280
315
  - utils/enveomics/Scripts/FastA.gc.pl
281
316
  - utils/enveomics/Scripts/FastA.interpose.pl
282
317
  - utils/enveomics/Scripts/FastA.length.pl
318
+ - utils/enveomics/Scripts/FastA.N50.pl
283
319
  - utils/enveomics/Scripts/FastA.per_file.pl
284
320
  - utils/enveomics/Scripts/FastA.qlen.pl
285
321
  - utils/enveomics/Scripts/FastA.rename.pl
@@ -296,21 +332,36 @@ files:
296
332
  - utils/enveomics/Scripts/FastQ.tag.rb
297
333
  - utils/enveomics/Scripts/FastQ.toFastA.awk
298
334
  - utils/enveomics/Scripts/GenBank.add_fields.rb
335
+ - utils/enveomics/Scripts/gi2tax.rb
299
336
  - utils/enveomics/Scripts/HMM.essential.rb
300
337
  - utils/enveomics/Scripts/HMMsearch.extractIds.rb
338
+ - utils/enveomics/Scripts/in_silico_GA_GI.pl
301
339
  - utils/enveomics/Scripts/JPlace.distances.rb
302
340
  - utils/enveomics/Scripts/JPlace.to_iToL.rb
341
+ - utils/enveomics/Scripts/lib/data/essential.hmm.gz
342
+ - utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb
343
+ - utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb
344
+ - utils/enveomics/Scripts/lib/enveomics_rb/og.rb
345
+ - utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb
346
+ - utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb
347
+ - utils/enveomics/Scripts/lib/enveomics_rb/stat.rb
348
+ - utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb
303
349
  - utils/enveomics/Scripts/M5nr.getSequences.rb
304
350
  - utils/enveomics/Scripts/MeTaxa.distribution.pl
305
351
  - utils/enveomics/Scripts/MyTaxa.fragsByTax.pl
306
352
  - utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb
307
353
  - utils/enveomics/Scripts/NCBIacc2tax.rb
308
354
  - utils/enveomics/Scripts/Newick.autoprune.R
355
+ - utils/enveomics/Scripts/ogs.annotate.rb
356
+ - utils/enveomics/Scripts/ogs.core-pan.rb
357
+ - utils/enveomics/Scripts/ogs.extract.rb
358
+ - utils/enveomics/Scripts/ogs.mcl.rb
359
+ - utils/enveomics/Scripts/ogs.rb
360
+ - utils/enveomics/Scripts/ogs.stats.rb
309
361
  - utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl
362
+ - utils/enveomics/Scripts/rbm.rb
310
363
  - utils/enveomics/Scripts/RefSeq.download.bash
311
364
  - utils/enveomics/Scripts/SRA.download.bash
312
- - utils/enveomics/Scripts/TRIBS.plot-test.R
313
- - utils/enveomics/Scripts/TRIBS.test.R
314
365
  - utils/enveomics/Scripts/Table.barplot.R
315
366
  - utils/enveomics/Scripts/Table.df2dist.R
316
367
  - utils/enveomics/Scripts/Table.filter.pl
@@ -319,37 +370,10 @@ files:
319
370
  - utils/enveomics/Scripts/Table.round.rb
320
371
  - utils/enveomics/Scripts/Table.split.pl
321
372
  - utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb
373
+ - utils/enveomics/Scripts/TRIBS.plot-test.R
374
+ - utils/enveomics/Scripts/TRIBS.test.R
322
375
  - utils/enveomics/Scripts/VCF.KaKs.rb
323
376
  - utils/enveomics/Scripts/VCF.SNPs.rb
324
- - utils/enveomics/Scripts/aai.rb
325
- - utils/enveomics/Scripts/ani.rb
326
- - utils/enveomics/Scripts/gi2tax.rb
327
- - utils/enveomics/Scripts/in_silico_GA_GI.pl
328
- - utils/enveomics/Scripts/lib/data/essential.hmm.gz
329
- - utils/enveomics/Scripts/lib/enveomics.R
330
- - utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb
331
- - utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb
332
- - utils/enveomics/Scripts/lib/enveomics_rb/og.rb
333
- - utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb
334
- - utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb
335
- - utils/enveomics/Scripts/lib/enveomics_rb/stat.rb
336
- - utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb
337
- - utils/enveomics/Scripts/ogs.annotate.rb
338
- - utils/enveomics/Scripts/ogs.core-pan.rb
339
- - utils/enveomics/Scripts/ogs.extract.rb
340
- - utils/enveomics/Scripts/ogs.mcl.rb
341
- - utils/enveomics/Scripts/ogs.rb
342
- - utils/enveomics/Scripts/ogs.stats.rb
343
- - utils/enveomics/Scripts/rbm.rb
344
- - utils/enveomics/Tests/Makefile
345
- - utils/enveomics/Tests/Mgen_M2288.faa
346
- - utils/enveomics/Tests/Mgen_M2288.fna
347
- - utils/enveomics/Tests/Mgen_M2321.fna
348
- - utils/enveomics/Tests/Nequ_Kin4M.faa
349
- - utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata
350
- - utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt
351
- - utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv
352
- - utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv
353
377
  - utils/enveomics/Tests/a_mg.cds-go.blast.tsv
354
378
  - utils/enveomics/Tests/a_mg.reads-cds.blast.tsv
355
379
  - utils/enveomics/Tests/a_mg.reads-cds.counts.tsv
@@ -362,6 +386,11 @@ files:
362
386
  - utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv
363
387
  - utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim
364
388
  - utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec
389
+ - utils/enveomics/Tests/Makefile
390
+ - utils/enveomics/Tests/Mgen_M2288.faa
391
+ - utils/enveomics/Tests/Mgen_M2288.fna
392
+ - utils/enveomics/Tests/Mgen_M2321.fna
393
+ - utils/enveomics/Tests/Nequ_Kin4M.faa
365
394
  - utils/enveomics/Tests/phyla_counts.tsv
366
395
  - utils/enveomics/Tests/primate_lentivirus.ogs
367
396
  - utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm
@@ -370,65 +399,10 @@ files:
370
399
  - utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm
371
400
  - utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm
372
401
  - utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm
373
- - utils/enveomics/build_enveomics_r.bash
374
- - utils/enveomics/enveomics.R/DESCRIPTION
375
- - utils/enveomics/enveomics.R/NAMESPACE
376
- - utils/enveomics/enveomics.R/R/autoprune.R
377
- - utils/enveomics/enveomics.R/R/barplot.R
378
- - utils/enveomics/enveomics.R/R/cliopts.R
379
- - utils/enveomics/enveomics.R/R/df2dist.R
380
- - utils/enveomics/enveomics.R/R/growthcurve.R
381
- - utils/enveomics/enveomics.R/R/recplot.R
382
- - utils/enveomics/enveomics.R/R/recplot2.R
383
- - utils/enveomics/enveomics.R/R/tribs.R
384
- - utils/enveomics/enveomics.R/R/utils.R
385
- - utils/enveomics/enveomics.R/README.md
386
- - utils/enveomics/enveomics.R/data/growth.curves.rda
387
- - utils/enveomics/enveomics.R/data/phyla.counts.rda
388
- - utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd
389
- - utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd
390
- - utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd
391
- - utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd
392
- - utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd
393
- - utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd
394
- - utils/enveomics/enveomics.R/man/enve.__tribs.Rd
395
- - utils/enveomics/enveomics.R/man/enve.barplot.Rd
396
- - utils/enveomics/enveomics.R/man/enve.cliopts.Rd
397
- - utils/enveomics/enveomics.R/man/enve.col.alpha.Rd
398
- - utils/enveomics/enveomics.R/man/enve.col2alpha.Rd
399
- - utils/enveomics/enveomics.R/man/enve.df2dist.Rd
400
- - utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd
401
- - utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd
402
- - utils/enveomics/enveomics.R/man/enve.growthcurve.Rd
403
- - utils/enveomics/enveomics.R/man/enve.prune.dist.Rd
404
- - utils/enveomics/enveomics.R/man/enve.recplot.Rd
405
- - utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd
406
- - utils/enveomics/enveomics.R/man/enve.recplot2.Rd
407
- - utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd
408
- - utils/enveomics/enveomics.R/man/enve.recplot2.__findPeak.Rd
409
- - utils/enveomics/enveomics.R/man/enve.recplot2.__findPeaks.Rd
410
- - utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd
411
- - utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd
412
- - utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd
413
- - utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd
414
- - utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd
415
- - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd
416
- - utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd
417
- - utils/enveomics/enveomics.R/man/enve.tribs.Rd
418
- - utils/enveomics/enveomics.R/man/enve.tribs.test.Rd
419
- - utils/enveomics/enveomics.R/man/enveomics.R-package.Rd
420
- - utils/enveomics/enveomics.R/man/growth.curves.Rd
421
- - utils/enveomics/enveomics.R/man/phyla.counts.Rd
422
- - utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd
423
- - utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd
424
- - utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd
425
- - utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd
426
- - utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd
427
- - utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd
428
- - utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd
429
- - utils/enveomics/enveomics.R/man/z$-methods.Rd
430
- - utils/enveomics/globals.mk
431
- - utils/enveomics/manifest.json
402
+ - utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata
403
+ - utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt
404
+ - utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv
405
+ - utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv
432
406
  - utils/index_metadata.rb
433
407
  - utils/mytaxa_scan.R
434
408
  - utils/mytaxa_scan.rb
@@ -438,6 +412,31 @@ files:
438
412
  - utils/subclades-compile.rb
439
413
  - utils/subclades-nj.R
440
414
  - utils/subclades.R
415
+ - bin/miga
416
+ - actions/about.rb
417
+ - actions/add.rb
418
+ - actions/add_result.rb
419
+ - actions/daemon.rb
420
+ - actions/date.rb
421
+ - actions/files.rb
422
+ - actions/find.rb
423
+ - actions/get.rb
424
+ - actions/init.rb
425
+ - actions/ln.rb
426
+ - actions/ls.rb
427
+ - actions/new.rb
428
+ - actions/plugins.rb
429
+ - actions/rm.rb
430
+ - actions/run.rb
431
+ - actions/stats.rb
432
+ - actions/tax_dist.rb
433
+ - actions/tax_index.rb
434
+ - actions/tax_set.rb
435
+ - actions/tax_test.rb
436
+ - Gemfile
437
+ - Rakefile
438
+ - README.md
439
+ - LICENSE
441
440
  homepage: http://enve-omics.ce.gatech.edu/miga
442
441
  licenses:
443
442
  - Artistic-2.0
@@ -446,25 +445,25 @@ post_install_message:
446
445
  rdoc_options:
447
446
  - lib
448
447
  - README.md
449
- - "--main"
448
+ - --main
450
449
  - README.md
451
- - "--title"
450
+ - --title
452
451
  - MiGA
453
452
  require_paths:
454
453
  - lib
455
454
  required_ruby_version: !ruby/object:Gem::Requirement
456
455
  requirements:
457
- - - ">="
456
+ - - '>='
458
457
  - !ruby/object:Gem::Version
459
458
  version: '1.9'
460
459
  required_rubygems_version: !ruby/object:Gem::Requirement
461
460
  requirements:
462
- - - ">="
461
+ - - '>='
463
462
  - !ruby/object:Gem::Version
464
463
  version: '0'
465
464
  requirements: []
466
465
  rubyforge_project:
467
- rubygems_version: 2.6.11
466
+ rubygems_version: 2.0.14
468
467
  signing_key:
469
468
  specification_version: 4
470
469
  summary: MiGA
data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl DELETED
@@ -1 +0,0 @@
1
- utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.N50.pl
data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl DELETED
@@ -1 +0,0 @@
1
- utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.filterN.pl
data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl DELETED
@@ -1 +0,0 @@
1
- utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.length.pl
data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl DELETED
@@ -1 +0,0 @@
1
- utils/enveomics/Pipelines/blast.pbs/../../Scripts/FastA.split.pl
data/utils/enveomics/Scripts/lib/enveomics.R DELETED
@@ -1 +0,0 @@
1
- utils/enveomics/Scripts/lib/../../enveomics.R