miga-base 0.7.12.0 → 0.7.13.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: f99f8fd530489d42672cdd96123f321725b9437ee4a81e822a07854ec924ad53
-  data.tar.gz: c4d6607a4b6062b45cc94985b8bc920bb25307232851b20436ee4b9cd8a8986b
+  metadata.gz: 36fd2b4078044d448feccc3a1c08f4299663692c3f564fd0d390808a2d2f07e7
+  data.tar.gz: b57924e0a40b316f186d5089455e1d2221f3e11f559d91c0d9f5d8e8e621b257
 SHA512:
-  metadata.gz: '03478c56a40e948ad9eb4cb09fbedc72bac331072ccf46ce5468f1f78a08e891260684771e455b92841d8af454fcab997d7d51a68360b8337ffa13c8c2ec88a4'
-  data.tar.gz: e992d10e5de206a85ac425e15c7594629f86e8088ec6f59ba820c5ecaf6c8901af0142455501a1d8af03902a3ca559d0374692e4df9f41acdceaf45d5d750b1f
+  metadata.gz: 47038d85b7680fff3d74b176e1fc46125b0b76f5c7044c6ae3153f2192584e7934c480c901ab538a926ab9f5b2af9ac9d54c16ce88231043cb2e5bb0c0ad40d8
+  data.tar.gz: b1878fb728f2e3414e8c9ffdc8af436d50f66c64588ecbff4b991bb2df93528e7b4fd3177b47ad4a136e45a972ea07c2c48328234ec1b5579795311bcd20c2d6

data/lib/miga/cli.rb

@@ -189,8 +189,9 @@ class MiGA::Cli < MiGA::MiGA
   end
 
   ##
-  # Perform the task requested (see #task)
-  def launch
+  # Perform the task requested (see #task); if +abort_on_error+, abort on
+  # error
+  def launch(abort_on_error = false)
     begin
       raise "See `miga -h`" if action.nil?
 
@@ -199,6 +200,7 @@ class MiGA::Cli < MiGA::MiGA
       $stderr.puts "Exception: #{err}"
       $stderr.puts ''
       err.backtrace.each { |l| $stderr.puts "DEBUG: #{l}" }
+      abort if abort_on_error
       err
     end
   end

data/lib/miga/cli/action/browse.rb

@@ -46,7 +46,9 @@ class MiGA::Cli::Action::Browse < MiGA::Cli::Action
 
     # Summaries
     summaries = Dir["#{p.path}/*.tsv"].map do |i|
-      "<li><a href='file://#{i}'>#{File.basename(i)}</a></li>"
+      b = File.basename(i, '.tsv')
+      generate_summary_page(i, p)
+      "<li><a href='s-#{b}.html'>#{format_name(b)}</a></li>"
     end.join('')
 
     # Project index page
@@ -59,6 +61,32 @@ class MiGA::Cli::Action::Browse < MiGA::Cli::Action
     write_file(p, 'index.html') { build_from_template('index.html', data) }
   end
 
+  ##
+  # Create page for the summary +path+ in project +p+
+  def generate_summary_page(path, p)
+    b = File.basename(path, '.tsv')
+    table = '<table class="table table-hover table-responsive">'
+    File.open(path, 'r') do |fh|
+      fh.each do |ln|
+        r = ln.chomp.split("\t")
+        if $. == 1
+          table += '<thead><tr>' +
+            r.map { |i| "<th scope=col>#{format_name(i)}</th>" }.join(' ') +
+            '</tr></thead><tbody>'
+        else
+          table += "<tr><th scope=row>#{r.shift}</th>" +
+            r.map { |i| "<td>#{i}</td>" }.join(' ') + "</tr>"
+        end
+      end
+    end
+    table += '</tbody></table>'
+    write_file(p, "s-#{b}.html") do
+      build_from_template(
+        'summary.html', file: "#{b}.tsv", name: format_name(b), table: table
+      )
+    end
+  end
+
   ##
   # Create page for dataset +d+ within project +p+
   def generate_dataset_page(p, d)
@@ -162,7 +190,7 @@ class MiGA::Cli::Action::Browse < MiGA::Cli::Action
     links = []
     res.each_file do |key, _|
       name = format_name(key)
-      links << "<a href='file://#{res.file_path(key)}'>#{name}</a><br/>"
+      links << "<a href='../#{res.file_path(key, true)}'>#{name}</a><br/>"
     end
     links.empty? ? nil : links.join('')
   end

data/lib/miga/cli/action/browse/about.html

@@ -0,0 +1,31 @@
+<h1 class="h2 border-bottom pt-3 pb-2 mb-3">About MiGA</h1>
+<p>
+MiGA is developed and maintained by
+<a href='https://rodriguez-r.com/'>Luis M. Rodriguez-R</a>.
+
+The MiGA codebase is
+<a href='http://code.microbial-genomes.org/miga'>freely available</a> under the
+terms of the terms of the
+<a href='http://code.microbial-genomes.org/miga/blob/master/LICENSE'>Artistic License 2.0</a>.
+</p>
+
+<p>
+MiGA is the result of a collaboration between the
+<a href='http://enve-omics.gatech.edu/'>Kostas Lab</a>
+(<a href='http://www.gatech.edu/'>Georgia Institute of Technology</a>) and the
+<a href='http://rdp.cme.msu.edu/'>RDP team</a>
+(<a href='http://cme.msu.edu/'>Center for Microbial Ecology</a>,
+<a href='https://msu.edu/'>Michigan State University</a>).
+The MiGA project is funded by the
+<a href='http://nsf.gov/'>US National Science Foundation</a>
+(Awards <a href='http://nsf.gov/awardsearch/showAward?AWD_ID=1356288'>#1356288</a> &amp;
+<a href='https://xras.xsede.org/public/requests/31162-XSEDE-MCB190042-1190572'>#MCB190042</a>).
+</p>
+
+<h1 class="h2 border-bottom pt-3 pb-2 mb-3">Citation</h1>
+If you use MiGA in your work, consider citing:
+<blockquote class='border-left p-3'>
+{{citation}}
+</blockquote>
+
+

data/lib/miga/cli/action/browse/dataset.html

@@ -0,0 +1,5 @@
+<h1 class="h2 border-bottom pt-3 pb-2 mb-3">{{unmiga_name}}</h1>
+{{information}}
+
+<h1 class="h2 border-bottom pt-3 pb-2 mb-3">Results</h1>
+{{results}}

data/lib/miga/cli/action/browse/dataset_menu_item.html

@@ -0,0 +1,3 @@
+<li class="nav-item">
+  <a class="nav-link" href="ds_{{name}}.html">{{unmiga_name}}</a>
+</li>

data/lib/miga/cli/action/browse/datasets.html

@@ -0,0 +1,4 @@
+<h1 class="h2 border-bottom pt-3 pb-2 mb-3">{{type_name}} Datasets</h1>
+<ul>
+  {{list}}
+</ul>

data/lib/miga/cli/action/browse/index.html

@@ -0,0 +1,8 @@
+<h1 class="h2 border-bottom pt-3 pb-2 mb-3">Project Information</h1>
+{{information}}
+
+<h1 class="h2 border-bottom pt-3 pb-2 mb-3">Summaries</h1>
+{{summaries}}
+
+<h1 class="h2 border-bottom pt-3 pb-2 mb-3">Project Results</h1>
+{{results}}

data/lib/miga/cli/action/browse/layout.html

@@ -0,0 +1,57 @@
+<!doctype html>
+<head>
+  <meta charset="utf-8">
+  <title>MiGA | {{project_name}}</title>
+
+  <!-- Remote assets -->
+  <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.5.0/css/bootstrap.min.css" integrity="sha384-9aIt2nRpC12Uk9gS9baDl411NQApFmC26EwAOH8WgZl5MYYxFfc+NcPb1dKGj7Sk" crossorigin="anonymous">
+  <script src="https://code.jquery.com/jquery-3.5.1.slim.min.js" integrity="sha384-DfXdz2htPH0lsSSs5nCTpuj/zy4C+OGpamoFVy38MVBnE+IbbVYUew+OrCXaRkfj" crossorigin="anonymous"></script>
+  <script src="https://cdn.jsdelivr.net/npm/popper.js@1.16.0/dist/umd/popper.min.js" integrity="sha384-Q6E9RHvbIyZFJoft+2mJbHaEWldlvI9IOYy5n3zV9zzTtmI3UksdQRVvoxMfooAo" crossorigin="anonymous"></script>
+  <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.5.0/js/bootstrap.min.js" integrity="sha384-OgVRvuATP1z7JjHLkuOU7Xw704+h835Lr+6QL9UvYjZE3Ipu6Tp75j7Bh/kR0JKI" crossorigin="anonymous"></script>
+
+  <!-- Local assets -->
+  <link href="style.css" rel="stylesheet">
+  <link rel="icon" href="favicon-32.png" sizes="32x32" type="image/png">
+</head>
+<body>
+  <nav class="navbar navbar-dark sticky-top bg-dark flex-md-nowrap p-0 shadow">
+    <a class="navbar-brand col-md-12 col-lg-12 mr-0 px-3"
+          href="index.html">MiGA | {{project_name}}</a>
+    <button class="navbar-toggler position-absolute d-md-none collapsed"
+          type="button" data-toggle="collapse" data-target="#sidebarMenu"
+          aria-controls="sidebarMenu" aria-expanded="false"
+          aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+  </nav>
+  <div class="container-fluid">
+  <div class="row">
+    <nav id="sidebarMenu" class="col-md-3 col-lg-2 d-md-block bg-light sidebar collapse">
+      <div class="sidebar-sticky pt-3">
+        <ul class="nav flex-column">
+          <li class="nav-item">
+            <a class="nav-link {{project_active}}" href="index.html">Project</a>
+          </li>
+          <li class="nav-item">
+            <a class="nav-link {{ref_datasets_active}}"
+                  href="ref_datasets.html">Reference datasets</a>
+          </li>
+          <li class="nav-item">
+            <a class="nav-link {{qry_datasets_active}}"
+                  href="qry_datasets.html">Query datasets</a>
+          </li>
+          <li class="nav-item border-top mt-4">
+            <a class="nav-link {{about_miga_active}}"
+                  href="about.html">About MiGA</a>
+          </li>
+        </ul>
+      </div>
+    </nav>
+
+    <main role="main" class="col-md-9 ml-sm-auto col-lg-10 px-md-4">
+      {{content}}
+    </main>
+  </div>
+</div>
+</body>
+

data/lib/miga/cli/action/browse/redirect.html

@@ -0,0 +1,11 @@
+<!doctype html>
+<head>
+  <title>MiGA Project</title>
+  <meta http-equiv = "refresh" content = "1; url = browse/index.html" />
+</head>
+<body>
+  <div style='font-size:200%; margin-top: 5em; text-align: center;'>
+    Redirecting to <a href='browse/index.html'>Project page</a>...
+  </div>
+</body>
+

data/lib/miga/cli/action/browse/style.css

@@ -0,0 +1,97 @@
+body {
+  font-size: .875rem;
+}
+
+/*
+ * Sidebar
+ */
+
+.sidebar {
+  position: fixed;
+  top: 0;
+  bottom: 0;
+  left: 0;
+  z-index: 100; /* Behind the navbar */
+  padding: 48px 0 0; /* Height of navbar */
+  box-shadow: inset -1px 0 0 rgba(0, 0, 0, .1);
+}
+
+@media (max-width: 767.98px) {
+  .sidebar {
+    top: 3rem;
+  }
+}
+
+.sidebar-sticky {
+  position: relative;
+  top: 0;
+  height: calc(100vh - 48px);
+  padding-top: .5rem;
+  overflow-x: hidden;
+  overflow-y: auto; /* Scrollable contents if viewport is shorter than content. */
+}
+
+@supports ((position: -webkit-sticky) or (position: sticky)) {
+  .sidebar-sticky {
+    position: -webkit-sticky;
+    position: sticky;
+  }
+}
+
+.sidebar .nav-link {
+  font-weight: 500;
+  color: #333;
+}
+
+.sidebar .nav-link .feather {
+  margin-right: 4px;
+  color: #999;
+}
+
+.sidebar .nav-link.active {
+  color: #007bff;
+}
+
+.sidebar .nav-link:hover .feather,
+.sidebar .nav-link.active .feather {
+  color: inherit;
+}
+
+.sidebar-heading {
+  font-size: .75rem;
+  text-transform: uppercase;
+}
+
+/*
+ * Navbar
+ */
+
+.navbar-brand {
+  padding-top: .75rem;
+  padding-bottom: .75rem;
+  font-size: 1rem;
+  background-color: rgba(0, 0, 0, .25);
+  box-shadow: inset -1px 0 0 rgba(0, 0, 0, .25);
+}
+
+.navbar .navbar-toggler {
+  top: .25rem;
+  right: 1rem;
+}
+
+.navbar .form-control {
+  padding: .75rem 1rem;
+  border-width: 0;
+  border-radius: 0;
+}
+
+.form-control-dark {
+  color: #fff;
+  background-color: rgba(255, 255, 255, .1);
+  border-color: rgba(255, 255, 255, .1);
+}
+
+.form-control-dark:focus {
+  border-color: transparent;
+  box-shadow: 0 0 0 3px rgba(255, 255, 255, .25);
+}

data/lib/miga/cli/action/browse/summary.html

@@ -0,0 +1,5 @@
+<h1 class="h2 border-bottom pt-3 pb-2 mb-3">Summary: {{name}}</h1>
+<p class='m-2 mb-3'>
+  Based on <a href='../{{file}}'>{{file}}</a>
+</p>
+{{table}}

data/lib/miga/cli/action/derep_wf.rb

@@ -27,10 +27,13 @@ class MiGA::Cli::Action::DerepWf < MiGA::Cli::Action
         '--threshold FLOAT', Float,
         "Metric threshold (%) to dereplicate. By default: #{cli[:threshold]}"
       ) { |v| cli[:threshold] = v }
+      opt.on(
+        '--quality',
+        'Use genome with highest quality as clade representatives (default)'
+      ) { |v| cli[:criterion] = :quality }
       opt.on(
         '--medoids',
-        'Use medoids as clade representatives',
-        'By default: Use genome with the highest quality'
+        'Use medoids as clade representatives'
       ) { |v| cli[:criterion] = :medoids }
       opt.on(
         '--no-collection',
@@ -47,12 +50,18 @@ class MiGA::Cli::Action::DerepWf < MiGA::Cli::Action
 
   def perform
     # Input data
-    p = create_project(:assembly,
-                       { run_project_stats: false, run_clades: false,
-                         gsp_metric: cli[:metric], :"gsp_#{cli[:metric]}" => cli[:threshold] },
-                       { run_mytaxa_scan: false, run_ssu: false })
+    p = create_project(
+      :assembly,
+      {
+        run_project_stats: false,
+        run_clades: false,
+        gsp_metric: cli[:metric],
+        :"gsp_#{cli[:metric]}" => cli[:threshold]
+      },
+      { run_mytaxa_scan: false, run_ssu: false }
+    )
     unless cli[:threshold] >= 0.0 && cli[:threshold] <= 100.0
-      raise "The threshold of identity must be in the range [0,100]"
+      raise 'The threshold of identity must be in the range [0,100]'
     end
 
     # Run
@@ -65,8 +74,8 @@ class MiGA::Cli::Action::DerepWf < MiGA::Cli::Action
   private
 
   def dereplicate(p)
-    cli.say "Extracting genomospecies clades"
-    r = p.result(:clade_finding) or raise "Result unavailable: run failed"
+    cli.say 'Extracting genomospecies clades'
+    r = p.result(:clade_finding) or raise 'Result unavailable: run failed'
     c_f = r.file_path(:clades_gsp) or raise 'Result incomplete: run failed'
     clades = File.readlines(c_f).map { |i| i.chomp.split("\t") }
     rep = representatives(p)
@@ -87,7 +96,7 @@ class MiGA::Cli::Action::DerepWf < MiGA::Cli::Action
   end
 
   def representatives(p)
-    cli.say "Identifying representatives"
+    cli.say 'Identifying representatives'
     f = File.expand_path('representatives.txt', cli[:outdir])
     if cli[:criterion] == :medoids
       FileUtils.cp(p.result(:clade_finding).file_path(:medoids_gsp), f)

data/lib/miga/daemon.rb

@@ -91,7 +91,8 @@ class MiGA::Daemon < MiGA::MiGA
     flush!
     if (loop_i % 12).zero?
       purge!
-      recalculate_status!
+      # TEMPORARILY DISABLED:
+      # recalculate_status!
     end
     save_status
     sleep(latency)

data/lib/miga/result.rb

@@ -81,20 +81,22 @@ class MiGA::Result < MiGA::MiGA
   end
 
   ##
-  # Directory containing the result
-  def dir
-    File.dirname(path)
+  # Directory containing the result; by default an absolute path, if
+  # +relative+ is true returns the path relative to the parent project
+  def dir(relative = false)
+    relative ? relative_dir : File.dirname(path)
   end
 
   ##
-  # Absolute path to the file(s) defined by symbol +k+
-  def file_path(k)
+  # Absolute path to the file(s) defined by symbol +k+, or relative
+  # path if +relative+ is true
+  def file_path(k, relative = false)
     k = k.to_sym
     f = self[:files].nil? ? nil : self[:files][k]
     return nil if f.nil?
-    return File.expand_path(f, dir) unless f.is_a? Array
+    return File.join(dir(relative), f) unless f.is_a? Array
 
-    f.map { |fi| File.expand_path(fi, dir) }
+    f.map { |fi| File.join(dir(relative), fi) }
   end
 
   ##

data/lib/miga/version.rb

@@ -8,7 +8,7 @@ module MiGA
   # - Float representing the major.minor version.
   # - Integer representing gem releases of the current version.
   # - Integer representing minor changes that require new version number.
-  VERSION = [0.7, 12, 0]
+  VERSION = [0.7, 13, 2]
 
   ##
   # Nickname for the current major.minor version.
@@ -16,7 +16,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2020, 7, 22)
+  VERSION_DATE = Date.new(2020, 8, 4)
 
   ##
   # Reference of MiGA.

data/scripts/aai_distances.bash

@@ -13,17 +13,20 @@ echo -n "" > miga-project.log
 DS=$(miga ls -P "$PROJECT" --ref --no-multi --active)
 
 # Extract values
-echo "metric a b value sd n omega" | tr " " "\\t" >miga-project.txt
-for i in $DS ; do
-  echo "SELECT CASE WHEN omega!=0 THEN 'AAI' ELSE 'hAAI_AAI' END," \
-    " seq1, seq2, aai, sd, n, omega from aai;" \
-    | sqlite3 "$i.db" | tr "\\|" "\\t" >>miga-project.txt
-  echo "$i" >> miga-project.log
-done
+rm -f miga-project.txt
+(
+  echo "metric a b value sd n omega" | tr " " "\\t"
+  for i in $DS ; do
+    echo "SELECT CASE WHEN omega!=0 THEN 'AAI' ELSE 'hAAI_AAI' END," \
+      " seq1, seq2, aai, sd, n, omega from aai;" \
+      | sqlite3 "$i.db" | tr "\\|" "\\t"
+    echo "$i" >> miga-project.log
+  done
+) | gzip -9c > miga-project.txt.gz
 
 # R-ify
 echo "
-aai <- read.table('miga-project.txt', sep='\\t', h=T, as.is=TRUE);
+aai <- read.table(gzfile('miga-project.txt.gz'), sep='\\t', h=T, as.is=TRUE);
 save(aai, file='miga-project.Rdata');
 if(sum(aai[,'a'] != aai[,'b']) > 0){
   h <- hist(aai[aai[,'a'] != aai[,'b'], 'value'], breaks=100, plot=FALSE);
@@ -35,9 +38,6 @@ if(sum(aai[,'a'] != aai[,'b']) > 0){
 }
 " | R --vanilla
 
-# Gzip
-gzip -9 -f miga-project.txt
-
 # Finalize
 miga date > "miga-project.done"
 miga add_result -P "$PROJECT" -r "$SCRIPT" -f

data/scripts/ani_distances.bash

@@ -13,16 +13,19 @@ echo -n "" > miga-project.log
 DS=$(miga ls -P "$PROJECT" --ref --no-multi --active)
 
 # Extract values
-echo "metric a b value sd n omega" | tr " " "\\t" >miga-project.txt
-for i in $DS ; do
-  echo "SELECT 'ANI', seq1, seq2, ani, sd, n, omega from ani ;" \
-    | sqlite3 "$i.db" | tr "\\|" "\\t" >>miga-project.txt
-  echo "$i" >> miga-project.log
-done
+rm -f miga-project.txt
+(
+  echo "metric a b value sd n omega" | tr " " "\\t"
+  for i in $DS ; do
+    echo "SELECT 'ANI', seq1, seq2, ani, sd, n, omega from ani ;" \
+      | sqlite3 "$i.db" | tr "\\|" "\\t"
+    echo "$i" >> miga-project.log
+  done
+) | gzip -9c > miga-project.txt.gz
 
 # R-ify
 echo "
-ani <- read.table('miga-project.txt', sep='\\t', h=T, as.is=TRUE);
+ani <- read.table(gzfile('miga-project.txt.gz'), sep='\\t', h=T, as.is=TRUE);
 save(ani, file='miga-project.Rdata');
 if(sum(ani[,'a'] != ani[,'b']) > 0){
   h <- hist(ani[ani[,'a'] != ani[,'b'], 'value'], breaks=100, plot=FALSE);
@@ -34,9 +37,6 @@ if(sum(ani[,'a'] != ani[,'b']) > 0){
 }
 " | R --vanilla
 
-# Gzip
-gzip -9 -f miga-project.txt
-
 # Finalize
 miga date > "miga-project.done"
 miga add_result -P "$PROJECT" -r "$SCRIPT" -f

data/scripts/haai_distances.bash

@@ -17,30 +17,30 @@ echo -n "" > miga-project.log
 DS=$(miga ls -P "$PROJECT" --ref --no-multi --active)
 
 # Extract values
-echo "metric a b value sd n omega" | tr " " "\\t" >miga-project.txt
-for i in $DS ; do
-  echo "SELECT 'hAAI', seq1, seq2, aai, sd, n, omega from aai ;" \
-    | sqlite3 "$i.db" | tr "\\|" "\\t" >>miga-project.txt
-  echo "$i" >> miga-project.log
-done
+rm -f miga-project.txt
+(
+  echo "metric a b value sd n omega" | tr " " "\\t"
+  for i in $DS ; do
+    echo "SELECT 'hAAI', seq1, seq2, aai, sd, n, omega from aai ;" \
+      | sqlite3 "$i.db" | tr "\\|" "\\t"
+    echo "$i" >> miga-project.log
+  done
+) | gzip -9c > miga-project.txt.gz
 
 # R-ify
 echo "
-haai <- read.table('miga-project.txt', sep='\\t', h=T, as.is=TRUE);
+haai <- read.table(gzfile('miga-project.txt.gz'), sep='\\t', h=T, as.is=TRUE);
 save(haai, file='miga-project.Rdata');
 if(sum(haai[,'a'] != haai[,'b']) > 0){
   h <- hist(haai[haai[,'a'] != haai[,'b'], 'value'], breaks=100, plot=FALSE);
   write.table(
     cbind(h[['breaks']][-length(h[['breaks']])],
-      h[['breaks']][-1],h[['counts']]),
+      h[['breaks']][-1], h[['counts']]),
     file='miga-project.hist', quote=FALSE, sep='\\t',
     col.names=FALSE, row.names=FALSE);
 }
 " | R --vanilla
 
-# Gzip
-gzip -9 -f miga-project.txt
-
 # Finalize
 miga date > "miga-project.done"
 miga add_result -P "$PROJECT" -r "$SCRIPT" -f

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.12.0
+  version: 0.7.13.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-07-22 00:00:00.000000000 Z
+date: 2020-08-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -119,6 +119,16 @@ files:
 - lib/miga/cli/action/add_result.rb
 - lib/miga/cli/action/archive.rb
 - lib/miga/cli/action/browse.rb
+- lib/miga/cli/action/browse/about.html
+- lib/miga/cli/action/browse/dataset.html
+- lib/miga/cli/action/browse/dataset_menu_item.html
+- lib/miga/cli/action/browse/datasets.html
+- lib/miga/cli/action/browse/favicon-32.png
+- lib/miga/cli/action/browse/index.html
+- lib/miga/cli/action/browse/layout.html
+- lib/miga/cli/action/browse/redirect.html
+- lib/miga/cli/action/browse/style.css
+- lib/miga/cli/action/browse/summary.html
 - lib/miga/cli/action/classify_wf.rb
 - lib/miga/cli/action/console.rb
 - lib/miga/cli/action/daemon.rb