sequenceserver 3.0.1 → 3.1.0

data/views/tblastx_options.erb

@@ -4,15 +4,15 @@
         characters per line to preserve formatting.
 %>
 
-<h5>Input Query Options</h5>
-<ul class="list-unstyled">
+<h5 class="text-lg py-4 font-medium">Input Query Options</h5>
+<ul class="list-unstyled space-y-2">
 <li>
-<pre><%= ERB::Util.h %q|-strand <String, `both', `minus', `plus'>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-strand <String, `both', `minus', `plus'>
   Query strand(s) to search against database/subject
   Default = 'both'|%></pre>
   </li>
 <li>
-<pre><%= ERB::Util.h %q|-query_gencode <Integer, values between: 1-6, 9-16, 21-31, 33>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-query_gencode <Integer, values between: 1-6, 9-16, 21-31, 33>
   Genetic code to use to translate query (see https://www.ncbi.nlm.nih.gov/Taxonomy/
    taxonomyhome.html/index.cgi?chapter=cgencodes for details)
   Default = '1'|%></pre>
@@ -21,60 +21,60 @@
 
 <br />
 
-<h5>General Search Options</h5>
-<ul class="list-unstyled">
+<h5 class="text-lg py-4 font-medium">General Search Options</h5>
+<ul class="list-unstyled space-y-2">
   <li>
-<pre><%= ERB::Util.h %q|-evalue <Real>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-evalue <Real>
   Expectation value (E) threshold for saving hits
   Default = '10'| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-word_size <Integer, >=2>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-word_size <Integer, >=2>
   Word size for wordfinder algorithm| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-max_intron_length <Integer, >=0>
-  Length of the largest intron allowed in a translated nucleotide sequence when 
-   linking multiple distinct alignments 
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-max_intron_length <Integer, >=0>
+  Length of the largest intron allowed in a translated nucleotide sequence when
+   linking multiple distinct alignments
   Default = '0'| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-matrix <String>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-matrix <String>
   Scoring matrix name (normally BLOSUM62)| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-threshold <Real, >=0>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-threshold <Real, >=0>
   Minimum word score such that the word is added to the BLAST lookup table| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-db_gencode <Integer, values between: 1-6, 9-16, 21-31, 33>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-db_gencode <Integer, values between: 1-6, 9-16, 21-31, 33>
   Genetic code to use to translate database/subjects (see user manual for details)
   Default = '1' | %></pre>
   </li>
 </ul>
   <br />
 
-<h5>Formatting Options</h5>
-<ul class="list-unstyled">
+<h5 class="text-lg py-4 font-medium">Formatting Options</h5>
+<ul class="list-unstyled space-y-2">
    <li>
-<pre><%= ERB::Util.h %q|-show_gis
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-show_gis
   Show NCBI GIs in deflines?| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-num_descriptions <Integer, >=0>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-num_descriptions <Integer, >=0>
   Number of database sequences to show one-line descriptions for
   Not applicable for outfmt > 4
   Default = '500'
   * Incompatible with:  max_target_seqs| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q| -num_alignments <Integer, >=0>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q| -num_alignments <Integer, >=0>
   Number of database sequences to show alignments for
   Default = '250'
   * Incompatible with:  max_target_seqs| %></pre>
   </li>
     <li>
-<pre><%= ERB::Util.h %q| -sorthits <Integer, (>=0 and =<4)>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q| -sorthits <Integer, (>=0 and =<4)>
   Sorting option for hits:
    alignment view options:
      0 = Sort by evalue,
@@ -85,7 +85,7 @@
    Not applicable for outfmt > 4| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q| -sorthsps <Integer, (>=0 and =<4)>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q| -sorthsps <Integer, (>=0 and =<4)>
   Sorting option for hps:
      0 = Sort by hsp evalue,
      1 = Sort by hsp score,
@@ -98,52 +98,52 @@
 
 <br/>
 
-<h5>Query filtering options</h5>
-<ul class="list-unstyled">
+<h5 class="text-lg py-4 font-medium">Query filtering options</h5>
+<ul class="list-unstyled space-y-2">
   <li>
-<pre><%= ERB::Util.h %q|-seg <String>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-seg <String>
   Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
   or 'no' to disable)
   Default = '12 2.2 2.5'| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-soft_masking <Boolean>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-soft_masking <Boolean>
   Apply filtering locations as soft masks
   Default ='false'| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-lcase_masking
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-lcase_masking
   Use lower case filtering in query and subject sequence(s)?| %></pre>
   </li>
 </ul>
 
 <br/>
 
-<h5>Restrict search or results</h5>
-<ul class="list-unstyled">
+<h5 class="text-lg py-4 font-medium">Restrict search or results</h5>
+<ul class="list-unstyled space-y-2">
   <li>
-<pre><%= ERB::Util.h %q|-gilist <String>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-gilist <String>
   Restrict search of database to list of GIs
   * Incompatible with:  seqidlist, taxids, taxidlist, negative_gilist,
    negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
    subject_loc| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-seqidlist <String>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-seqidlist <String>
   Restrict search of database to list of SeqIDs
   * Incompatible with:  gilist, taxids, taxidlist, negative_gilist,
    negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
    subject_loc| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-negative_gilist <String>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-negative_gilist <String>
   Restrict search of database to everything except the specified GIs
   * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
    negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
    subject_loc| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-negative_seqidlist <String>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-negative_seqidlist <String>
   Restrict search of database to everything except the specified SeqIDs
   * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
    negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
@@ -151,78 +151,78 @@
   </li>
   <li>
   <li>
-<pre><%= ERB::Util.h %q|-taxids <String>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-taxids <String>
   Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')
   * Incompatible with:  gilist, seqidlist, taxidlist, negative_gilist,
    negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
    subject_loc| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-negative_taxids <String>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-negative_taxids <String>
   Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')
   * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
    negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
    subject_loc| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-taxidlist <String>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-taxidlist <String>
   Restrict search of database to include only the specified taxonomy IDs
   * Incompatible with:  gilist, seqidlist, taxids, negative_gilist,
    negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
    subject_loc| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-negative_taxidlist <String>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-negative_taxidlist <String>
   Restrict search of database to everything except the specified taxonomy IDs
   * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
    negative_gilist, negative_seqidlist, negative_taxids, remote, subject,
    subject_loc| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-entrez_query <String>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-entrez_query <String>
   Restrict search with the given Entrez query
   * Requires:  remote| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-db_soft_mask <String>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-db_soft_mask <String>
   Filtering algorithm ID to apply to the BLAST database as soft masking
   * Incompatible with:  db_hard_mask, subject, subject_loc| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-db_hard_mask <String>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-db_hard_mask <String>
   Filtering algorithm ID to apply to the BLAST database as hard masking
   * Incompatible with:  db_soft_mask, subject, subject_loc| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-qcov_hsp_perc <Real, 0..100>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-qcov_hsp_perc <Real, 0..100>
   Percent query coverage per hsp| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-max_hsps <Integer, >=1>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-max_hsps <Integer, >=1>
   Set maximum number of HSPs per subject sequence to save for each query| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-culling_limit <Integer, >=0>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-culling_limit <Integer, >=0>
   If the query range of a hit is enveloped by that of at least this
   many higher-scoring hits, delete the hit
   * Incompatible with:  best_hit_overhang, best_hit_score_edge| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-best_hit_overhang <Real, (>0 and <0.5)>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-best_hit_overhang <Real, (>0 and <0.5)>
   Best Hit algorithm overhang value (recommended value: 0.1)
   * Incompatible with:  culling_limit| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-best_hit_score_edge <Real, (>0 and <0.5)>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-best_hit_score_edge <Real, (>0 and <0.5)>
   Best Hit algorithm score edge value (recommended value: 0.1)
   * Incompatible with:  culling_limit| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-subject_besthit
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-subject_besthit
   Turn on best hit per subject sequence| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-max_target_seqs <Integer, >=1>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-max_target_seqs <Integer, >=1>
   Maximum number of aligned sequences to keep (value of 5 or more is recommended)
   Default = '500'
   * Incompatible with:  num_descriptions, num_alignments| %></pre>
@@ -231,61 +231,61 @@
 
 <br/>
 
-<h5>Statistical options</h5>
-<ul class="list-unstyled">
+<h5 class="text-lg py-4 font-medium">Statistical options</h5>
+<ul class="list-unstyled space-y-2">
   <li>
-<pre><%= ERB::Util.h %q|-dbsize <Int8>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-dbsize <Int8>
   Effective length of the database| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-searchsp <Int8, >=0>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-searchsp <Int8, >=0>
   Effective length of the search space| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-sum_stats <Boolean>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-sum_stats <Boolean>
   Use sum statistics| %></pre>
   </li>
 </ul>
 
 <br/>
 
-<h5>Search Strategy options</h5>
-<ul class="list-unstyled">
+<h5 class="text-lg py-4 font-medium">Search Strategy options</h5>
+<ul class="list-unstyled space-y-2">
   <li>
-<pre><%= ERB::Util.h %q|-import_search_strategy <File_In>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-import_search_strategy <File_In>
   Search strategy to use
   * Incompatible with:  export_search_strategy| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-export_search_strategy <File_Out>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-export_search_strategy <File_Out>
   File name to record the search strategy used
   * Incompatible with:  import_search_strategy| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-sum_stats <Boolean>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-sum_stats <Boolean>
   Use sum statistics| %></pre>
   </li>
 </ul>
 
 <br/>
 
-<h5>Extension options</h5>
-<ul class="list-unstyled">
+<h5 class="text-lg py-4 font-medium">Extension options</h5>
+<ul class="list-unstyled space-y-2">
   <li>
-<pre><%= ERB::Util.h %q|-xdrop_ungap <Real>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-xdrop_ungap <Real>
   X-dropoff value (in bits) for ungapped extensions| %></pre>
   </li>
   <li>
-<pre><%= ERB::Util.h %q|-window_size <Integer, >=0>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-window_size <Integer, >=0>
   Multiple hits window size, use 0 to specify 1-hit algorithm| %></pre>
   </li>
- 
+
 </ul>
 <br />
-<h5>Miscellaneous options</h5>
-<ul class="list-unstyled">
+<h5 class="text-lg py-4 font-medium">Miscellaneous options</h5>
+<ul class="list-unstyled space-y-2">
   <li>
-<pre><%= ERB::Util.h %q|-parse_deflines <Real>
+<pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-parse_deflines <Real>
   Should the query and subject defline(s) be parsed?| %></pre>
   </li>
 </ul>

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 3.0.1
+  version: 3.1.0
 platform: ruby
 authors:
 - Queen Mary University of London
@@ -9,7 +9,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-02-13 00:00:00.000000000 Z
+date: 2024-06-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: json_pure
@@ -165,20 +165,20 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.15'
+        version: '3.40'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.15.1
+        version: 3.40.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.15'
+        version: '3.40'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.15.1
+        version: 3.40.0
 - !ruby/object:Gem::Dependency
   name: capybara-screenshot
   requirement: !ruby/object:Gem::Requirement
@@ -233,20 +233,20 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.7'
+        version: '3.13'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.7.0
+        version: 3.13.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.7'
+        version: '3.13'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.7.0
+        version: 3.13.0
 - !ruby/object:Gem::Dependency
   name: rubocop
   requirement: !ruby/object:Gem::Requirement
@@ -273,40 +273,40 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 4.15.0
+        version: 4.18.0
     - - ">="
       - !ruby/object:Gem::Version
-        version: 4.15.0
+        version: 4.18.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 4.15.0
+        version: 4.18.0
     - - ">="
       - !ruby/object:Gem::Version
-        version: 4.15.0
+        version: 4.18.1
 - !ruby/object:Gem::Dependency
   name: simplecov
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.17.0
+        version: 0.22.0
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.17.0
+        version: 0.22.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.17.0
+        version: 0.22.0
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.17.0
+        version: 0.22.0
 description: |
   SequenceServer lets you rapidly set up a BLAST+ server with an intuitive
   user interface for use locally or over the web.
@@ -331,6 +331,7 @@ files:
 - lib/sequenceserver/blast/job.rb
 - lib/sequenceserver/blast/query.rb
 - lib/sequenceserver/blast/report.rb
+- lib/sequenceserver/blast/tasks.rb
 - lib/sequenceserver/config.rb
 - lib/sequenceserver/database.rb
 - lib/sequenceserver/doctor.rb
@@ -339,7 +340,6 @@ files:
 - lib/sequenceserver/job_remover.rb
 - lib/sequenceserver/links.rb
 - lib/sequenceserver/logger.rb
-- lib/sequenceserver/makeblastdb-modified-with-cache.rb
 - lib/sequenceserver/makeblastdb.rb
 - lib/sequenceserver/pool.rb
 - lib/sequenceserver/refinements.rb
@@ -351,8 +351,9 @@ files:
 - lib/sequenceserver/version.rb
 - lib/sequenceserver/zip_file_generator.rb
 - public/404.html
-- public/SequenceServer_logo.png
 - public/config.js
+- public/css/app.css
+- public/css/app.min.css
 - public/css/fonts.css
 - public/css/grapher.css
 - public/css/sequenceserver.css
@@ -376,6 +377,7 @@ files:
 - public/js/alignment_exporter.js
 - public/js/circos.js
 - public/js/cloud_share_modal.js
+- public/js/collapse_preferences.js
 - public/js/databases.js
 - public/js/databases_tree.js
 - public/js/dnd.js
@@ -394,8 +396,12 @@ files:
 - public/js/length_distribution.js
 - public/js/mailto.js
 - public/js/null_plugins/download_links.js
+- public/js/null_plugins/grapher/histogram.js
 - public/js/null_plugins/hit_buttons.js
+- public/js/null_plugins/options.js
+- public/js/null_plugins/query_stats.js
 - public/js/null_plugins/report_plugins.js
+- public/js/null_plugins/search_header_plugin.js
 - public/js/options.js
 - public/js/query.js
 - public/js/report.js
@@ -407,12 +413,13 @@ files:
 - public/js/share_url.js
 - public/js/sidebar.js
 - public/js/svgExporter.js
-- public/js/tests/advanced_parameters.spec.js
 - public/js/tests/database.spec.js
+- public/js/tests/form.spec.js
 - public/js/tests/mock_data/databases.json
 - public/js/tests/mock_data/long_response.json
 - public/js/tests/mock_data/sequences.js
 - public/js/tests/mock_data/short_response.json
+- public/js/tests/mocks/circos.js
 - public/js/tests/report.spec.js
 - public/js/tests/search_button.spec.js
 - public/js/tests/search_query.spec.js
@@ -422,6 +429,7 @@ files:
 - public/packages/jquery-ui@1.11.4.js
 - public/sequenceserver-report.min.js
 - public/sequenceserver-search.min.js
+- public/sequenceserver_logo.webp
 - public/vendor/github/components/jquery@2.1.4.js
 - public/vendor/github/components/jquery@2.1.4/README.md
 - public/vendor/github/components/jquery@2.1.4/bower.json
@@ -3496,6 +3504,7 @@ files:
 - views/layout.erb
 - views/report.erb
 - views/search.erb
+- views/search_layout.erb
 - views/tblastn_options.erb
 - views/tblastx_options.erb
 homepage: https://sequenceserver.com
@@ -3530,7 +3539,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.4.10
+rubygems_version: 3.5.6
 signing_key:
 specification_version: 4
 summary: BLAST search made easy!