sequenceserver 2.0.0.rc3 → 2.0.0.rc8
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- checksums.yaml +4 -4
- data/bin/chromedriver +0 -0
- data/bin/geckodriver +0 -0
- data/bin/sequenceserver +39 -29
- data/lib/sequenceserver.rb +48 -22
- data/lib/sequenceserver/blast/job.rb +11 -1
- data/lib/sequenceserver/database.rb +7 -168
- data/lib/sequenceserver/exceptions.rb +14 -0
- data/lib/sequenceserver/makeblastdb.rb +323 -0
- data/lib/sequenceserver/routes.rb +6 -1
- data/lib/sequenceserver/sequence.rb +1 -1
- data/lib/sequenceserver/version.rb +1 -1
- data/public/css/sequenceserver.css +10 -3
- data/public/css/sequenceserver.min.css +1 -1
- data/public/js/error_modal.js +27 -29
- data/public/js/hit.js +14 -5
- data/public/js/jquery_world.js +1 -1
- data/public/js/query.js +31 -15
- data/public/js/report.js +13 -6
- data/public/js/search.js +44 -24
- data/public/js/sequence_modal.js +10 -5
- data/public/js/sidebar.js +52 -28
- data/public/sequenceserver-report.min.js +17 -17
- data/public/sequenceserver-search.min.js +2 -2
- data/views/layout.erb +5 -1
- data/views/report.erb +1 -1
- data/views/search.erb +1 -1
- metadata +9 -450
- data/.bootstrap/config.json +0 -433
- data/.codeclimate.yml +0 -31
- data/.csslintrc +0 -2
- data/.eslintignore +0 -1
- data/.eslintrc.json +0 -36
- data/.gitignore +0 -56
- data/.mailmap +0 -5
- data/.rspec +0 -3
- data/.rubocop.yml +0 -61
- data/.travis.yml +0 -74
- data/AppImage/recipe.yml +0 -15
- data/AppImage/sequenceserver.desktop +0 -8
- data/AppImage/sequenceserver.png +0 -0
- data/AppImage/sequenceserver.sh +0 -16
- data/Dockerfile +0 -23
- data/LICENSE.txt +0 -661
- data/LICENSE/Apache.txt +0 -176
- data/LICENSE/d3.txt +0 -26
- data/README.md +0 -161
- data/package.json +0 -48
- data/public/vendor/.dependencies.json +0 -18
- data/public/vendor/.loaderversions +0 -1
- data/public/vendor/github/components/jquery@2.1.4/.gitignore +0 -1
- data/public/vendor/github/components/jquery@2.1.4/.jspm-hash +0 -1
- data/public/vendor/github/components/jquery@2.1.4/.jspm.json +0 -37
- data/public/vendor/github/components/jqueryui@1.11.4/.gitignore +0 -4
- data/public/vendor/github/components/jqueryui@1.11.4/.jspm-hash +0 -1
- data/public/vendor/github/components/jqueryui@1.11.4/.jspm.json +0 -136
- data/public/vendor/github/components/jqueryui@1.11.4/ui/.jshintrc +0 -24
- data/public/vendor/github/jspm/nodelibs-buffer@0.1.0/.jspm-hash +0 -1
- data/public/vendor/github/jspm/nodelibs-buffer@0.1.0/.jspm.json +0 -10
- data/public/vendor/github/jspm/nodelibs-events@0.1.1/.jspm-hash +0 -1
- data/public/vendor/github/jspm/nodelibs-events@0.1.1/.jspm.json +0 -10
- data/public/vendor/github/jspm/nodelibs-fs@0.1.2/.jspm-hash +0 -1
- data/public/vendor/github/jspm/nodelibs-module@0.1.0/.jspm-hash +0 -1
- data/public/vendor/github/jspm/nodelibs-module@0.1.0/.jspm.json +0 -3
- data/public/vendor/github/jspm/nodelibs-path@0.1.0/.jspm-hash +0 -1
- data/public/vendor/github/jspm/nodelibs-path@0.1.0/.jspm.json +0 -10
- data/public/vendor/github/jspm/nodelibs-process@0.1.1/.jspm-hash +0 -1
- data/public/vendor/github/jspm/nodelibs-stream@0.1.0/.jspm-hash +0 -1
- data/public/vendor/github/jspm/nodelibs-stream@0.1.0/.jspm.json +0 -10
- data/public/vendor/github/jspm/nodelibs-util@0.1.0/.jspm-hash +0 -1
- data/public/vendor/github/jspm/nodelibs-util@0.1.0/.jspm.json +0 -10
- data/public/vendor/github/mbostock/d3@3.5.6/.jspm-hash +0 -1
- data/public/vendor/github/mbostock/d3@3.5.6/.jspm.json +0 -76
- data/public/vendor/github/nicgirault/circosJs@1.7.0/.gitignore +0 -10
- data/public/vendor/github/nicgirault/circosJs@1.7.0/.jspm-hash +0 -1
- data/public/vendor/github/systemjs/plugin-css@0.1.15/.gitignore +0 -1
- data/public/vendor/github/systemjs/plugin-css@0.1.15/.jspm-hash +0 -1
- data/public/vendor/github/systemjs/plugin-css@0.1.15/.jspm.json +0 -4
- data/public/vendor/github/systemjs/plugin-json@0.1.0/.jspm-hash +0 -1
- data/public/vendor/github/twbs/bootstrap@3.3.5/.jspm-hash +0 -1
- data/public/vendor/github/twbs/bootstrap@3.3.5/.jspm.json +0 -100
- data/public/vendor/npm/amdefine@1.0.0/.jspm-hash +0 -1
- data/public/vendor/npm/amdefine@1.0.0/.jspm.json +0 -55
- data/public/vendor/npm/babel-core@5.8.23/.jspm-hash +0 -1
- data/public/vendor/npm/babel-runtime@5.8.20/.jspm-hash +0 -1
- data/public/vendor/npm/babel-runtime@5.8.20/.npmignore +0 -2
- data/public/vendor/npm/base62@0.1.1/.jspm-hash +0 -1
- data/public/vendor/npm/base62@0.1.1/.jspm.json +0 -49
- data/public/vendor/npm/base62@0.1.1/.travis.yml +0 -4
- data/public/vendor/npm/base64-js@0.0.8/.jspm-hash +0 -1
- data/public/vendor/npm/base64-js@0.0.8/.jspm.json +0 -77
- data/public/vendor/npm/base64-js@0.0.8/.travis.yml +0 -5
- data/public/vendor/npm/buffer@3.4.3/.jspm-hash +0 -1
- data/public/vendor/npm/buffer@3.4.3/.jspm.json +0 -105
- data/public/vendor/npm/buffer@3.4.3/.npmignore +0 -1
- data/public/vendor/npm/buffer@3.4.3/.travis.yml +0 -8
- data/public/vendor/npm/buffer@3.4.3/.zuul.yml +0 -20
- data/public/vendor/npm/core-js@1.1.2/.eslintrc +0 -36
- data/public/vendor/npm/core-js@1.1.2/.gitattributes +0 -1
- data/public/vendor/npm/core-js@1.1.2/.jspm-hash +0 -1
- data/public/vendor/npm/core-js@1.1.2/.npmignore +0 -10
- data/public/vendor/npm/core-js@1.1.2/.travis.yml +0 -3
- data/public/vendor/npm/core-util-is@1.0.1/.jspm-hash +0 -1
- data/public/vendor/npm/core-util-is@1.0.1/.jspm.json +0 -58
- data/public/vendor/npm/envify@3.4.0/.jspm-hash +0 -1
- data/public/vendor/npm/envify@3.4.0/.jspm.json +0 -72
- data/public/vendor/npm/envify@3.4.0/.npmignore +0 -2
- data/public/vendor/npm/esprima-fb@13001.1001.0-dev-harmony-fb/.jspm-hash +0 -1
- data/public/vendor/npm/esprima-fb@13001.1001.0-dev-harmony-fb/.jspm.json +0 -102
- data/public/vendor/npm/events@1.0.2/.jspm-hash +0 -1
- data/public/vendor/npm/events@1.0.2/.jspm.json +0 -67
- data/public/vendor/npm/events@1.0.2/.npmignore +0 -1
- data/public/vendor/npm/events@1.0.2/.travis.yml +0 -7
- data/public/vendor/npm/events@1.0.2/.zuul.yml +0 -12
- data/public/vendor/npm/font-awesome@4.4.0/.jspm-hash +0 -1
- data/public/vendor/npm/font-awesome@4.4.0/.jspm.json +0 -81
- data/public/vendor/npm/font-awesome@4.4.0/.npmignore +0 -42
- data/public/vendor/npm/ieee754@1.1.6/.jspm-hash +0 -1
- data/public/vendor/npm/ieee754@1.1.6/.jspm.json +0 -70
- data/public/vendor/npm/ieee754@1.1.6/.travis.yml +0 -7
- data/public/vendor/npm/ieee754@1.1.6/.zuul.yml +0 -20
- data/public/vendor/npm/inherits@2.0.1/.jspm-hash +0 -1
- data/public/vendor/npm/inherits@2.0.1/.jspm.json +0 -60
- data/public/vendor/npm/is-array@1.0.1/.jepso-ci.json +0 -3
- data/public/vendor/npm/is-array@1.0.1/.jspm-hash +0 -1
- data/public/vendor/npm/is-array@1.0.1/.jspm.json +0 -42
- data/public/vendor/npm/is-array@1.0.1/.npmignore +0 -0
- data/public/vendor/npm/isarray@0.0.1/.jspm-hash +0 -1
- data/public/vendor/npm/isarray@0.0.1/.jspm.json +0 -51
- data/public/vendor/npm/jstransform@10.1.0/.jshintrc +0 -28
- data/public/vendor/npm/jstransform@10.1.0/.jspm-hash +0 -1
- data/public/vendor/npm/jstransform@10.1.0/.jspm.json +0 -95
- data/public/vendor/npm/jstransform@10.1.0/.npmignore +0 -4
- data/public/vendor/npm/jstransform@10.1.0/.travis.yml +0 -8
- data/public/vendor/npm/path-browserify@0.0.0/.jspm-hash +0 -1
- data/public/vendor/npm/path-browserify@0.0.0/.jspm.json +0 -56
- data/public/vendor/npm/process@0.10.1/.jspm-hash +0 -1
- data/public/vendor/npm/react@0.13.3/.jspm-hash +0 -1
- data/public/vendor/npm/react@0.13.3/.jspm.json +0 -77
- data/public/vendor/npm/readable-stream@1.1.13/.jspm-hash +0 -1
- data/public/vendor/npm/readable-stream@1.1.13/.jspm.json +0 -95
- data/public/vendor/npm/readable-stream@1.1.13/.npmignore +0 -5
- data/public/vendor/npm/source-map@0.1.31/.jspm-hash +0 -1
- data/public/vendor/npm/source-map@0.1.31/.jspm.json +0 -133
- data/public/vendor/npm/source-map@0.1.31/.npmignore +0 -2
- data/public/vendor/npm/source-map@0.1.31/.travis.yml +0 -4
- data/public/vendor/npm/stream-browserify@1.0.0/.jspm-hash +0 -1
- data/public/vendor/npm/stream-browserify@1.0.0/.jspm.json +0 -77
- data/public/vendor/npm/stream-browserify@1.0.0/.travis.yml +0 -4
- data/public/vendor/npm/string_decoder@0.10.31/.jspm-hash +0 -1
- data/public/vendor/npm/string_decoder@0.10.31/.jspm.json +0 -58
- data/public/vendor/npm/string_decoder@0.10.31/.npmignore +0 -2
- data/public/vendor/npm/through@2.3.8/.jspm-hash +0 -1
- data/public/vendor/npm/through@2.3.8/.jspm.json +0 -72
- data/public/vendor/npm/through@2.3.8/.travis.yml +0 -5
- data/public/vendor/npm/underscore@1.8.3/.jspm-hash +0 -1
- data/public/vendor/npm/underscore@1.8.3/.jspm.json +0 -74
- data/public/vendor/npm/util@0.10.3/.jspm-hash +0 -1
- data/public/vendor/npm/util@0.10.3/.jspm.json +0 -58
- data/public/vendor/npm/util@0.10.3/.npmignore +0 -1
- data/public/vendor/npm/util@0.10.3/.travis.yml +0 -8
- data/public/vendor/npm/util@0.10.3/.zuul.yml +0 -10
- data/public/vendor/npm/webshim@1.15.8/.gitattributes +0 -12
- data/public/vendor/npm/webshim@1.15.8/.jspm-hash +0 -1
- data/public/vendor/npm/webshim@1.15.8/.jspm.json +0 -92
- data/public/vendor/npm/webshim@1.15.8/.npmignore +0 -16
- data/public/vendor/npm/webshim@1.15.8/.project +0 -12
- data/public/vendor/npm/webshim@1.15.8/demos/demos/filereader/upload/.keep +0 -0
- data/sequenceserver.gemspec +0 -55
- data/spec/blast_versions/blast_2.2.30/blast_2.2.30_spec.rb +0 -228
- data/spec/blast_versions/blast_2.2.30/import_spec_capybara_local_2.2.30.rb +0 -583
- data/spec/blast_versions/blast_2.2.31/blast_2.2.31_spec.rb +0 -228
- data/spec/blast_versions/blast_2.2.31/import_spec_capybara_local_2.2.31.rb +0 -587
- data/spec/blast_versions/blast_2.3.0/blast_2.3.0_spec.rb +0 -229
- data/spec/blast_versions/blast_2.3.0/import_spec_capybara_local_2.3.0.rb +0 -587
- data/spec/blast_versions/blast_2.4.0/blast_2.4.0_spec.rb +0 -228
- data/spec/blast_versions/blast_2.4.0/import_spec_capybara_local_2.4.0.rb +0 -588
- data/spec/blast_versions/blast_2.5.0/blast_2.5.0_spec.rb +0 -228
- data/spec/blast_versions/blast_2.5.0/import_spec_capybara_local_2.5.0.rb +0 -587
- data/spec/blast_versions/blast_2.6.0/blast_2.6.0_spec.rb +0 -228
- data/spec/blast_versions/blast_2.6.0/import_spec_capybara_local_2.6.0.rb +0 -587
- data/spec/blast_versions/blast_2.7.1/blast_2.7.1_spec.rb +0 -228
- data/spec/blast_versions/blast_2.7.1/import_spec_capybara_local_2.7.1.rb +0 -587
- data/spec/blast_versions/blast_2.8.1/blast_2.8.1_spec.rb +0 -228
- data/spec/blast_versions/blast_2.8.1/import_spec_capybara_local_2.8.1.rb +0 -587
- data/spec/blast_versions/blast_2.9.0/blast_2.9.0_spec.rb +0 -228
- data/spec/blast_versions/blast_2.9.0/import_spec_capybara_local_2.9.0.rb +0 -585
- data/spec/blast_versions/diamond_0.9.24/diamond_0.9.24_spec.rb +0 -176
- data/spec/blast_versions/diamond_0.9.24/import_spec_capybara_local_0.9.24.rb +0 -237
- data/spec/capybara_spec.rb +0 -334
- data/spec/config_spec.rb +0 -87
- data/spec/database/funky_ids/funky_ids.fa +0 -16
- data/spec/database/funky_ids/funky_ids.fa.nhd +0 -8
- data/spec/database/funky_ids/funky_ids.fa.nhi +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nhr +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nin +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nog +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nsd +0 -15
- data/spec/database/funky_ids/funky_ids.fa.nsi +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nsq +0 -0
- data/spec/database/funky_sequences/README.md +0 -14
- data/spec/database/funky_sequences/funky_aa_sequences.fa +0 -7
- data/spec/database/funky_sequences/funky_aa_sequences.fa.phd +0 -3
- data/spec/database/funky_sequences/funky_aa_sequences.fa.phi +0 -0
- data/spec/database/funky_sequences/funky_aa_sequences.fa.phr +0 -0
- data/spec/database/funky_sequences/funky_aa_sequences.fa.pin +0 -0
- data/spec/database/funky_sequences/funky_aa_sequences.fa.pog +0 -0
- data/spec/database/funky_sequences/funky_aa_sequences.fa.psd +0 -6
- data/spec/database/funky_sequences/funky_aa_sequences.fa.psi +0 -0
- data/spec/database/funky_sequences/funky_aa_sequences.fa.psq +0 -0
- data/spec/database/funky_sequences/funky_na_sequences.fa +0 -2
- data/spec/database/funky_sequences/funky_na_sequences.fa.nhr +0 -0
- data/spec/database/funky_sequences/funky_na_sequences.fa.nin +0 -0
- data/spec/database/funky_sequences/funky_na_sequences.fa.nog +0 -0
- data/spec/database/funky_sequences/funky_na_sequences.fa.nsd +0 -2
- data/spec/database/funky_sequences/funky_na_sequences.fa.nsi +0 -0
- data/spec/database/funky_sequences/funky_na_sequences.fa.nsq +0 -0
- data/spec/database/ox_parse_error/query.fa +0 -1
- data/spec/database/ox_parse_error/rand1.fa +0 -2
- data/spec/database/ox_parse_error/rand1.fa.nhd +0 -1
- data/spec/database/ox_parse_error/rand1.fa.nhi +0 -0
- data/spec/database/ox_parse_error/rand1.fa.nhr +0 -0
- data/spec/database/ox_parse_error/rand1.fa.nin +0 -0
- data/spec/database/ox_parse_error/rand1.fa.nog +0 -0
- data/spec/database/ox_parse_error/rand1.fa.nsd +0 -2
- data/spec/database/ox_parse_error/rand1.fa.nsi +0 -0
- data/spec/database/ox_parse_error/rand1.fa.nsq +0 -0
- data/spec/database/ox_parse_error/rand2.fa +0 -2
- data/spec/database/ox_parse_error/rand2.fa.nhd +0 -1
- data/spec/database/ox_parse_error/rand2.fa.nhi +0 -0
- data/spec/database/ox_parse_error/rand2.fa.nhr +0 -0
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- data/spec/database/ox_parse_error_unique_ids/query.fa +0 -1
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- data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.txt +0 -8
- data/spec/database/sample/links.rb +0 -23
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta +0 -6449
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phd +0 -1189
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Copyright (c) 2010-2015, Michael Bostock
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this list of conditions and the following disclaimer in the documentation
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* The name Michael Bostock may not be used to endorse or promote products
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL MICHAEL BOSTOCK BE LIABLE FOR ANY DIRECT,
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EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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[![gem version](https://img.shields.io/badge/version-1.0.x%20(old%20stable)-green.svg)](http://rubygems.org/gems/sequenceserver)
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[![build status](https://secure.travis-ci.org/wurmlab/sequenceserver.png?branch=1.0.x)](https://travis-ci.org/wurmlab/sequenceserver)
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[![total downloads](http://ruby-gem-downloads-badge.herokuapp.com/sequenceserver?type=total&color=brightgreen)](http://rubygems.org/gems/sequenceserver)
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[![gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/wurmlab/sequenceserver)
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**Beta version:**
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[![new gem version](https://img.shields.io/badge/version-2.0%20(beta)-yellowgreen.svg)](http://rubygems.org/gems/sequenceserver) **GitHub Master:** [![build status](https://secure.travis-ci.org/wurmlab/sequenceserver.png)](https://travis-ci.org/wurmlab/sequenceserver)
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<!--[![code climate](https://codeclimate.com/github/wurmlab/sequenceserver/badges/gpa.svg)](https://codeclimate.com/github/wurmlab/sequenceserver)-->
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<!--[![coverage](https://codeclimate.com/github/wurmlab/sequenceserver/badges/coverage.svg)](https://codeclimate.com/github/wurmlab/sequenceserver)-->
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<!--[![browser matrix](https://saucelabs.com/browser-matrix/yeban.svg)](https://saucelabs.com/u/yeban)-->
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# SequenceServer - BLAST searching made easy!
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SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for personal or group use.
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If you use SequenceServer, please cite:
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> [Sequenceserver: A modern graphical user interface for custom BLAST
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databases. Molecular Biology and Evolution
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(2019).](https://doi.org/10.1093/molbev/msz185)
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## Stable (version 1.0.11)
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- Release date: June 2017
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- Works with BLAST 2.2.30
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### Installation
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https://sequenceserver.com/#installation.
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'Develop and contribute' section below.
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## Beta (version 2.0)
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We have changed the underlying architecture so that BLAST jobs submisions are asynchronous and so that raw BLAST results are available in the browser in JSON format. Asynchronous job submission facilitates handling of BLAST searches that take a while to compute. For SequenceServer instances running on PCs or fat servers, this means not having to worry about network timeouts when running searches that take more than 5-10 minutes. However, asynchronous job architecture also facilitates hooking SequenceServer to grid engines (e.g., qsub) to run BLAST searches that will take hours or even days. Availability of raw BLAST results (details about each query, hit, and hsps) in the browser in JSON format means that the rich ecosystem of JavaScript visualisation libraries can be used.
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**Key features**
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and older versions of BLAST+ (till 2.2.30)
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* Visualisations for each level of results:
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- Summary overview of top hits in a circos plot
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- Length distribution of hits per query
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- Relative length and position of matching regions for
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each query-hit pair (Kablammo)
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* Ability to pre-set advanced parameters for different BLAST algorithms
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**Beta to stable**
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1. Fix visual bugs in reports page
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The new beta releases are announced on [GitHub release page](https://github.com/wurmlab/sequenceserver/releases) and on [Google Group](https://groups.google.com/forum/#!forum/sequenceserver)/
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Development priorities are being coordinated through the following Google Doc: [SequenceServer 2.0 roadmap](https://docs.google.com/document/d/1Vt2MmaD5h5oN8XrmokLVnjUfRLWqKVWeEja3w9SIeBw) (comments welcome)
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### Install and configure
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To get the latest 2.0 (beta) release, run:
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gem install --pre sequenceserver
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section on our website http://sequenceserver.com.
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'Develop and contribute' section below.
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### Develop and contribute
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To develop and contribute, you will need to run SequenceServer from source.
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#### Run SequenceServer from source code
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# Install bundler gem to install Ruby dependencies
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gem install bundler
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cd sequenceserver
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bundle install
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# Use bundler to run SequenceServer
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bundle exec bin/sequenceserver
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by running `bundle install --without=development`.
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#### Making changes to the code
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During development, you should use `-D` option to run SequenceServer in development mode. In this mode, SequenceServer logs verbosely and uses raw front-end files.
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# Run SequenceServer in development mode
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bundle exec bin/sequenceserver -D
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npm install
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npm run-script build
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#### Testing
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We use RSpec and Capybara for testing. Our test suite covers 95% of the codebase. Running all tests can take considerable time (~2 hrs). We recommend using Travis to automatically run all tests when you push your code to your fork. Tests are also run automatically when you open a pull-request (see Getting code merged section below). Although, it may be desirable sometimes to run a single test, whole file, or all tests locally.
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To run a single test (a.k.a, scenario):
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bundle exec rspec spec/foo_spec.rb
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To run all tests:
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bundle exec rspec spec/**/*spec*
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#### Getting code merged
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Please open a pull-request on GitHub to get code merged. Our test suite and the CodeClimate static code analysis system will be automatically run on your pull-request. These should pass for your code to be merged. If you want to add a new feature to SequenceServer, please also add tests. In addition, code should be `rubocop` and `eslint` compliant, and hard-wrapped to 80 chars per line.
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If you change frontend code (JavaScript and CSS), please build (i.e., minify and compress) and commit the resulting JS and CSS bundles before opening a pull-request. This is because SequenceServer is run in production mode by the test suite.
|
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## Docker builds
|
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Both the old stable and new beta versions of SequenceServer are available as
|
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Docker images.
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```
|
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# With database fasta files inside a folder named db
|
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docker run --rm -ti -p 4567:4567 -v $(pwd)/db:/db wurmlab/sequenceserver
|
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```
|
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This will use the new beta release of SequenceServer. To use the old stable
|
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release, add the version tag to the command:
|
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|
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```
|
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# With database fasta files inside a folder named db
|
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docker run --rm -ti -p 4567:4567 -v $(pwd)/db:/db wurmlab/sequenceserver:1.0.11
|
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```
|
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## Contact
|
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* Anurag Priyam (architect) - [email](mailto:anurag08priyam@gmail.com) | [@yeban](//twitter.com/yeban)
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* Yannick Wurm (PI) - [email](mailto:yannickwurm@gmail.com) | [@yannick\_\_](//twitter.com/yannick__)
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* [Mailing list / forum](https://groups.google.com/forum/#!forum/sequenceserver)
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data/package.json
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{
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"name": "SequenceServer",
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"description": "BLAST searching made easy!",
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"version": "2.0.0-beta",
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"homepage": "http://www.sequenceserver.com",
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"repository": "https://github.com/yannickwurm/sequenceserver",
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"author": {
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"name": "Anurag Priyam",
|
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"email": "anurag08priyam@gmail.com"
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"dependencies": {},
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"devDependencies": {
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"clean-css": "^3.4.1",
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"eslint": "^6.5.1",
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"eslint-plugin-react": "^7.16.0",
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"jspm": "^0.16.2"
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},
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"scripts": {
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"build": "jspm bundle-sfx --minify --skip-source-maps js/search.js public/sequenceserver-search.min.js && jspm bundle-sfx --minify --skip-source-maps js/report.js public/sequenceserver-report.min.js && cleancss public/css/sequenceserver.css > public/css/sequenceserver.min.css"
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},
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"jspm": {
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"baseURL": "public",
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"packages": "public/vendor"
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"dependencies": {
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"bootstrap": "github:twbs/bootstrap@^3.3.5",
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"d3": "github:mbostock/d3@^3.5.6",
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"font-awesome": "npm:font-awesome@^4.4.0",
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"jquery-ui": "github:components/jqueryui@^1.11.4",
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"nicgirault/circosJs": "github:nicgirault/circosJs@^1.7.0",
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"react": "npm:react@^0.13.3",
|
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"underscore": "npm:underscore@^1.8.3",
|
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"webshim": "npm:webshim@^1.15.8"
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},
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"devDependencies": {
|
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"babel": "npm:babel-core@^5.8.22",
|
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"babel-runtime": "npm:babel-runtime@^5.8.20",
|
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"core-js": "npm:core-js@^1.1.0"
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},
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"overrides": {
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"main": "js-webshim/minified/polyfiller"
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@@ -1,18 +0,0 @@
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{
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"github:nicgirault/circosJs@1.7.0": {},
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"npm:babel-core@5.8.23": {},
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"npm:babel-runtime@5.8.20": {
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"process": "github:jspm/nodelibs-process@^0.1.0"
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},
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"process": "github:jspm/nodelibs-process@^0.1.0",
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"systemjs-json": "github:systemjs/plugin-json@^0.1.0",
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"fs": "github:jspm/nodelibs-fs@^0.1.0"
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},
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"github:jspm/nodelibs-fs@0.1.2": {},
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"github:systemjs/plugin-json@0.1.0": {},
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"github:jspm/nodelibs-process@0.1.1": {
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"process": "npm:process@^0.10.0"
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}
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@@ -1 +0,0 @@
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0.19.30
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@@ -1 +0,0 @@
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build
|
@@ -1 +0,0 @@
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1
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7b1d1104656a092423fbfba13c5920e9bbba290c44ca7a5ccba37a3d7d6ab2331f3a6540jspm-github@0.13.10.16
|
@@ -1,37 +0,0 @@
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{
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"name": "jquery",
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"description": "JavaScript library for DOM operations",
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"version": "2.1.4",
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"homepage": "http://jquery.com",
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"author": {
|
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"name": "jQuery Foundation and other contributors",
|
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"url": "https://github.com/jquery/jquery/blob/master/AUTHORS.txt"
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},
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"repository": {
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"type": "git",
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"url": "https://github.com/jquery/jquery.git"
|
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},
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"keywords": [
|
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"jquery",
|
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"browser",
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"bugs": {
|
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"url": "http://bugs.jquery.com"
|
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},
|
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"licenses": [
|
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{
|
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"type": "MIT",
|
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"url": "https://github.com/jquery/jquery/blob/master/MIT-LICENSE.txt"
|
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}
|
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],
|
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"spm": {
|
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"main": "jquery.js"
|
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|
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"jspm": {
|
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"main": "jquery"
|
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},
|
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"main": "jquery",
|
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"registry": "github"
|
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}
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