RubyGems - sequenceserver - Versions diffs - 2.0.0.rc7 → 2.0.0.rc8 - Mend

sequenceserver 2.0.0.rc7 → 2.0.0.rc8

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data/LICENSE/d3.txt DELETED

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-Copyright (c) 2010-2015, Michael Bostock
-All rights reserved.
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
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-  list of conditions and the following disclaimer.
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-  this list of conditions and the following disclaimer in the documentation
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-OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
-EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

data/README.md DELETED

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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)
-[![build status](https://secure.travis-ci.org/wurmlab/sequenceserver.png?branch=1.0.x)](https://travis-ci.org/wurmlab/sequenceserver)
-[![total downloads](http://ruby-gem-downloads-badge.herokuapp.com/sequenceserver?type=total&color=brightgreen)](http://rubygems.org/gems/sequenceserver)
-[![gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/wurmlab/sequenceserver)
-**Beta version:**
-[![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)
-<!--[![code climate](https://codeclimate.com/github/wurmlab/sequenceserver/badges/gpa.svg)](https://codeclimate.com/github/wurmlab/sequenceserver)-->
-<!--[![coverage](https://codeclimate.com/github/wurmlab/sequenceserver/badges/coverage.svg)](https://codeclimate.com/github/wurmlab/sequenceserver)-->
-<!--[![browser matrix](https://saucelabs.com/browser-matrix/yeban.svg)](https://saucelabs.com/u/yeban)-->
-# SequenceServer - BLAST searching made easy!
-SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for personal or group use.
-If you use SequenceServer, please cite:
-> [Sequenceserver: A modern graphical user interface for custom BLAST
-  databases. Molecular Biology and Evolution
-  (2019).](https://doi.org/10.1093/molbev/msz185)
-## Stable (version 1.0.11)
-- Release date: June 2017
-- Works with BLAST 2.2.30
-### Installation
-For installation instructions and how to use SequenceServer please see
-https://sequenceserver.com/#installation.
-If you want to run SequenceServer directly from source code, please see
-'Develop and contribute' section below.
-## Beta (version 2.0)
-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.
-**Key features**
-* Supports BLAST 2.9.0 and the new v5 BLAST database format
-* Ability to import and visualise XML output from DIAMOND
-   and older versions of BLAST+ (till 2.2.30)
-* Ability to bookmark and share the results page
-* Visualisations for each level of results:
-    - Summary overview of top hits in a circos plot
-    - Length distribution of hits per query
-    - Relative length and position of matching regions for
-      each query-hit pair (Kablammo)
-* Ability to pre-set advanced parameters for different BLAST algorithms
-**Beta to stable**
-1. Fix visual bugs in reports page
-2. Performance optimisation
-3. User reported bug fixes
-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)/
-Development priorities are being coordinated through the following Google Doc: [SequenceServer 2.0 roadmap](https://docs.google.com/document/d/1Vt2MmaD5h5oN8XrmokLVnjUfRLWqKVWeEja3w9SIeBw) (comments welcome)
-### Install and configure
-To get the latest 2.0 (beta) release, run:
-    gem install --pre sequenceserver
-If you are new to the above command, please consult the 'Install or update'
-section on our website http://sequenceserver.com.
-If you want to run SequenceServer beta directly from source code, please see
-'Develop and contribute' section below.
-### Develop and contribute
-To develop and contribute, you will need to run SequenceServer from source.
-#### Run SequenceServer from source code
-You will need [Ruby](https://www.ruby-lang.org/en/) and [RubyGems](https://rubygems.org/):
-    # Install bundler gem to install Ruby dependencies
-    gem install bundler
-    # Move to where you downloaded or cloned seqserv
-    cd sequenceserver
-    # Use bundler to install Ruby dependencies
-    bundle install
-    # Use bundler to run SequenceServer
-    bundle exec bin/sequenceserver
-If you do not plan to develop, you can skip installing development dependencies
-by running `bundle install --without=development`.
-#### Making changes to the code
-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.
-    # Run SequenceServer in development mode
-    bundle exec bin/sequenceserver -D
-You will need [Node and npm](https://nodejs.org/) if you want to modify and build frontend code:
-    # Install frontend dependencies
-    npm install
-    # Build minified JS and CSS bundles
-    npm run-script build
-#### Testing
-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.
-To run a single test (a.k.a, scenario):
-    bundle exec rspec spec/foo_spec.rb -e 'bar'
-To run all tests in a single file:
-    bundle exec rspec spec/foo_spec.rb
-To run all tests:
-    bundle exec rspec spec/**/*spec*
-#### Getting code merged
-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.
-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.
-## Docker builds
-Both the old stable and new beta versions of SequenceServer are available as
-Docker images.
-```
-# With database fasta files inside a folder named db
-docker run --rm -ti -p 4567:4567 -v $(pwd)/db:/db wurmlab/sequenceserver
-```
-This will use the new beta release of SequenceServer. To use the old stable
-release, add the version tag to the command:
-```
-# With database fasta files inside a folder named db
-docker run --rm -ti -p 4567:4567 -v $(pwd)/db:/db wurmlab/sequenceserver:1.0.11
-```
-## Contact
-* Anurag Priyam (architect) - [email](mailto:anurag08priyam@gmail.com) | [@yeban](//twitter.com/yeban)
-* Yannick Wurm  (PI) - [email](mailto:yannickwurm@gmail.com) | [@yannick\_\_](//twitter.com/yannick__)
-* [Mailing list / forum](https://groups.google.com/forum/#!forum/sequenceserver)

data/package.json DELETED

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-{
-  "name": "SequenceServer",
-  "description": "BLAST searching made easy!",
-  "version": "2.0.0-beta",
-  "homepage": "http://www.sequenceserver.com",
-  "repository": "https://github.com/yannickwurm/sequenceserver",
-  "author": {
-    "name": "Anurag Priyam",
-    "email": "anurag08priyam@gmail.com"
-  },
-  "dependencies": {},
-  "devDependencies": {
-    "clean-css": "^3.4.1",
-    "eslint": "^6.5.1",
-    "eslint-plugin-react": "^7.16.0",
-    "jspm": "^0.16.2"
-  },
-  "scripts": {
-    "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"
-  },
-  "jspm": {
-    "directories": {
-      "baseURL": "public",
-      "packages": "public/vendor"
-    },
-    "dependencies": {
-      "bootstrap": "github:twbs/bootstrap@^3.3.5",
-      "d3": "github:mbostock/d3@^3.5.6",
-      "font-awesome": "npm:font-awesome@^4.4.0",
-      "jquery": "github:components/jquery@^2.1.4",
-      "jquery-ui": "github:components/jqueryui@^1.11.4",
-      "nicgirault/circosJs": "github:nicgirault/circosJs@^1.7.0",
-      "react": "npm:react@^0.13.3",
-      "underscore": "npm:underscore@^1.8.3",
-      "webshim": "npm:webshim@^1.15.8"
-    },
-    "devDependencies": {
-      "babel": "npm:babel-core@^5.8.22",
-      "babel-runtime": "npm:babel-runtime@^5.8.20",
-      "core-js": "npm:core-js@^1.1.0"
-    },
-    "overrides": {
-      "npm:webshim@1.15.8": {
-        "main": "js-webshim/minified/polyfiller"
-      }
-    }
-  }
-}

data/public/vendor/.dependencies.json DELETED

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-{
-  "github:nicgirault/circosJs@1.7.0": {},
-  "npm:babel-core@5.8.23": {},
-  "npm:babel-runtime@5.8.20": {
-    "process": "github:jspm/nodelibs-process@^0.1.0"
-  },
-  "npm:core-js@1.1.2": {
-    "process": "github:jspm/nodelibs-process@^0.1.0",
-    "systemjs-json": "github:systemjs/plugin-json@^0.1.0",
-    "fs": "github:jspm/nodelibs-fs@^0.1.0"
-  },
-  "github:jspm/nodelibs-fs@0.1.2": {},
-  "github:systemjs/plugin-json@0.1.0": {},
-  "github:jspm/nodelibs-process@0.1.1": {
-    "process": "npm:process@^0.10.0"
-  },
-  "npm:process@0.10.1": {}
-}

data/public/vendor/.loaderversions DELETED

	@@ -1 +0,0 @@
1	- 0.19.30

data/public/vendor/github/components/jquery@2.1.4/.gitignore DELETED

	@@ -1 +0,0 @@
1	- build

data/public/vendor/github/components/jquery@2.1.4/.jspm-hash DELETED

	@@ -1 +0,0 @@
1	- 7b1d1104656a092423fbfba13c5920e9bbba290c44ca7a5ccba37a3d7d6ab2331f3a6540jspm-github@0.13.10.16

data/public/vendor/github/components/jquery@2.1.4/.jspm.json DELETED

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-{
-  "name": "jquery",
-  "description": "JavaScript library for DOM operations",
-  "version": "2.1.4",
-  "homepage": "http://jquery.com",
-  "author": {
-    "name": "jQuery Foundation and other contributors",
-    "url": "https://github.com/jquery/jquery/blob/master/AUTHORS.txt"
-  },
-  "repository": {
-    "type": "git",
-    "url": "https://github.com/jquery/jquery.git"
-  },
-  "keywords": [
-    "jquery",
-    "javascript",
-    "browser",
-    "library"
-  ],
-  "bugs": {
-    "url": "http://bugs.jquery.com"
-  },
-  "licenses": [
-    {
-      "type": "MIT",
-      "url": "https://github.com/jquery/jquery/blob/master/MIT-LICENSE.txt"
-    }
-  ],
-  "spm": {
-    "main": "jquery.js"
-  },
-  "jspm": {
-    "main": "jquery"
-  },
-  "main": "jquery",
-  "registry": "github"
-}