ruby-igv 0.0.5 → 0.0.6

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Files changed (5) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +14 -5
  3. data/lib/igv/version.rb +1 -1
  4. data/lib/igv.rb +2 -2
  5. metadata +3 -3
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data/README.md CHANGED
@@ -1,19 +1,22 @@
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- # Ruby-IGV
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+ # ruby-igv
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  [![Gem Version](https://badge.fury.io/rb/ruby-igv.svg)](https://badge.fury.io/rb/ruby-igv)
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  [![Docs Latest](https://img.shields.io/badge/docs-latest-blue.svg)](https://rubydoc.info/gems/ruby-igv)
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  [![The MIT License](https://img.shields.io/badge/license-MIT-orange.svg)](LICENSE.txt)
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-
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- Controlling [Integrative Genomics Viewer (IGV)](http://software.broadinstitute.org/software/igv/) with the [Ruby](https://github.com/ruby/ruby) language.
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+ [![DOI](https://zenodo.org/badge/281373245.svg)](https://zenodo.org/badge/latestdoi/281373245)
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  ## Installation
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+ Requirement: [IGV (Integrative Genomics Viewer)](http://software.broadinstitute.org/software/igv/) and [Ruby](https://github.com/ruby/ruby).
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+
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  ```ruby
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  gem install ruby-igv
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  ```
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  ## Usage
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+ [Enable IGV to listen on the port](https://software.broadinstitute.org/software/igv/Preferences#Advanced): Preference > Advanced > Enable port
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+
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  ```ruby
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  igv = IGV.new
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  igv.genome 'hg19'
@@ -26,7 +29,7 @@ igv.save 'region.jpg' # save to /tmp/r2/region.png
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  igv.send 'echo' # whatever you want
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  ```
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- * [Controlling IGV through a Port](https://software.broadinstitute.org/software/igv/PortCommands)
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+ See [the list of Batch commands](https://github.com/igvteam/igv/wiki/Batch-commands).
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  ## Contributing
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@@ -35,7 +38,13 @@ igv.send 'echo' # whatever you want
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  * Write, clarify, or fix documentation
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  * Suggest or add new features
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- # Acknowledgement
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+ ```
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+ Do you need commit rights to my repository?
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+ Do you want to get admin rights and take over the project?
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+ If so, please feel free to contact me @kojix2.
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+ ```
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+
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+ ## Acknowledgement
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  This gem is strongly inspired by a Python script developed by Brent Pedersen.
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  * [brentp/bio-playground/igv](https://github.com/brentp/bio-playground).
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data/lib/igv/version.rb CHANGED
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  # frozen_string_literal: true
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  class IGV
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- VERSION = '0.0.5'
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+ VERSION = '0.0.6'
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  end
data/lib/igv.rb CHANGED
@@ -63,11 +63,11 @@ class IGV
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  send "sort #{option}"
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  end
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- def expand(_track = '')
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+ def expand(track = '')
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  send "expand #{track}"
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  end
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- def collapse(_track = '')
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+ def collapse(track = '')
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  send "collapse #{track}"
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  end
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metadata CHANGED
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  --- !ruby/object:Gem::Specification
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  name: ruby-igv
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  version: !ruby/object:Gem::Version
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- version: 0.0.5
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+ version: 0.0.6
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  platform: ruby
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  authors:
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  - kojix2
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2020-12-10 00:00:00.000000000 Z
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+ date: 2022-08-02 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bundler
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  - !ruby/object:Gem::Version
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  version: '0'
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  requirements: []
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- rubygems_version: 3.1.4
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+ rubygems_version: 3.3.7
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  signing_key:
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  specification_version: 4
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  summary: Control IGV (Integrative Genomics Viewer) with Ruby.