ruby-igv 0.0.5 → 0.0.6

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
1
1
  ---
2
2
  SHA256:
3
- metadata.gz: a162dd0aa5d26fd45b3da87eb9c8e4faec6bc47f6922dc850dc5f5f556405c26
4
- data.tar.gz: 6ceb747c0f8b5b697f561c2836c8e021d29fd2bcc0cc5bc91cc7916bc24b0c61
3
+ metadata.gz: e0cb49945b7684826529fbdd82ae84de01c45f3b309f1cf41e096dab651ca261
4
+ data.tar.gz: a345c80a98c564cf7de1cb62768214f8273abf033b1c24ebb8575bb69fe00026
5
5
  SHA512:
6
- metadata.gz: 0e05cd137522d371629790616283c5f2c31f96f9882979d64f46ab83530ccf14569bc039213ddda103653ad009d9818e50f1e95e5f3738cb985903da6d8c6ed2
7
- data.tar.gz: 361d5f9e770f4f78304e4b99672e6e5e2c116bd8994b5d57076b808b40b27ae5fa493c74842923d4165adef2b79827ae85e5d711d9ce279f001afddb0676df95
6
+ metadata.gz: db09a0dc972eb58b3c90412be2a7503015ca3b32152ea2f4be89065833ed94d674fb4bce97a19a5ba8721b59be14b8c8beb00849db865d6b9ee9cfe3ea0afffc
7
+ data.tar.gz: b97c8c53963c3a9460a38c06bde171fd5f9494c7bdbc8b575ded5b17a854b0038ac421da45628f42865d9cecef7824485adc80e92af9281541bac6dc96466102
data/README.md CHANGED
@@ -1,19 +1,22 @@
1
- # Ruby-IGV
1
+ # ruby-igv
2
2
 
3
3
  [![Gem Version](https://badge.fury.io/rb/ruby-igv.svg)](https://badge.fury.io/rb/ruby-igv)
4
4
  [![Docs Latest](https://img.shields.io/badge/docs-latest-blue.svg)](https://rubydoc.info/gems/ruby-igv)
5
5
  [![The MIT License](https://img.shields.io/badge/license-MIT-orange.svg)](LICENSE.txt)
6
-
7
- Controlling [Integrative Genomics Viewer (IGV)](http://software.broadinstitute.org/software/igv/) with the [Ruby](https://github.com/ruby/ruby) language.
6
+ [![DOI](https://zenodo.org/badge/281373245.svg)](https://zenodo.org/badge/latestdoi/281373245)
8
7
 
9
8
  ## Installation
10
9
 
10
+ Requirement: [IGV (Integrative Genomics Viewer)](http://software.broadinstitute.org/software/igv/) and [Ruby](https://github.com/ruby/ruby).
11
+
11
12
  ```ruby
12
13
  gem install ruby-igv
13
14
  ```
14
15
 
15
16
  ## Usage
16
17
 
18
+ [Enable IGV to listen on the port](https://software.broadinstitute.org/software/igv/Preferences#Advanced): Preference > Advanced > Enable port
19
+
17
20
  ```ruby
18
21
  igv = IGV.new
19
22
  igv.genome 'hg19'
@@ -26,7 +29,7 @@ igv.save 'region.jpg' # save to /tmp/r2/region.png
26
29
  igv.send 'echo' # whatever you want
27
30
  ```
28
31
 
29
- * [Controlling IGV through a Port](https://software.broadinstitute.org/software/igv/PortCommands)
32
+ See [the list of Batch commands](https://github.com/igvteam/igv/wiki/Batch-commands).
30
33
 
31
34
  ## Contributing
32
35
 
@@ -35,7 +38,13 @@ igv.send 'echo' # whatever you want
35
38
  * Write, clarify, or fix documentation
36
39
  * Suggest or add new features
37
40
 
38
- # Acknowledgement
41
+ ```
42
+ Do you need commit rights to my repository?
43
+ Do you want to get admin rights and take over the project?
44
+ If so, please feel free to contact me @kojix2.
45
+ ```
46
+
47
+ ## Acknowledgement
39
48
  This gem is strongly inspired by a Python script developed by Brent Pedersen.
40
49
  * [brentp/bio-playground/igv](https://github.com/brentp/bio-playground).
41
50
 
data/lib/igv/version.rb CHANGED
@@ -1,5 +1,5 @@
1
1
  # frozen_string_literal: true
2
2
 
3
3
  class IGV
4
- VERSION = '0.0.5'
4
+ VERSION = '0.0.6'
5
5
  end
data/lib/igv.rb CHANGED
@@ -63,11 +63,11 @@ class IGV
63
63
  send "sort #{option}"
64
64
  end
65
65
 
66
- def expand(_track = '')
66
+ def expand(track = '')
67
67
  send "expand #{track}"
68
68
  end
69
69
 
70
- def collapse(_track = '')
70
+ def collapse(track = '')
71
71
  send "collapse #{track}"
72
72
  end
73
73
 
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: ruby-igv
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.0.5
4
+ version: 0.0.6
5
5
  platform: ruby
6
6
  authors:
7
7
  - kojix2
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2020-12-10 00:00:00.000000000 Z
11
+ date: 2022-08-02 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: bundler
@@ -96,7 +96,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
96
96
  - !ruby/object:Gem::Version
97
97
  version: '0'
98
98
  requirements: []
99
- rubygems_version: 3.1.4
99
+ rubygems_version: 3.3.7
100
100
  signing_key:
101
101
  specification_version: 4
102
102
  summary: Control IGV (Integrative Genomics Viewer) with Ruby.