bio-sambamba 0.0.4 → 0.0.5
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- data/.travis.yml +8 -7
- data/Gemfile +9 -3
- data/README.md +1 -1
- data/VERSION +1 -1
- metadata +24 -13
data/.travis.yml
CHANGED
@@ -2,11 +2,12 @@ language: ruby
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|
2
2
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rvm:
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3
3
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- 1.9.2
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4
4
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- 1.9.3
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5
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-
- jruby-19mode
|
6
|
-
- rbx-19mode
|
7
|
-
# - 1.8.7
|
8
|
-
# - jruby-18mode # JRuby in 1.8 mode
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9
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-
# - rbx-18mode
|
5
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+
# - jruby-19mode -- the same problems as with BioRuby, related to popen3
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6
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+
# - rbx-19mode -- msgpack extension doesn't work with Rubinius
|
10
7
|
|
11
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-
|
12
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-
|
8
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+
jdk:
|
9
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+
- oraclejdk7
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10
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+
|
11
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+
before_install:
|
12
|
+
- wget https://github.com/downloads/lomereiter/sambamba/sambamba-0.2.6_i386.deb
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13
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+
- sudo dpkg -i sambamba-0.2.6_i386.deb
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data/Gemfile
CHANGED
@@ -1,11 +1,17 @@
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|
1
1
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source "http://rubygems.org"
|
2
2
|
|
3
|
-
gem "bio", "
|
4
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-
|
3
|
+
gem "bio", ">= 1.4.2"
|
4
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+
|
5
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+
if defined?(JRUBY_VERSION)
|
6
|
+
gem "msgpack-jruby", ">= 1.2.0"
|
7
|
+
else
|
8
|
+
gem "msgpack", ">= 0.4.7"
|
9
|
+
end
|
5
10
|
|
6
11
|
group :development do
|
12
|
+
gem "rake"
|
7
13
|
gem "bundler", "~> 1.1.4"
|
8
14
|
gem "jeweler", "~> 1.8.3"
|
9
15
|
gem "rspec", "~> 2.7.0"
|
10
|
-
gem "cucumber", "
|
16
|
+
gem "cucumber", ">= 0"
|
11
17
|
end
|
data/README.md
CHANGED
@@ -14,7 +14,7 @@ Note: this software is under active development!
|
|
14
14
|
rake install
|
15
15
|
```
|
16
16
|
|
17
|
-
In order to use the gem, you also need <code>sambamba</code> tool installed (version >= 0.2.
|
17
|
+
In order to use the gem, you also need <code>sambamba</code> tool installed (version >= 0.2.6).
|
18
18
|
|
19
19
|
If you use Debian, you can download a package for your architecture from
|
20
20
|
[github downloads](http://github.com/lomereiter/sambamba/downloads).
|
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
|
-
0.0.
|
1
|
+
0.0.5
|
metadata
CHANGED
@@ -2,7 +2,7 @@
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|
2
2
|
name: bio-sambamba
|
3
3
|
version: !ruby/object:Gem::Version
|
4
4
|
prerelease:
|
5
|
-
version: 0.0.
|
5
|
+
version: 0.0.5
|
6
6
|
platform: ruby
|
7
7
|
authors:
|
8
8
|
- Artem Tarasov
|
@@ -17,7 +17,7 @@ dependencies:
|
|
17
17
|
requirement: &id001 !ruby/object:Gem::Requirement
|
18
18
|
none: false
|
19
19
|
requirements:
|
20
|
-
- -
|
20
|
+
- - ">="
|
21
21
|
- !ruby/object:Gem::Version
|
22
22
|
version: 1.4.2
|
23
23
|
type: :runtime
|
@@ -28,56 +28,67 @@ dependencies:
|
|
28
28
|
requirement: &id002 !ruby/object:Gem::Requirement
|
29
29
|
none: false
|
30
30
|
requirements:
|
31
|
-
- -
|
31
|
+
- - ">="
|
32
32
|
- !ruby/object:Gem::Version
|
33
33
|
version: 0.4.7
|
34
34
|
type: :runtime
|
35
35
|
prerelease: false
|
36
36
|
version_requirements: *id002
|
37
37
|
- !ruby/object:Gem::Dependency
|
38
|
-
name:
|
38
|
+
name: rake
|
39
39
|
requirement: &id003 !ruby/object:Gem::Requirement
|
40
40
|
none: false
|
41
41
|
requirements:
|
42
|
-
- -
|
42
|
+
- - ">="
|
43
43
|
- !ruby/object:Gem::Version
|
44
|
-
version:
|
44
|
+
version: "0"
|
45
45
|
type: :development
|
46
46
|
prerelease: false
|
47
47
|
version_requirements: *id003
|
48
48
|
- !ruby/object:Gem::Dependency
|
49
|
-
name:
|
49
|
+
name: bundler
|
50
50
|
requirement: &id004 !ruby/object:Gem::Requirement
|
51
51
|
none: false
|
52
52
|
requirements:
|
53
53
|
- - ~>
|
54
54
|
- !ruby/object:Gem::Version
|
55
|
-
version: 1.
|
55
|
+
version: 1.1.4
|
56
56
|
type: :development
|
57
57
|
prerelease: false
|
58
58
|
version_requirements: *id004
|
59
59
|
- !ruby/object:Gem::Dependency
|
60
|
-
name:
|
60
|
+
name: jeweler
|
61
61
|
requirement: &id005 !ruby/object:Gem::Requirement
|
62
62
|
none: false
|
63
63
|
requirements:
|
64
64
|
- - ~>
|
65
65
|
- !ruby/object:Gem::Version
|
66
|
-
version:
|
66
|
+
version: 1.8.3
|
67
67
|
type: :development
|
68
68
|
prerelease: false
|
69
69
|
version_requirements: *id005
|
70
70
|
- !ruby/object:Gem::Dependency
|
71
|
-
name:
|
71
|
+
name: rspec
|
72
72
|
requirement: &id006 !ruby/object:Gem::Requirement
|
73
73
|
none: false
|
74
74
|
requirements:
|
75
75
|
- - ~>
|
76
76
|
- !ruby/object:Gem::Version
|
77
|
-
version:
|
77
|
+
version: 2.7.0
|
78
78
|
type: :development
|
79
79
|
prerelease: false
|
80
80
|
version_requirements: *id006
|
81
|
+
- !ruby/object:Gem::Dependency
|
82
|
+
name: cucumber
|
83
|
+
requirement: &id007 !ruby/object:Gem::Requirement
|
84
|
+
none: false
|
85
|
+
requirements:
|
86
|
+
- - ">="
|
87
|
+
- !ruby/object:Gem::Version
|
88
|
+
version: "0"
|
89
|
+
type: :development
|
90
|
+
prerelease: false
|
91
|
+
version_requirements: *id007
|
81
92
|
description: New Sambamba library comes with a command-line tool for working with SAM/BAM files. This gem brings some of its functionality to Ruby.
|
82
93
|
email: lomereiter@gmail.com
|
83
94
|
executables: []
|
@@ -144,7 +155,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
144
155
|
requirements:
|
145
156
|
- - ">="
|
146
157
|
- !ruby/object:Gem::Version
|
147
|
-
hash: -
|
158
|
+
hash: -4515808283139857040
|
148
159
|
segments:
|
149
160
|
- 0
|
150
161
|
version: "0"
|