cagnut_core 0.3.0 → 0.3.1
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- checksums.yaml +4 -4
- data/lib/cagnut/cli/pipeline.rb +2 -0
- data/lib/cagnut/configuration/checks/tools.rb +7 -8
- data/lib/cagnut/configuration.rb +1 -1
- data/lib/cagnut/version.rb +1 -1
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: a3043c0169386288bb33ba28308bc79a662bfb06
|
4
|
+
data.tar.gz: d53e358ea09299895646b483dc43507545ac94a9
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 703c7e9017043a9aebd258a7bc6269135dd9d544de6b6dcbfd32d07b55b670311fe64c149cc26bcabe82ba18452342a251e4391862ac615e351e6dc62f86ed15
|
7
|
+
data.tar.gz: a5a0550a1f044d42a0b8bcf3b2d8395fd75b109b348d6386415dd5e74f355a70f7e16c20b2169394ed29a787f3b79ee2da20e63f450e00241989e352a3f87b53
|
data/lib/cagnut/cli/pipeline.rb
CHANGED
@@ -20,20 +20,24 @@ module Cagnut
|
|
20
20
|
tools = @config['tools']
|
21
21
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refs = @config['refs']
|
22
22
|
puts 'Start Checking...'
|
23
|
-
|
23
|
+
check_execute_system
|
24
24
|
check_ref_fasta refs['ref_fasta']
|
25
25
|
check_java tools['java']
|
26
26
|
check_r tools['R']
|
27
27
|
check_tool tools, refs
|
28
28
|
end
|
29
29
|
|
30
|
+
def check_execute_system
|
31
|
+
puts "Using Local System"
|
32
|
+
end
|
33
|
+
|
30
34
|
def check_tool tools_path, refs=nil
|
31
35
|
end
|
32
36
|
|
33
37
|
def check_tool_ver tool
|
34
38
|
ver = yield if block_given?
|
35
|
-
@check_completed = false if ver.
|
36
|
-
ver = ver.
|
39
|
+
@check_completed = false if ver.blank?
|
40
|
+
ver = ver.blank? ? 'Not Found' : ver.chomp!
|
37
41
|
puts "Using #{tool} (#{ver})"
|
38
42
|
end
|
39
43
|
|
@@ -59,11 +63,6 @@ module Cagnut
|
|
59
63
|
end
|
60
64
|
end
|
61
65
|
|
62
|
-
def check_queueing_system queueing_system
|
63
|
-
system = queueing_system.nil? ? 'Local' : queueing_system['system']
|
64
|
-
puts "Using Queueing System: #{system}"
|
65
|
-
end
|
66
|
-
|
67
66
|
def check_ref_fasta ref_path
|
68
67
|
puts 'Checking Reference Files...'
|
69
68
|
return if File.exist?(ref_path)
|
data/lib/cagnut/configuration.rb
CHANGED
@@ -28,7 +28,7 @@ module Cagnut
|
|
28
28
|
def load_config config_name, options
|
29
29
|
@config ||= check_and_load_yml fetch_system_config_path(options[:config])
|
30
30
|
@params ||= check_and_load_yml fetch_tools_config_path(config_name, options[:params])
|
31
|
-
config_check config_name, options[:
|
31
|
+
config_check config_name, options[:no_check]
|
32
32
|
end
|
33
33
|
|
34
34
|
private
|
data/lib/cagnut/version.rb
CHANGED
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: cagnut_core
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.3.
|
4
|
+
version: 0.3.1
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Shi-Gang Wang
|
@@ -9,7 +9,7 @@ authors:
|
|
9
9
|
autorequire:
|
10
10
|
bindir: exe
|
11
11
|
cert_chain: []
|
12
|
-
date: 2016-11-
|
12
|
+
date: 2016-11-07 00:00:00.000000000 Z
|
13
13
|
dependencies:
|
14
14
|
- !ruby/object:Gem::Dependency
|
15
15
|
name: activesupport
|