workflow_manager 0.3.8 → 0.3.9
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- checksums.yaml +4 -4
- data/bin/workflow_manager +6 -2
- data/lib/workflow_manager/cluster.rb +6 -1
- data/lib/workflow_manager/version.rb +1 -1
- metadata +3 -3
checksums.yaml
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
---
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|
2
2
|
SHA1:
|
|
3
|
-
metadata.gz:
|
|
4
|
-
data.tar.gz:
|
|
3
|
+
metadata.gz: 18ae8afa0d8c422d163839c81a930793a149361e
|
|
4
|
+
data.tar.gz: 72f450e946fdc603978f710eb520dbb8c41d261a
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|
5
5
|
SHA512:
|
|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: bf583dd83202286eac771eebba6b3263c9a5d17a3a8ea7caeb6e165907623b517560592738647d513a98e9a85b165a6b657746605fff5a28029b5ac61ff3bc71
|
|
7
|
+
data.tar.gz: e4babb61dc0f21012f1bee086e522985b232bf3301b20cfca676c46ebc6fe52675a1339acb6edafe2e2274afa725714e5898f5978695e62478d6c69186010607
|
data/bin/workflow_manager
CHANGED
|
@@ -17,8 +17,12 @@ if opt.mode =~ /[development|production]/
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|
|
17
17
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config = File.join(File.dirname(File.expand_path(__FILE__)), "../config/environments/#{opt.mode}.rb")
|
|
18
18
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opt.mode = nil unless File.exist?(config)
|
|
19
19
|
end
|
|
20
|
-
|
|
21
|
-
|
|
20
|
+
puts "version = #{Version}"
|
|
21
|
+
puts "mode = #{opt.mode}"
|
|
22
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+
ruby_path = File.join(RbConfig.expand("$(bindir)"), "ruby")
|
|
23
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+
puts "ruby = #{ruby_path}"
|
|
24
|
+
gem_path = Gem::path
|
|
25
|
+
puts "GEM_PATH = #{gem_path.join(',')}"
|
|
22
26
|
if opt.mode
|
|
23
27
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config_dir = "./config/environments/"
|
|
24
28
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FileUtils.mkdir_p config_dir
|
|
@@ -92,7 +92,8 @@ module WorkflowManager
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|
|
92
92
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|
|
93
93
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class FGCZCluster < Cluster
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|
94
94
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def submit_job(script_file, script_content, option='')
|
|
95
|
-
if script_name = File.basename(script_file) and script_name =~ /\.sh
|
|
95
|
+
if script_name = File.basename(script_file) and script_name =~ /\.sh/
|
|
96
|
+
script_name = script_name.split(/\.sh/).first + ".sh"
|
|
96
97
|
new_job_script = generate_new_job_script(script_name, script_content)
|
|
97
98
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new_job_script_base = File.basename(new_job_script)
|
|
98
99
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log_file = File.join(@log_dir, new_job_script_base + "_o.log")
|
|
@@ -101,6 +102,10 @@ module WorkflowManager
|
|
|
101
102
|
job_id = `#{command}`
|
|
102
103
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job_id = job_id.match(/Your job (\d+) \(/)[1]
|
|
103
104
|
[job_id, log_file, command]
|
|
105
|
+
else
|
|
106
|
+
err_msg = "FGCZCluster#submit_job, ERROR: script_name is not *.sh: #{File.basename(script_file)}"
|
|
107
|
+
warn err_msg
|
|
108
|
+
raise err_msg
|
|
104
109
|
end
|
|
105
110
|
end
|
|
106
111
|
def job_running?(job_id)
|
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: workflow_manager
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.3.
|
|
4
|
+
version: 0.3.9
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Functional Genomics Center Zurich
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date:
|
|
11
|
+
date: 2018-03-01 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: bundler
|
|
@@ -102,7 +102,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
|
102
102
|
version: '0'
|
|
103
103
|
requirements: []
|
|
104
104
|
rubyforge_project:
|
|
105
|
-
rubygems_version: 2.
|
|
105
|
+
rubygems_version: 2.6.14
|
|
106
106
|
signing_key:
|
|
107
107
|
specification_version: 4
|
|
108
108
|
summary: Workflow Manager manages job submissions using dRuby.
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