workflow_manager 0.8.0 → 0.9.0
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- checksums.yaml +4 -4
- data/Gemfile.lock +11 -10
- data/lib/workflow_manager/cluster.rb +11 -9
- data/lib/workflow_manager/server.rb +2 -2
- data/lib/workflow_manager/version.rb +1 -1
- data/start_workflow_manager.sh +3 -2
- metadata +6 -6
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 120bc6b3498d6366882d6274765b9996bf6a66b992067716dd5d34b0d12537d7
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4
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+
data.tar.gz: 84b9d14e46363cc6e8e8d93409cd1edca162da3697e590ea68427a02ee8de9c7
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5
5
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SHA512:
|
6
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-
metadata.gz:
|
7
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-
data.tar.gz:
|
6
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+
metadata.gz: b070889a1ee8d888475c96b40f8ee3b7a42d98654f57507a5bf82536e5936ba56eb9f1ecac632de247d4ea9faf90c1cefa30de5c42bae31f8cb894704399e807
|
7
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+
data.tar.gz: 5ddfb1618cdd7b92908d5d76ce5a3ecd5ef3311ab65d5e50abba49be42c1b313be336d55d34551c47f3125a21e60fe32a3dd533707751d91923bae4b5e4b7d5c
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data/Gemfile.lock
CHANGED
@@ -1,25 +1,26 @@
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1
1
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PATH
|
2
2
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remote: .
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3
3
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specs:
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4
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-
workflow_manager (0.
|
4
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+
workflow_manager (0.8.1)
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5
5
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6
6
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GEM
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7
7
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remote: https://rubygems.org/
|
8
8
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specs:
|
9
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-
concurrent-ruby (1.2.
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10
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-
connection_pool (2.
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11
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-
rack (3.0.
|
12
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-
redis (5.0.
|
13
|
-
redis-client (>= 0.
|
14
|
-
redis-client (0.
|
9
|
+
concurrent-ruby (1.2.3)
|
10
|
+
connection_pool (2.4.1)
|
11
|
+
rack (3.0.9)
|
12
|
+
redis (5.0.8)
|
13
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+
redis-client (>= 0.17.0)
|
14
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+
redis-client (0.19.1)
|
15
15
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connection_pool
|
16
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-
sidekiq (7.
|
16
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+
sidekiq (7.2.1)
|
17
17
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concurrent-ruby (< 2)
|
18
18
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connection_pool (>= 2.3.0)
|
19
19
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rack (>= 2.2.4)
|
20
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-
redis-client (>= 0.
|
20
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+
redis-client (>= 0.19.0)
|
21
21
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|
22
22
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PLATFORMS
|
23
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+
ruby
|
23
24
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x86_64-linux
|
24
25
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|
25
26
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DEPENDENCIES
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@@ -28,4 +29,4 @@ DEPENDENCIES
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|
28
29
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workflow_manager!
|
29
30
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|
30
31
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BUNDLED WITH
|
31
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-
2.
|
32
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+
2.5.5
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@@ -28,7 +28,7 @@ module WorkflowManager
|
|
28
28
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end
|
29
29
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def job_pending?(job_id)
|
30
30
|
end
|
31
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-
def copy_commands(org_dir, dest_parent_dir, now=nil)
|
31
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+
def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
|
32
32
|
end
|
33
33
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def kill_command(job_id)
|
34
34
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end
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@@ -75,7 +75,7 @@ module WorkflowManager
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|
75
75
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result = `#{command}`
|
76
76
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result.to_s.empty? ? false : true
|
77
77
|
end
|
78
|
-
def copy_commands(org_dir, dest_parent_dir, now=nil)
|
78
|
+
def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
|
79
79
|
commands = []
|
80
80
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commands << "mkdir -p #{dest_parent_dir}"
|
81
81
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commands << "cp -r #{org_dir} #{dest_parent_dir}"
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@@ -199,7 +199,7 @@ module WorkflowManager
|
|
199
199
|
end
|
200
200
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qstat_flag
|
201
201
|
end
|
202
|
-
def copy_commands(org_dir, dest_parent_dir, now=nil)
|
202
|
+
def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
|
203
203
|
commands = if now == "force"
|
204
204
|
target_file = File.join(dest_parent_dir, File.basename(org_dir))
|
205
205
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["g-req copynow -f #{org_dir} #{dest_parent_dir}"]
|
@@ -300,7 +300,7 @@ module WorkflowManager
|
|
300
300
|
end
|
301
301
|
|
302
302
|
class FGCZCourseCluster < FGCZCluster
|
303
|
-
def copy_commands(org_dir, dest_parent_dir, now=nil)
|
303
|
+
def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
|
304
304
|
commands = ["cp -r #{org_dir} #{dest_parent_dir}"]
|
305
305
|
end
|
306
306
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def delete_command(target)
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@@ -333,7 +333,7 @@ module WorkflowManager
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|
333
333
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def job_pending?(job_id)
|
334
334
|
# TODO
|
335
335
|
end
|
336
|
-
def copy_commands(org_dir, dest_parent_dir, now=nil)
|
336
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+
def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
|
337
337
|
# TODO
|
338
338
|
end
|
339
339
|
def kill_command(job_id)
|
@@ -411,7 +411,7 @@ module WorkflowManager
|
|
411
411
|
end
|
412
412
|
qstat_flag
|
413
413
|
end
|
414
|
-
def copy_commands(org_dir, dest_parent_dir, now=nil)
|
414
|
+
def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
|
415
415
|
commands = if now == "force"
|
416
416
|
target_file = File.join(dest_parent_dir, File.basename(org_dir))
|
417
417
|
["g-req copynow -f #{org_dir} #{dest_parent_dir}"]
|
@@ -521,14 +521,16 @@ module WorkflowManager
|
|
521
521
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end
|
522
522
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qstat_flag
|
523
523
|
end
|
524
|
-
def copy_commands(org_dir, dest_parent_dir, now=nil)
|
524
|
+
def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
|
525
525
|
commands = if now == "force"
|
526
526
|
target_file = File.join(dest_parent_dir, File.basename(org_dir))
|
527
527
|
["g-req copynow -f #{org_dir} #{dest_parent_dir}"]
|
528
528
|
elsif now
|
529
529
|
["g-req copynow #{org_dir} #{dest_parent_dir}"]
|
530
|
-
|
530
|
+
elsif queue.nil? or queue == "light"
|
531
531
|
["g-req -w copy #{org_dir} #{dest_parent_dir}"]
|
532
|
+
else
|
533
|
+
["g-req -w copy -f heavy #{org_dir} #{dest_parent_dir}"]
|
532
534
|
end
|
533
535
|
end
|
534
536
|
def kill_command(job_id)
|
@@ -546,7 +548,7 @@ module WorkflowManager
|
|
546
548
|
end
|
547
549
|
|
548
550
|
class FGCZDebian10DemoCluster < FGCZDebian10Cluster
|
549
|
-
def copy_commands(org_dir, dest_parent_dir, now=nil)
|
551
|
+
def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
|
550
552
|
commands = ["cp -r #{org_dir} #{dest_parent_dir}"]
|
551
553
|
end
|
552
554
|
def delete_command(target)
|
@@ -202,8 +202,8 @@ module WorkflowManager
|
|
202
202
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def hello
|
203
203
|
'hello hoge hoge bar boo bundle, '+ @cluster.name
|
204
204
|
end
|
205
|
-
def copy_commands(org_dir, dest_parent_dir, now=nil)
|
206
|
-
@cluster.copy_commands(org_dir, dest_parent_dir, now)
|
205
|
+
def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
|
206
|
+
@cluster.copy_commands(org_dir, dest_parent_dir, now, queue)
|
207
207
|
end
|
208
208
|
def kill_job(job_id)
|
209
209
|
status(job_id, 'FAIL')
|
data/start_workflow_manager.sh
CHANGED
@@ -1,7 +1,8 @@
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|
1
1
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#!/usr/bin/bash
|
2
2
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source /usr/local/ngseq/etc/lmod_profile
|
3
|
-
module load Dev/Ruby/3.
|
4
|
-
module load Tools/Redis/7.
|
3
|
+
module load Dev/Ruby/3.2.3
|
4
|
+
module load Tools/Redis/7.2.4
|
5
|
+
. "/usr/local/ngseq/miniconda3/etc/profile.d/conda.sh"
|
5
6
|
conda activate gtools_env
|
6
7
|
which python
|
7
8
|
which g-sub
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
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--- !ruby/object:Gem::Specification
|
2
2
|
name: workflow_manager
|
3
3
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version: !ruby/object:Gem::Version
|
4
|
-
version: 0.
|
4
|
+
version: 0.9.0
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Functional Genomics Center Zurich
|
8
|
-
autorequire:
|
8
|
+
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date:
|
11
|
+
date: 2024-02-06 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: bundler
|
@@ -98,7 +98,7 @@ homepage: ''
|
|
98
98
|
licenses:
|
99
99
|
- MIT
|
100
100
|
metadata: {}
|
101
|
-
post_install_message:
|
101
|
+
post_install_message:
|
102
102
|
rdoc_options: []
|
103
103
|
require_paths:
|
104
104
|
- lib
|
@@ -113,8 +113,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
113
113
|
- !ruby/object:Gem::Version
|
114
114
|
version: '0'
|
115
115
|
requirements: []
|
116
|
-
rubygems_version: 3.
|
117
|
-
signing_key:
|
116
|
+
rubygems_version: 3.5.5
|
117
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+
signing_key:
|
118
118
|
specification_version: 4
|
119
119
|
summary: Workflow Manager manages job submissions using dRuby.
|
120
120
|
test_files:
|