workflow_manager 0.7.9 → 0.8.1
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- checksums.yaml +4 -4
- data/.gitignore +0 -1
- data/Gemfile.lock +31 -0
- data/config/environments/redis.conf +9 -5
- 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 +5 -4
- metadata +7 -6
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
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---
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2
2
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SHA256:
|
3
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-
metadata.gz:
|
4
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-
data.tar.gz:
|
3
|
+
metadata.gz: 46119a1d4da028cc76b16a56545512607afa923742d982f2b5f1941ce42bacd3
|
4
|
+
data.tar.gz: 922c122276a8e6842017288a643eb4dbe208b4f69907f690d4a8c00adb1649b3
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 1a2e0eea78ab77f45b1b80e558f880ef362c2668cb3d30b67039dc078fd45a27d49401d802c46caeb55352053b25f22a05f7d50d5ff0b6d970e22e8fdd73b043
|
7
|
+
data.tar.gz: ec74fee4bebb6c4014535e228a1c2c6b229a8a7151c540c9fb9853635a207e05a177ec9f8dcce4cf7f5eb331294a6ef1eed213f6893404155d030c4595ada2c9
|
data/.gitignore
CHANGED
data/Gemfile.lock
ADDED
@@ -0,0 +1,31 @@
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1
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+
PATH
|
2
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+
remote: .
|
3
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+
specs:
|
4
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+
workflow_manager (0.8.1)
|
5
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+
|
6
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+
GEM
|
7
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+
remote: https://rubygems.org/
|
8
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+
specs:
|
9
|
+
concurrent-ruby (1.2.2)
|
10
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+
connection_pool (2.4.1)
|
11
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+
rack (3.0.8)
|
12
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+
redis (5.0.6)
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13
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+
redis-client (>= 0.9.0)
|
14
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+
redis-client (0.17.0)
|
15
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+
connection_pool
|
16
|
+
sidekiq (7.1.4)
|
17
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+
concurrent-ruby (< 2)
|
18
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+
connection_pool (>= 2.3.0)
|
19
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+
rack (>= 2.2.4)
|
20
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+
redis-client (>= 0.14.0)
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21
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+
|
22
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+
PLATFORMS
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23
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+
x86_64-linux
|
24
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+
|
25
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+
DEPENDENCIES
|
26
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+
redis
|
27
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+
sidekiq
|
28
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+
workflow_manager!
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29
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+
|
30
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+
BUNDLED WITH
|
31
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+
2.3.26
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@@ -1,9 +1,13 @@
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1
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-
|
2
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-
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1
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+
# example: https://raw.githubusercontent.com/redis/redis/7.0/redis.conf
|
2
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+
# default, for production
|
3
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+
port 6379
|
4
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+
# for test
|
5
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+
#port 6380
|
6
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+
loglevel notice
|
7
|
+
logfile ../logs/redis.log
|
3
8
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databases 5
|
4
|
-
save 300 10
|
9
|
+
save 3600 1 300 10 60 1000
|
5
10
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rdbcompression yes
|
6
|
-
dir ./dbs
|
7
11
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dbfilename redis.rdb
|
12
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+
dir dbs
|
8
13
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maxmemory 10gb
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9
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-
port 6379
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@@ -28,7 +28,7 @@ module WorkflowManager
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|
28
28
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end
|
29
29
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def job_pending?(job_id)
|
30
30
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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
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-
def copy_commands(org_dir, dest_parent_dir, now=nil)
|
78
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+
def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
|
79
79
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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
|
qstat_flag
|
201
201
|
end
|
202
|
-
def copy_commands(org_dir, dest_parent_dir, now=nil)
|
202
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+
def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
|
203
203
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commands = if now == "force"
|
204
204
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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}"]
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@@ -300,7 +300,7 @@ module WorkflowManager
|
|
300
300
|
end
|
301
301
|
|
302
302
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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)
|
@@ -333,7 +333,7 @@ module WorkflowManager
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|
333
333
|
def job_pending?(job_id)
|
334
334
|
# TODO
|
335
335
|
end
|
336
|
-
def copy_commands(org_dir, dest_parent_dir, now=nil)
|
336
|
+
def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
|
337
337
|
# TODO
|
338
338
|
end
|
339
339
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def kill_command(job_id)
|
@@ -411,7 +411,7 @@ module WorkflowManager
|
|
411
411
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end
|
412
412
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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
|
end
|
522
522
|
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
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+
else
|
533
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+
["g-req -w copy -f heavy #{org_dir} #{dest_parent_dir}"]
|
532
534
|
end
|
533
535
|
end
|
534
536
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def kill_command(job_id)
|
@@ -546,7 +548,7 @@ module WorkflowManager
|
|
546
548
|
end
|
547
549
|
|
548
550
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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
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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
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+
@cluster.copy_commands(org_dir, dest_parent_dir, now, queue)
|
207
207
|
end
|
208
208
|
def kill_job(job_id)
|
209
209
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status(job_id, 'FAIL')
|
data/start_workflow_manager.sh
CHANGED
@@ -1,11 +1,12 @@
|
|
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/
|
4
|
-
module load Tools/Redis/
|
5
|
-
conda activate gtools_env
|
3
|
+
module load Dev/Ruby/3.1.3
|
4
|
+
module load Tools/Redis/7.0.8
|
5
|
+
#conda activate gtools_env
|
6
6
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which python
|
7
7
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which g-sub
|
8
8
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which g-req
|
9
9
|
mkdir -p logs
|
10
10
|
mkdir -p dbs
|
11
|
-
bundle exec workflow_manager -d druby://fgcz-h-
|
11
|
+
#bundle exec workflow_manager -d druby://fgcz-h-031:40001
|
12
|
+
bundle exec workflow_manager -d druby://fgcz-h-032:40001
|
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
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+
version: 0.8.1
|
5
5
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platform: ruby
|
6
6
|
authors:
|
7
7
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- Functional Genomics Center Zurich
|
8
|
-
autorequire:
|
8
|
+
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date:
|
11
|
+
date: 2023-12-08 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: bundler
|
@@ -59,6 +59,7 @@ files:
|
|
59
59
|
- ".gitignore"
|
60
60
|
- ".rspec"
|
61
61
|
- Gemfile
|
62
|
+
- Gemfile.lock
|
62
63
|
- LICENSE.txt
|
63
64
|
- README.md
|
64
65
|
- Rakefile
|
@@ -97,7 +98,7 @@ homepage: ''
|
|
97
98
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licenses:
|
98
99
|
- MIT
|
99
100
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metadata: {}
|
100
|
-
post_install_message:
|
101
|
+
post_install_message:
|
101
102
|
rdoc_options: []
|
102
103
|
require_paths:
|
103
104
|
- lib
|
@@ -112,8 +113,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
112
113
|
- !ruby/object:Gem::Version
|
113
114
|
version: '0'
|
114
115
|
requirements: []
|
115
|
-
rubygems_version: 3.
|
116
|
-
signing_key:
|
116
|
+
rubygems_version: 3.3.26
|
117
|
+
signing_key:
|
117
118
|
specification_version: 4
|
118
119
|
summary: Workflow Manager manages job submissions using dRuby.
|
119
120
|
test_files:
|