workflow_manager 0.8.0 → 0.8.1
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- checksums.yaml +4 -4
- data/Gemfile.lock +7 -7
- 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 +2 -2
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: 46119a1d4da028cc76b16a56545512607afa923742d982f2b5f1941ce42bacd3
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4
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+
data.tar.gz: 922c122276a8e6842017288a643eb4dbe208b4f69907f690d4a8c00adb1649b3
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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:
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6
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+
metadata.gz: 1a2e0eea78ab77f45b1b80e558f880ef362c2668cb3d30b67039dc078fd45a27d49401d802c46caeb55352053b25f22a05f7d50d5ff0b6d970e22e8fdd73b043
|
7
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+
data.tar.gz: ec74fee4bebb6c4014535e228a1c2c6b229a8a7151c540c9fb9853635a207e05a177ec9f8dcce4cf7f5eb331294a6ef1eed213f6893404155d030c4595ada2c9
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data/Gemfile.lock
CHANGED
@@ -1,23 +1,23 @@
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|
1
1
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PATH
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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.
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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
|
7
7
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remote: https://rubygems.org/
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8
8
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specs:
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9
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-
concurrent-ruby (1.2.
|
10
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-
connection_pool (2.
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11
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-
rack (3.0.
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9
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+
concurrent-ruby (1.2.2)
|
10
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+
connection_pool (2.4.1)
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11
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+
rack (3.0.8)
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12
12
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redis (5.0.6)
|
13
13
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redis-client (>= 0.9.0)
|
14
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-
redis-client (0.
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14
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+
redis-client (0.17.0)
|
15
15
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connection_pool
|
16
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-
sidekiq (7.
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16
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+
sidekiq (7.1.4)
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17
17
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concurrent-ruby (< 2)
|
18
18
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connection_pool (>= 2.3.0)
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19
19
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rack (>= 2.2.4)
|
20
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-
redis-client (>= 0.
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20
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+
redis-client (>= 0.14.0)
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21
21
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22
22
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PLATFORMS
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23
23
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x86_64-linux
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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")
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32
32
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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
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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
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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
|
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
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|
300
300
|
end
|
301
301
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|
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
|
def delete_command(target)
|
@@ -333,7 +333,7 @@ module WorkflowManager
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|
333
333
|
def job_pending?(job_id)
|
334
334
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# 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
|
def kill_command(job_id)
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@@ -411,7 +411,7 @@ module WorkflowManager
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|
411
411
|
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
|
+
["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
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|
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
|
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
@@ -2,10 +2,11 @@
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|
2
2
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source /usr/local/ngseq/etc/lmod_profile
|
3
3
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module load Dev/Ruby/3.1.3
|
4
4
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module load Tools/Redis/7.0.8
|
5
|
-
conda activate gtools_env
|
5
|
+
#conda activate gtools_env
|
6
6
|
which python
|
7
7
|
which g-sub
|
8
8
|
which g-req
|
9
9
|
mkdir -p logs
|
10
10
|
mkdir -p dbs
|
11
|
-
bundle exec workflow_manager -d druby://fgcz-h-031:40001
|
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
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: workflow_manager
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.8.
|
4
|
+
version: 0.8.1
|
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: 2023-
|
11
|
+
date: 2023-12-08 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: bundler
|