sushi_fabric 0.7.2 → 0.7.3
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/lib/sushi_fabric/sushiApp.rb +36 -1
- data/lib/sushi_fabric/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: ed4f8e395298758aef808482287e2bf1c5a0bcfe
|
4
|
+
data.tar.gz: d97617cc762c64bf0835cb76a31a6a1dacd51e43
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 6ced57e208f262dd3c0018d5fb2f100961c10fd420a0d23b7330f93a9b6898cd5a2159775b81d313719f92549b0b66e4c22d36aff2a6c7281743d30f28eced28
|
7
|
+
data.tar.gz: d369c6a5bbaebaeff3b7b2522544cec99b5e092e1b9c3f4b6900a398e4be736327d1f90728103e4011f2c05f9b3498af030c003f4f6c8af891785b6549b80091
|
@@ -1,6 +1,6 @@
|
|
1
1
|
#!/usr/bin/env ruby
|
2
2
|
# encoding: utf-8
|
3
|
-
# Version = '
|
3
|
+
# Version = '20170410-034927'
|
4
4
|
|
5
5
|
require 'csv'
|
6
6
|
require 'fileutils'
|
@@ -17,6 +17,7 @@ module SushiFabric
|
|
17
17
|
config.gstore_dir = File.join(default_root, 'public/gstore/projects')
|
18
18
|
config.sushi_app_dir = default_root
|
19
19
|
config.scratch_dir = '/tmp/scratch'
|
20
|
+
config.module_source = nil
|
20
21
|
end
|
21
22
|
|
22
23
|
# load custmized parameters if there is
|
@@ -35,6 +36,7 @@ module SushiFabric
|
|
35
36
|
config.gstore_dir = File.join(#{default_root}, 'public/gstore/projects')
|
36
37
|
config.sushi_app_dir = #{default_root}
|
37
38
|
config.scratch_dir = '/tmp/scratch'
|
39
|
+
config.module_source = nil
|
38
40
|
end
|
39
41
|
end
|
40
42
|
EOF
|
@@ -46,6 +48,7 @@ end
|
|
46
48
|
GSTORE_DIR = config.gstore_dir
|
47
49
|
SUSHI_APP_DIR = config.sushi_app_dir
|
48
50
|
SCRATCH_DIR = config.scratch_dir
|
51
|
+
MODULE_SOURCE = config.module_source
|
49
52
|
|
50
53
|
unless File.exist?(GSTORE_DIR)
|
51
54
|
FileUtils.mkdir_p GSTORE_DIR
|
@@ -192,6 +195,7 @@ class SushiApp
|
|
192
195
|
attr_reader :analysis_category
|
193
196
|
attr_reader :description
|
194
197
|
attr_reader :name
|
198
|
+
attr_reader :modules
|
195
199
|
attr_accessor :dataset_tsv_file
|
196
200
|
attr_accessor :parameterset_tsv_file
|
197
201
|
attr_accessor :dataset_sushi_id
|
@@ -217,6 +221,8 @@ class SushiApp
|
|
217
221
|
@params['process_mode'] = 'SAMPLE'
|
218
222
|
@job_ids = []
|
219
223
|
@required_columns = []
|
224
|
+
@module_source = MODULE_SOURCE
|
225
|
+
@modules = []
|
220
226
|
#@workflow_manager = workflow_manager_instance||DRbObject.new_with_uri(WORKFLOW_MANAGER)
|
221
227
|
end
|
222
228
|
def set_input_dataset
|
@@ -360,6 +366,20 @@ class SushiApp
|
|
360
366
|
FileUtils.mkdir_p(@scratch_result_dir)
|
361
367
|
FileUtils.mkdir_p(@job_script_dir)
|
362
368
|
end
|
369
|
+
def check_latest_module_version(mod)
|
370
|
+
command = "module whatis #{mod}"
|
371
|
+
IO.popen(command) do |io|
|
372
|
+
latest_mod = nil
|
373
|
+
while line = io.gets
|
374
|
+
unless line.chomp.strip.empty?
|
375
|
+
latest_mod = line.split.first
|
376
|
+
break
|
377
|
+
end
|
378
|
+
end
|
379
|
+
end
|
380
|
+
latest_mod = nil if latest_mod == "Failed"
|
381
|
+
latest_mod
|
382
|
+
end
|
363
383
|
def job_header
|
364
384
|
@scratch_dir = if @params['process_mode'] == 'SAMPLE'
|
365
385
|
@scratch_result_dir + "_" + @dataset['Name'] + '_temp$$'
|
@@ -372,6 +392,19 @@ class SushiApp
|
|
372
392
|
else
|
373
393
|
''
|
374
394
|
end
|
395
|
+
module_src_command = if @module_source and @modules and !@modules.empty?
|
396
|
+
"source #{@module_source}"
|
397
|
+
else
|
398
|
+
""
|
399
|
+
end
|
400
|
+
module_add_commands = if @modules and !@modules.empty?
|
401
|
+
#modules_with_version = @modules.map{|mod| check_latest_module_version(mod)}
|
402
|
+
#modules_with_version.compact!
|
403
|
+
#"module add #{modules_with_version.join(' ')}"
|
404
|
+
"module add #{@modules.join(' ')}"
|
405
|
+
else
|
406
|
+
""
|
407
|
+
end
|
375
408
|
@out.print <<-EOF
|
376
409
|
#!/bin/bash
|
377
410
|
#{hold_jid_option}
|
@@ -386,6 +419,8 @@ echo "Job runs on `hostname`"
|
|
386
419
|
echo "at $SCRATCH_DIR"
|
387
420
|
mkdir $SCRATCH_DIR || exit 1
|
388
421
|
cd $SCRATCH_DIR || exit 1
|
422
|
+
#{module_src_command}
|
423
|
+
#{module_add_commands}
|
389
424
|
|
390
425
|
EOF
|
391
426
|
end
|
data/lib/sushi_fabric/version.rb
CHANGED
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: sushi_fabric
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.7.
|
4
|
+
version: 0.7.3
|
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: 2017-
|
11
|
+
date: 2017-04-10 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: bundler
|