rbbt-util 5.26.14 → 5.26.15
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- checksums.yaml +4 -4
- data/lib/rbbt/hpc.rb +5 -0
- data/lib/rbbt/util/cmd.rb +8 -0
- data/lib/rbbt/util/misc/omics.rb +9 -3
- data/lib/rbbt/workflow.rb +9 -0
- data/lib/rbbt/workflow/definition.rb +1 -0
- data/test/rbbt/util/test_cmd.rb +3 -0
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 4ca1b6e54187f2a185a4808e193c8a7edf119c727ebd458a43de22c2ce459dbe
|
4
|
+
data.tar.gz: df37635156a96711ac3a17eb92ec342200d37561a24af7c159ef947f3b0b4520
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: d0f65a81a0bb09e76ed0dbb7460a3d3703d4bc4df4f1486ae40fec511b0fb931ea9d35b0db468a2ee8d266af367ca42ed61522c4b04c730b824695ecbf9bfb7c
|
7
|
+
data.tar.gz: 4265b0702cf71164fc828a8cc60c98c032be79734d0aa93f0b694d5698c82d89e599cab0456458aa778a649946e71da151c6a8888fa54ab85732b749b9844beb
|
data/lib/rbbt/hpc.rb
CHANGED
@@ -120,6 +120,11 @@ mkdir -p "$SINGULARITY_RUBY_INLINE"
|
|
120
120
|
# Prepare container dir
|
121
121
|
CONTAINER_DIR="#{contain}"
|
122
122
|
mkdir -p $CONTAINER_DIR/.rbbt/etc/
|
123
|
+
|
124
|
+
for dir in .ruby_inline git scratch home projects; do
|
125
|
+
mkdir -p $CONTAINER_DIR/$dir
|
126
|
+
done
|
127
|
+
|
123
128
|
for tmpd in persist_locks produce_locks R_sockets sensiblewrite sensiblewrite_locks step_info_locks tsv_open_locks; do
|
124
129
|
mkdir -p $CONTAINER_DIR/.rbbt/tmp/$tmpd
|
125
130
|
done
|
data/lib/rbbt/util/cmd.rb
CHANGED
@@ -4,6 +4,14 @@ require 'open3'
|
|
4
4
|
|
5
5
|
module CMD
|
6
6
|
|
7
|
+
def self.gzip_pipe(file)
|
8
|
+
Open.gzip?(file) ? "<(gunzip -c '#{file}')" : "'#{file}'"
|
9
|
+
end
|
10
|
+
|
11
|
+
def self.bash(cmd)
|
12
|
+
%Q(bash <<EOF\n#{cmd}\nEOF\n)
|
13
|
+
end
|
14
|
+
|
7
15
|
def self.process_cmd_options(options = {})
|
8
16
|
string = ""
|
9
17
|
options.each do |option, value|
|
data/lib/rbbt/util/misc/omics.rb
CHANGED
@@ -179,18 +179,24 @@ module Misc
|
|
179
179
|
"-" * (ref.length - m.length)
|
180
180
|
when (ref.length == 1 and m.length == 1)
|
181
181
|
m
|
182
|
+
when (ref == m)
|
183
|
+
nil
|
182
184
|
else
|
183
185
|
if ref == '-'
|
184
186
|
res = '+' + m
|
185
187
|
else
|
186
|
-
|
187
|
-
|
188
|
+
if ref[0] == m[0]
|
189
|
+
res = '+' << m[1..-1]
|
190
|
+
else
|
191
|
+
res = '-' * ref.length
|
192
|
+
res << m unless m == '-'
|
193
|
+
end
|
188
194
|
end
|
189
195
|
Log.debug{"Non-standard annotation: #{[ref, m]} (#{ muts }) => #{ res }"}
|
190
196
|
|
191
197
|
res
|
192
198
|
end
|
193
|
-
end
|
199
|
+
end.compact
|
194
200
|
|
195
201
|
[pos, muts]
|
196
202
|
end
|
data/lib/rbbt/workflow.rb
CHANGED
@@ -213,6 +213,15 @@ module Workflow
|
|
213
213
|
end
|
214
214
|
end
|
215
215
|
|
216
|
+
def import_task(workflow, orig, new)
|
217
|
+
new_task = workflow.tasks[orig].clone
|
218
|
+
new_task.workflow = self
|
219
|
+
new_task.name = new
|
220
|
+
tasks[new] = new_task
|
221
|
+
task_dependencies[new] = workflow.task_dependencies[orig]
|
222
|
+
task_description[new] = workflow.task_description[orig]
|
223
|
+
end
|
224
|
+
|
216
225
|
def workdir=(path)
|
217
226
|
path = Path.setup path.dup unless Path === path
|
218
227
|
@workdir = path
|
@@ -67,6 +67,7 @@ module Workflow
|
|
67
67
|
def dep_task(name, *dependency, &block)
|
68
68
|
dep(*dependency, &block)
|
69
69
|
task name do
|
70
|
+
raise RbbtException, "dependency not found in dep_task" if dependencies.empty?
|
70
71
|
dep = dependencies.last.join
|
71
72
|
set_info :result_type, dep.info[:result_type]
|
72
73
|
forget = config :forget_dep_tasks, :forget_dep_tasks, :default => FORGET_DEP_TASKS
|
data/test/rbbt/util/test_cmd.rb
CHANGED
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: rbbt-util
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 5.26.
|
4
|
+
version: 5.26.15
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2019-05-
|
11
|
+
date: 2019-05-31 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|