bio-pipengine 0.8.2 → 0.9.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/bin/pipengine +1 -0
- data/lib/bio/pipengine.rb +21 -0
- metadata +2 -2
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 383594042b8a168b00d40d54e32c5a7a65b80d33
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data.tar.gz: 4fbe9029f9164019773464d76dce673a9a295cc6
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: d808b81a9533dfe6ce2d63df335480dacf73b0b11166abcd7984be75f72867f7a842a7b44fc630190da216ed3a57ac32cbdf9080bcf86cd242956b39a1dbbc77
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7
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data.tar.gz: d0a27bf16ca3feac1f49c75ac7c9a8b06d08097178d32b9d05bd1a67eff6b549a18035ce3bbfa73e43f8ba8affb2a7a7c13ca9f43173a29567afb0b1e97fc259
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data/VERSION
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@@ -1 +1 @@
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1
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-
0.
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1
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0.9.0
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data/bin/pipengine
CHANGED
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@@ -34,6 +34,7 @@ when "run"
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opt :inspect_pipeline, "Show steps", :short => "i", :type => :string
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opt :log, "Log script activities, by default stdin. Options are fluentd", :type => :string, :default => "stdin"
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opt :log_adapter, "(stdin|syslog|fluentd) In case of fluentd use http://destination.hostname:port/yourtag", :type => :string
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opt :tag, "Overwrite tags present in samples.yml and pipeline.yml files (e.g. tag1=value1 tag2=value2)", :type => :strings
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end
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#when "jobs"
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# ARGV.shift
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data/lib/bio/pipengine.rb
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@@ -50,6 +50,24 @@ module Bio
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end
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end
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def self.parse_tag_option(option_tag)
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if !option_tag
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return {}
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else
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tags = {}
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option_tag.each do |tag|
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values = tag.split("=")
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if values.empty?
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@@logger_error.error "\nAbort! Unrecognized values for tag option, please provide the tags as follows: tag1=value1 tag2=value2".red
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exit
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else
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tags.merge! Hash[*values.flatten]
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end
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end
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return tags
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end
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end
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# handle steps that run on multiple samples (i.e. sample groups job)
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def self.check_and_run_multi(samples_file,pipeline,samples_list,options)
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step_multi = options[:steps].map {|s| Bio::Pipengine::Step.new(s,pipeline["steps"][s]).is_multi?}
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@@ -86,8 +104,11 @@ module Bio
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job.local = options[:tmp]
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job.custom_output = options[:output_dir]
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job.custom_name = (options[:name]) ? options[:name] : nil
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# Adding pipeline and samples resources
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job.add_resources pipeline["resources"]
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job.add_resources samples_file["resources"]
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# Adding resource tag from the command line which can overwrite resources defined in the pipeline and samples files
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job.add_resources parse_tag_option(options[:tag])
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#setting the logging system
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job.log = options[:log]
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job.log_adapter = options[:log_adapter]
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metadata
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@@ -1,7 +1,7 @@
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--- !ruby/object:Gem::Specification
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name: bio-pipengine
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version: !ruby/object:Gem::Version
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version: 0.
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version: 0.9.0
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platform: ruby
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authors:
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- Francesco Strozzi
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@@ -9,7 +9,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2016-04-
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date: 2016-04-14 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: trollop
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