cagnut_core 0.3.2 → 0.3.3
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/exe/{stat → stat_lsf_output} +0 -0
- data/lib/cagnut/configuration/checks/datasets.rb +15 -5
- data/lib/cagnut/version.rb +1 -1
- metadata +4 -4
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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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: a6516527142754d04d34191b4358b7a70a9db61d
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4
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data.tar.gz: 3ac9bbf7c0b568d4058fd40027e924d26d773c4f
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 2cac794d277b5b6075ca1df748c82c81ccd0a4c1396e7c30be2274f549af49cb79ce61a39f816ba2a36ef994cda25d693502fd8e4f2b050e550a72762d65a4ad
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7
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+
data.tar.gz: 7d8ffb98f78fd66f8d14ef5697e6c0d2683157160396a27962694e4bf619d5832e19509af0efa50a123287d6166c62028ff798e0d8cf89ab0000b058f4f513ed
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File without changes
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@@ -74,8 +74,10 @@ module Cagnut
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74
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def ln_seq_txt_file sample, qseq_dir
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75
75
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files =
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76
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Dir.glob("#{sample['path']}/*_sequence.txt*") + Dir.glob("#{sample['path']}/*_qseq.txt*")
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-
files
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-
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77
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+
check_file_size files
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files.each do |file|
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next unless file.match sample['name']
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80
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`ln -s #{file} #{qseq_dir} 2>/dev/null`
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end
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end
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@@ -86,19 +88,27 @@ module Cagnut
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end
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def ln_fastq_file sample, flist, fastq_dir
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91
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check_file_size flist
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if %w(ONEFASTQ ONEFASTQSE).include? @config['info']['data_type']
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files_to_much? flist
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file_type = link_name flist, sample['name']
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seq_file = "#{fastq_dir}/#{file_type}"
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`ln -s #{flist[0]} #{seq_file} 2>/dev/null` if flist[0].match sample['name']
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else
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95
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flist.each do |
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96
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-
next unless
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-
`ln -s #{
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flist.each do |file|
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next unless file.match sample['name']
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`ln -s #{file} #{fastq_dir} 2>/dev/null`
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end
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end
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end
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+
def check_file_size flist, previous_size=0
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106
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flist.each do |file|
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file_size = File.size(file)
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abort "#{file} is empty." unless file_size > 0
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end
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end
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def link_name flist, sample_name
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if flist[0].match '.gz'
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104
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"#{sample_name}_sequence.txt.gz"
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data/lib/cagnut/version.rb
CHANGED
metadata
CHANGED
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@@ -1,7 +1,7 @@
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--- !ruby/object:Gem::Specification
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name: cagnut_core
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version: !ruby/object:Gem::Version
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-
version: 0.3.
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version: 0.3.3
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platform: ruby
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authors:
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- Shi-Gang Wang
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@@ -9,7 +9,7 @@ authors:
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autorequire:
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bindir: exe
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cert_chain: []
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-
date: 2016-
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date: 2016-12-12 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: activesupport
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@@ -101,7 +101,7 @@ email:
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- tsechingho@goldenio.com
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executables:
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- cagnut
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-
-
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+
- stat_lsf_output
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extensions: []
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extra_rdoc_files: []
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files:
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@@ -117,7 +117,7 @@ files:
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- bin/setup
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- cagnut_core.gemspec
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- exe/cagnut
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-
- exe/
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+
- exe/stat_lsf_output
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- lib/cagnut.rb
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122
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- lib/cagnut/cli/new_project.rb
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123
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- lib/cagnut/cli/pipeline.rb
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