protk 1.2.6.pre3 → 1.2.6.pre4

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 CHANGED
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data/bin/interprophet.rb CHANGED
@@ -12,6 +12,7 @@ require 'protk/command_runner'
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  require 'protk/prophet_tool'
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  require 'protk/galaxy_util'
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14
 
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+ for_galaxy = GalaxyUtil.for_galaxy?
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16
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  # Setup specific command-line options for this tool. Other options are inherited from ProphetTool
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  #
@@ -72,13 +73,13 @@ if ( !Pathname.new(output_file).exist? || prophet_tool.over_write )
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  cmd << " MINPROB=#{prophet_tool.min_prob}" if ( prophet_tool.min_prob !="" )
73
74
 
74
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  inputs = ARGV.collect {|file_name|
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- input_name=file_name.chomp
76
- unless input_name !~/pep\.xml$/
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- input_name = GalaxyStager.new(input_name, :extension => ".pep.xml").staged_path
78
- end
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- input_name
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+ file_name.chomp
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  }
81
78
 
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+ if for_galaxy
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+ inputs = inputs.collect {|ip| GalaxyUtil.stage_pepxml(ip) }
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+ end
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+
82
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  cmd << " #{inputs.join(" ")} #{output_file}"
83
84
 
84
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  genv.log("Running #{cmd}",:info)
@@ -104,6 +104,8 @@ genv=Constants.new
104
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  #
105
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  msgf_bin="#{genv.msgfplusjar}"
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106
 
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+ throw "Could not find MSGFPlus.jar" if (msgf_bin==nil) || (msgf_bin.length==0)
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+
107
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  make_msgfdb_cmd=""
108
110
 
109
111
  case
@@ -12,7 +12,8 @@ require 'protk/command_runner'
12
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  require 'protk/prophet_tool'
13
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  require 'protk/galaxy_util'
14
14
 
15
- galaxy_util = GalaxyUtil.new
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+ for_galaxy = GalaxyUtil.for_galaxy?
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+ input_stager = nil
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17
 
17
18
  # Setup specific command-line options for this tool. Other options are inherited from ProphetTool
18
19
  #
@@ -120,15 +121,15 @@ genv=Constants.new
120
121
 
121
122
 
122
123
  inputs=ARGV.collect { |file_name| file_name.chomp}
123
- if galaxy_util.for_galaxy?
124
- inputs = inputs.collect {|ip| galaxy_util.stage_pepxml(ip) }
124
+ if for_galaxy
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+ inputs = inputs.collect {|ip| GalaxyUtil.stage_pepxml(ip) }
125
126
  end
126
127
 
127
128
  # Interrogate all the input files to obtain the database and search engine from them
128
129
  #
129
130
  genv.log("Determining search engine and database used to create input files ...",:info)
130
131
  file_info={}
131
- ARGV.each {|file_name|
132
+ inputs.each {|file_name|
132
133
  name=file_name.chomp
133
134
 
134
135
  engine=prophet_tool.extract_engine(name)
@@ -167,7 +168,7 @@ end
167
168
 
168
169
  def generate_command(genv,prophet_tool,inputs,output,database,engine)
169
170
 
170
- cmd="#{genv.xinteract} -N#{output} -l7 -eT -D'#{database}' "
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+ cmd="xinteract -N#{output} -l7 -eT -D'#{database}' "
171
172
 
172
173
  if prophet_tool.glyco
173
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  cmd << " -Og "
@@ -15,15 +15,6 @@ require 'protk/galaxy_util'
15
15
 
16
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  for_galaxy = GalaxyUtil.for_galaxy?
17
17
 
18
- if for_galaxy
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- # Stage files for galaxy
20
- original_input_file = ARGV[0]
21
- original_input_path = Pathname.new("#{original_input_file}")
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- input_stager = GalaxyStager.new("#{original_input_file}", :extension => '.pep.xml')
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- ARGV.push("-o")
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- ARGV.push("protein_prophet_results.prot.xml")
25
- end
26
-
27
18
  # Setup specific command-line options for this tool. Other options are inherited from ProphetTool
28
19
  #
29
20
  prophet_tool=ProphetTool.new([:glyco,:explicit_output,:over_write,:prefix_suffix])
@@ -112,12 +103,17 @@ p output_file
112
103
 
113
104
  if ( !Pathname.new(output_file).exist? || prophet_tool.over_write )
114
105
 
115
- cmd="#{genv.proteinprophet} "
106
+ cmd="ProteinProphet "
116
107
 
117
108
  inputs = ARGV.collect {|file_name|
118
109
  file_name.chomp
119
110
  }
120
111
 
112
+ if for_galaxy
113
+ inputs = inputs.collect {|ip| GalaxyUtil.stage_pepxml(ip) }
114
+ end
115
+
116
+
121
117
  cmd << " #{inputs.join(" ")} #{output_file}"
122
118
 
123
119
  if ( prophet_tool.glyco )
@@ -35,7 +35,9 @@ class Constants
35
35
  # This will be used for all constants other than paths
36
36
  #
37
37
  def method_missing(method)
38
- @env[method.to_s]
38
+ from_env = @env[method.to_s]
39
+ throw "#{method} is undefined" unless from_env!=nil
40
+ from_env
39
41
  end
40
42
 
41
43
  # Some constants are paths. They need to be translated into real paths before being returned
@@ -46,137 +48,33 @@ class Constants
46
48
  end
47
49
 
48
50
  def tpp_root
49
- path=@env['tpp_root']
50
- if ( path =~ /^\// )
51
- return path
52
- else
53
- return "#{@protk_dir}/#{@env['tpp_root']}"
54
- end
55
- end
56
-
57
- def xinteract
58
- return "#{self.tpp_root}/bin/xinteract"
59
- end
60
-
61
- def xtandem
62
- return "#{self.tpp_root}/bin/tandem"
63
- end
64
-
65
- def tandem2xml
66
- return "#{self.tpp_root}/bin/Tandem2XML"
67
- end
68
-
69
- def interprophetparser
70
- return "#{self.tpp_root}/bin/InterProphetParser"
71
- end
72
-
73
- def proteinprophet
74
- return "#{self.tpp_root}/bin/ProteinProphet"
75
- end
76
-
77
- def asapratiopeptideparser
78
- return "#{self.tpp_root}/bin/ASAPRatioPeptideParser"
51
+ "#{@protk_dir}/tools/tpp"
79
52
  end
80
53
 
81
- def asapratioproteinparser
82
- return "#{self.tpp_root}/bin/ASAPRatioProteinRatioParser"
83
- end
84
-
85
- def asaprationpvalueparser
86
- return "#{self.tpp_root}/bin/ASAPRatioPvalueParser"
87
- end
88
-
89
- def librapeptideparser
90
- return "#{self.tpp_root}/bin/LibraPeptideParser"
91
- end
92
-
93
- def libraproteinratioparser
94
- return "#{self.tpp_root}/bin/LibraProteinRatioParser"
95
- end
96
-
97
- def xpresspeptideparser
98
- return "#{self.tpp_root}/bin/XPressPeptideParser"
99
- end
100
-
101
- def xpressproteinratioparser
102
- return "#{self.tpp_root}/bin/XPressProteinRatioParser"
103
- end
104
-
105
- def mascot2xml
106
- return "#{self.tpp_root}/bin/Mascot2XML"
107
- end
108
54
 
109
55
  def omssa_root
110
- path=@env['omssa_root']
111
- if ( path =~ /^\// )
112
- return path
113
- else
114
- return "#{@protk_dir}/#{@env['omssa_root']}"
115
- end
116
- end
117
-
118
- def omssacl
119
- return "#{self.omssa_root}/omssacl"
120
- end
121
-
122
- def omssa2pepxml
123
- return "#{self.omssa_root}/omssa2pepXML"
56
+ "#{@protk_dir}/tools/omssa"
124
57
  end
125
58
 
126
59
  def msgfplus_root
127
- path=@env['msgfplus_root']
128
- if ( path =~ /^\// )
129
- return path
130
- else
131
- return "#{@protk_dir}/#{@env['msgfplus_root']}"
132
- end
60
+ "#{@protk_dir}/tools/msgfplus"
133
61
  end
134
62
 
135
63
  def msgfplusjar
136
- return %x[which MSGFPlus.jar]
64
+ msgfplus_path=%x[which MSGFPlus.jar]
65
+ msgfplus_path.chomp
137
66
  end
138
67
 
139
68
  def pwiz_root
140
- path=@env['pwiz_root']
141
- if ( path =~ /^\// )
142
- return path
143
- else
144
- return "#{@protk_dir}/#{@env['pwiz_root']}"
145
- end
146
- end
147
-
148
- def msconvert
149
- return "#{self.pwiz_root}/msconvert"
69
+ return "#{@protk_dir}/tools/pwiz"
150
70
  end
151
71
 
152
72
  def openms_root
153
- path=@env['openms_root']
154
- if ( path =~ /^\//)
155
- return path
156
- else
157
- return "#{@protk_dir}/#{@env['openms_root']}"
158
- end
159
- end
160
-
161
- def featurefinderisotopewavelet
162
- return "#{self.openms_root}/bin/FeatureFinderIsotopeWavelet"
163
- end
164
-
165
- def executepipeline
166
- return "#{self.openms_root}/bin/ExecutePipeline"
73
+ "#{@protk_dir}/tools/openms"
167
74
  end
168
75
 
169
76
  def tandem_root
170
- path=@env['tandem_root']
171
- if ( path =~ /^\//)
172
- return path
173
- else
174
- return "#{@protk_dir}/#{@env['tandem_root']}"
175
- end
176
- end
177
-
178
- def gpmtandem
179
- return "#{self.tandem_root}/bin/tandem"
77
+ "#{@protk_dir}/tools/tandem"
180
78
  end
181
79
 
182
80
  def protein_database_root
@@ -193,20 +91,7 @@ class Constants
193
91
  end
194
92
 
195
93
  def blast_root
196
- path=@env['blast_root']
197
- if ( path =~ /^\// )
198
- return path
199
- else
200
- return "#{@protk_dir}/#{@env['blast_root']}"
201
- end
202
- end
203
-
204
- def makeblastdb
205
- return "makeblastdb"
206
- end
207
-
208
- def searchblastdb
209
- return "#{self.blast_root}/bin/blastdbcmd"
94
+ "#{@protk_dir}/blast"
210
95
  end
211
96
 
212
97
  def log_file
@@ -247,7 +132,7 @@ class Constants
247
132
  @env=default_config_yml
248
133
  end
249
134
 
250
- protk_tool_dirs=["tpp","omssa","openms","msgfplus","blast","pwiz","tandem"]
135
+ protk_tool_dirs=["tpp/bin","omssa","openms/bin","msgfplus","blast/bin","pwiz","tandem/bin"]
251
136
 
252
137
  # Construct the PATH variable by prepending our preferred paths
253
138
  #
@@ -15,8 +15,8 @@ class GalaxyStager
15
15
  @staged_path = "#{@staged_base}#{@extension}"
16
16
  if options[:force_copy]
17
17
  FileUtils.copy(@original_path, @staged_path)
18
- else
19
- File.symlink(@original_path, @staged_path)
18
+ else
19
+ File.symlink(@original_path, @staged_path) unless File.symlink?@staged_path
20
20
  end
21
21
  end
22
22
 
@@ -6,18 +6,14 @@ require 'fileutils'
6
6
 
7
7
  class GalaxyUtil
8
8
 
9
- attr_accessor :for_galaxy
10
- attr_accessor :stagers
11
-
12
- def initialize()
13
- @for_galaxy= ARGV[0]=="--galaxy"
14
- ARGV.shift if @for_galaxy
15
- @stagers=[]
9
+ def self.for_galaxy?
10
+ fg = ARGV[0]=="--galaxy"
11
+ ARGV.shift if fg
12
+ fg
16
13
  end
17
14
 
18
- def stage_pepxml(input_pepxml_path)
15
+ def self.stage_pepxml(input_pepxml_path)
19
16
  stager = GalaxyStager.new(input_pepxml_path, :extension => ".pep.xml")
20
- @stagers << stager
21
17
  stager.staged_path
22
18
  end
23
19
 
@@ -133,10 +133,10 @@ task :perl_locallib => [perl_locallib_installed_file]
133
133
  #
134
134
  # TPP
135
135
  #
136
- tpp_version="4.6.2"
136
+ tpp_version="4.6.3"
137
137
  tpp_packagefile="TPP-#{tpp_version}.tgz"
138
- tpp_installed_file = "#{env.xinteract}"
139
- tpp_url = "https://dl.dropbox.com/u/226794/TPP-4.6.2.tgz"
138
+ tpp_installed_file = "#{env.tpp_root}/bin/xinteract"
139
+ tpp_url = "https://dl.dropbox.com/u/226794/TPP-4.6.3.tgz"
140
140
 
141
141
  tpp_download_file = download_task tpp_url, tpp_packagefile
142
142
 
@@ -198,7 +198,7 @@ def omssa_platform
198
198
  end
199
199
 
200
200
  omssa_packagefile="omssa-#{omssa_platform}.tar.gz"
201
- omssa_installed_file = "#{env.omssacl}"
201
+ omssa_installed_file = "#{env.omssa_root}/omssacl"
202
202
  omssa_url = "ftp://ftp.ncbi.nih.gov/pub/lewisg/omssa/CURRENT/omssa-#{omssa_platform}.tar.gz"
203
203
 
204
204
  download_task omssa_url, omssa_packagefile
@@ -229,7 +229,7 @@ end
229
229
  blast_version="2.2.27+"
230
230
  blast_packagefile="ncbi-blast-#{blast_version}-#{blast_platform}.tar.gz"
231
231
  blast_url="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/#{blast_version.chomp('+')}/#{blast_packagefile}"
232
- blast_installed_file="#{env.makeblastdb}"
232
+ blast_installed_file="#{env.blast_root}/bin/makeblastdb"
233
233
 
234
234
  download_task blast_url, blast_packagefile
235
235
 
@@ -248,10 +248,10 @@ task :blast => blast_installed_file
248
248
  #
249
249
  # MSGFPlus
250
250
  #
251
- msgfplus_version="20130410"
251
+ msgfplus_version="20140210"
252
252
  msgfplus_packagefile="MSGFPlus.#{msgfplus_version}.zip"
253
- msgfplus_url="http://proteomics.ucsd.edu/Downloads/MSGFPlus.#{msgfplus_version}.zip"
254
- msgfplus_installed_file="#{env.msgfplusjar}"
253
+ msgfplus_url="http://proteomics.ucsd.edu/Software/MSGFPlus/MSGFPlus.#{msgfplus_version}.zip"
254
+ msgfplus_installed_file="#{env.msgfplus_root}/MSGFPlus.jar"
255
255
 
256
256
  download_task msgfplus_url, msgfplus_packagefile
257
257
 
@@ -285,7 +285,7 @@ pwiz_version="3_0_4388"
285
285
  pwiz_folder_name="pwiz-bin-#{pwiz_platform}-release-#{pwiz_version}"
286
286
  pwiz_packagefile="#{pwiz_folder_name}.tar.bz2"
287
287
  pwiz_url="https://dl.dropbox.com/u/226794/#{pwiz_packagefile}"
288
- pwiz_installed_file="#{env.idconvert}"
288
+ pwiz_installed_file="#{env.pwiz_root}/idconvert"
289
289
 
290
290
  download_task pwiz_url, pwiz_packagefile
291
291
 
@@ -313,7 +313,7 @@ end
313
313
  openms_version="1.10.0"
314
314
  openms_packagefile="OpenMS-#{openms_version}.tar.gz"
315
315
  openms_url="https://dl.dropbox.com/u/226794/#{openms_packagefile}"
316
- openms_installed_file="#{env.featurefinderisotopewavelet}"
316
+ openms_installed_file="#{env.openms_root}/bin/FileConverter"
317
317
 
318
318
  download_task openms_url, openms_packagefile
319
319
 
@@ -340,10 +340,10 @@ def tandem_platform
340
340
  'linux'
341
341
  end
342
342
 
343
- tandem_version="13-02-01-1"
343
+ tandem_version="13-09-01-1"
344
344
  tandem_packagefile="tandem-#{tandem_platform}-#{tandem_version}.zip"
345
- tandem_url="ftp://ftp.thegpm.org/projects/tandem/source/#{tandem_packagefile}"
346
- tandem_installed_file="#{env.gpmxtandem}"
345
+ tandem_url="https://dl.dropboxusercontent.com/u/226794/galaxy/#{tandem_packagefile}"
346
+ tandem_installed_file="#{env.tandem_root}/bin/tandem.exe"
347
347
 
348
348
  download_task tandem_url, tandem_packagefile
349
349
 
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: protk
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.2.6.pre3
4
+ version: 1.2.6.pre4
5
5
  platform: ruby
6
6
  authors:
7
7
  - Ira Cooke