protk 1.1.11 → 1.1.12
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- data/lib/protk/constants.rb +11 -0
- data/lib/protk/setup_rakefile.rake +2 -2
- metadata +1 -1
data/lib/protk/constants.rb
CHANGED
@@ -232,6 +232,16 @@ class Constants
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232
232
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else
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233
233
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@env=default_config_yml
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234
234
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end
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235
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+
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236
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+
protk_roots = ["tpp","omssa","blast","pwiz","msgfplus","openms"]
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237
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+
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238
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+
protk_roots.each do |r|
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239
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+
env_value = ENV["PROTK_#{r.upcase}_ROOT"]
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240
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+
if ( env_value!=nil)
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241
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+
p "Using #{r} root #{env_value}"
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242
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+
@env["#{r}_root"]=env_value
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243
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+
end
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244
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+
end
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235
245
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236
246
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throw "No data found in config file" unless @env!=nil
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237
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@info_level=default_config_yml['message_level']
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@@ -240,6 +250,7 @@ class Constants
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240
250
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241
251
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end
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242
252
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253
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+
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243
254
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def update_user_config(dict)
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244
255
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user_config_yml = YAML.load_file "#{self.protk_dir}/config.yml" if File.exist? "#{self.protk_dir}/config.yml"
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245
256
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@@ -274,7 +274,7 @@ def platform_bunzip
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274
274
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'bunzip2'
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275
275
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end
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276
276
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277
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-
pwiz_version="
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277
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+
pwiz_version="3_0_4388"
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278
278
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pwiz_packagefile="pwiz-bin-#{pwiz_platform}-release-#{pwiz_version}.tar.bz2"
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279
279
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pwiz_url="https://dl.dropbox.com/u/226794/#{pwiz_packagefile}"
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280
280
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pwiz_installed_file="#{env.idconvert}"
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@@ -286,7 +286,7 @@ file pwiz_installed_file => [@build_dir,"#{@download_dir}/#{pwiz_packagefile}"]
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286
286
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sh %{cd #{@build_dir}; #{platform_bunzip} -f #{pwiz_packagefile}}
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287
287
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sh %{cd #{@build_dir}; tar -xvf #{pwiz_packagefile.chomp('.bz2')}}
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288
288
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sh %{mkdir -p #{env.pwiz_root}}
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289
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-
sh %{cd #{@build_dir}; cp idconvert msconvert #{env.pwiz_root}/}
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289
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+
sh %{cd #{@build_dir}; cp chainsaw idconvert msaccess mscat msdiff msistats peakaboo pepsum txt2mzml idcat msbenchmark msconvert msdir mspicture pepcat sldout unimod_2.xsd license #{env.pwiz_root}/}
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290
290
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end
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291
291
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292
292
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task :pwiz => pwiz_installed_file
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