MARQ 0.0.1

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  1. data/LICENSE +20 -0
  2. data/R/CustomDS.R +80 -0
  3. data/R/GEO.R +249 -0
  4. data/R/MA.R +359 -0
  5. data/README.rdoc +29 -0
  6. data/bin/marq_config +170 -0
  7. data/install_scripts/CustomDS/Rakefile +223 -0
  8. data/install_scripts/GEO/Rakefile +258 -0
  9. data/install_scripts/GEO/platforms/GPL100.yaml +7 -0
  10. data/install_scripts/GEO/platforms/GPL1002.yaml +7 -0
  11. data/install_scripts/GEO/platforms/GPL1007.yaml +7 -0
  12. data/install_scripts/GEO/platforms/GPL101.yaml +7 -0
  13. data/install_scripts/GEO/platforms/GPL1010.yaml +7 -0
  14. data/install_scripts/GEO/platforms/GPL1073.yaml +7 -0
  15. data/install_scripts/GEO/platforms/GPL1074.yaml +4 -0
  16. data/install_scripts/GEO/platforms/GPL1090.yaml +7 -0
  17. data/install_scripts/GEO/platforms/GPL1104.yaml +7 -0
  18. data/install_scripts/GEO/platforms/GPL118.yaml +7 -0
  19. data/install_scripts/GEO/platforms/GPL1205.yaml +4 -0
  20. data/install_scripts/GEO/platforms/GPL1211.yaml +7 -0
  21. data/install_scripts/GEO/platforms/GPL1213.yaml +7 -0
  22. data/install_scripts/GEO/platforms/GPL1219.yaml +4 -0
  23. data/install_scripts/GEO/platforms/GPL1223.yaml +7 -0
  24. data/install_scripts/GEO/platforms/GPL1226.yaml +7 -0
  25. data/install_scripts/GEO/platforms/GPL1229.yaml +7 -0
  26. data/install_scripts/GEO/platforms/GPL1230.yaml +7 -0
  27. data/install_scripts/GEO/platforms/GPL1231.yaml +7 -0
  28. data/install_scripts/GEO/platforms/GPL1232.yaml +7 -0
  29. data/install_scripts/GEO/platforms/GPL1260.yaml +4 -0
  30. data/install_scripts/GEO/platforms/GPL1261.yaml +4 -0
  31. data/install_scripts/GEO/platforms/GPL127.yaml +4 -0
  32. data/install_scripts/GEO/platforms/GPL128.yaml +7 -0
  33. data/install_scripts/GEO/platforms/GPL1290.yaml +7 -0
  34. data/install_scripts/GEO/platforms/GPL1292.yaml +7 -0
  35. data/install_scripts/GEO/platforms/GPL1293.yaml +7 -0
  36. data/install_scripts/GEO/platforms/GPL1294.yaml +7 -0
  37. data/install_scripts/GEO/platforms/GPL1295.yaml +7 -0
  38. data/install_scripts/GEO/platforms/GPL13.yaml +4 -0
  39. data/install_scripts/GEO/platforms/GPL1310.yaml +7 -0
  40. data/install_scripts/GEO/platforms/GPL1313.yaml +7 -0
  41. data/install_scripts/GEO/platforms/GPL1323.yaml +7 -0
  42. data/install_scripts/GEO/platforms/GPL1331.yaml +7 -0
  43. data/install_scripts/GEO/platforms/GPL1352.yaml +4 -0
  44. data/install_scripts/GEO/platforms/GPL1355.yaml +4 -0
  45. data/install_scripts/GEO/platforms/GPL1382.yaml +7 -0
  46. data/install_scripts/GEO/platforms/GPL1387.yaml +7 -0
  47. data/install_scripts/GEO/platforms/GPL1397.yaml +4 -0
  48. data/install_scripts/GEO/platforms/GPL14.yaml +7 -0
  49. data/install_scripts/GEO/platforms/GPL1412.yaml +7 -0
  50. data/install_scripts/GEO/platforms/GPL1415.yaml +7 -0
  51. data/install_scripts/GEO/platforms/GPL1420.yaml +7 -0
  52. data/install_scripts/GEO/platforms/GPL144.yaml +7 -0
  53. data/install_scripts/GEO/platforms/GPL1449.yaml +7 -0
  54. data/install_scripts/GEO/platforms/GPL1458.yaml +7 -0
  55. data/install_scripts/GEO/platforms/GPL1523.yaml +7 -0
  56. data/install_scripts/GEO/platforms/GPL1524.yaml +7 -0
  57. data/install_scripts/GEO/platforms/GPL1528.yaml +7 -0
  58. data/install_scripts/GEO/platforms/GPL153.yaml +7 -0
  59. data/install_scripts/GEO/platforms/GPL1530.yaml +7 -0
  60. data/install_scripts/GEO/platforms/GPL1535.yaml +4 -0
  61. data/install_scripts/GEO/platforms/GPL155.yaml +7 -0
  62. data/install_scripts/GEO/platforms/GPL163.yaml +7 -0
  63. data/install_scripts/GEO/platforms/GPL168.yaml +7 -0
  64. data/install_scripts/GEO/platforms/GPL169.yaml +7 -0
  65. data/install_scripts/GEO/platforms/GPL1704.yaml +4 -0
  66. data/install_scripts/GEO/platforms/GPL1708.yaml +7 -0
  67. data/install_scripts/GEO/platforms/GPL1739.yaml +7 -0
  68. data/install_scripts/GEO/platforms/GPL1740.yaml +4 -0
  69. data/install_scripts/GEO/platforms/GPL1749.yaml +7 -0
  70. data/install_scripts/GEO/platforms/GPL177.yaml +7 -0
  71. data/install_scripts/GEO/platforms/GPL1790.yaml +7 -0
  72. data/install_scripts/GEO/platforms/GPL1792.yaml +7 -0
  73. data/install_scripts/GEO/platforms/GPL181.yaml +7 -0
  74. data/install_scripts/GEO/platforms/GPL1818.yaml +7 -0
  75. data/install_scripts/GEO/platforms/GPL1820.yaml +4 -0
  76. data/install_scripts/GEO/platforms/GPL1823.yaml +7 -0
  77. data/install_scripts/GEO/platforms/GPL1826.yaml +7 -0
  78. data/install_scripts/GEO/platforms/GPL183.yaml +7 -0
  79. data/install_scripts/GEO/platforms/GPL1831.yaml +7 -0
  80. data/install_scripts/GEO/platforms/GPL1833.yaml +7 -0
  81. data/install_scripts/GEO/platforms/GPL1872.yaml +4 -0
  82. data/install_scripts/GEO/platforms/GPL1911.yaml +7 -0
  83. data/install_scripts/GEO/platforms/GPL1914.yaml +4 -0
  84. data/install_scripts/GEO/platforms/GPL1928.yaml +7 -0
  85. data/install_scripts/GEO/platforms/GPL1942.yaml +7 -0
  86. data/install_scripts/GEO/platforms/GPL1945.yaml +7 -0
  87. data/install_scripts/GEO/platforms/GPL1964.yaml +7 -0
  88. data/install_scripts/GEO/platforms/GPL198.yaml +4 -0
  89. data/install_scripts/GEO/platforms/GPL1981.yaml +4 -0
  90. data/install_scripts/GEO/platforms/GPL200.yaml +7 -0
  91. data/install_scripts/GEO/platforms/GPL2006.yaml +7 -0
  92. data/install_scripts/GEO/platforms/GPL201.yaml +4 -0
  93. data/install_scripts/GEO/platforms/GPL2011.yaml +7 -0
  94. data/install_scripts/GEO/platforms/GPL2026.yaml +7 -0
  95. data/install_scripts/GEO/platforms/GPL205.yaml +7 -0
  96. data/install_scripts/GEO/platforms/GPL207.yaml +7 -0
  97. data/install_scripts/GEO/platforms/GPL2136.yaml +7 -0
  98. data/install_scripts/GEO/platforms/GPL220.yaml +7 -0
  99. data/install_scripts/GEO/platforms/GPL226.yaml +7 -0
  100. data/install_scripts/GEO/platforms/GPL24.yaml +4 -0
  101. data/install_scripts/GEO/platforms/GPL246.yaml +4 -0
  102. data/install_scripts/GEO/platforms/GPL247.yaml +7 -0
  103. data/install_scripts/GEO/platforms/GPL2507.yaml +4 -0
  104. data/install_scripts/GEO/platforms/GPL2529.yaml +4 -0
  105. data/install_scripts/GEO/platforms/GPL2531.yaml +7 -0
  106. data/install_scripts/GEO/platforms/GPL254.yaml +7 -0
  107. data/install_scripts/GEO/platforms/GPL2569.yaml +7 -0
  108. data/install_scripts/GEO/platforms/GPL257.yaml +7 -0
  109. data/install_scripts/GEO/platforms/GPL2598.yaml +7 -0
  110. data/install_scripts/GEO/platforms/GPL260.yaml +7 -0
  111. data/install_scripts/GEO/platforms/GPL2614.yaml +4 -0
  112. data/install_scripts/GEO/platforms/GPL2622.yaml +7 -0
  113. data/install_scripts/GEO/platforms/GPL2623.yaml +7 -0
  114. data/install_scripts/GEO/platforms/GPL2660.yaml +7 -0
  115. data/install_scripts/GEO/platforms/GPL2670.yaml +7 -0
  116. data/install_scripts/GEO/platforms/GPL2677.yaml +7 -0
  117. data/install_scripts/GEO/platforms/GPL2700.yaml +4 -0
  118. data/install_scripts/GEO/platforms/GPL2721.yaml +7 -0
  119. data/install_scripts/GEO/platforms/GPL2727.yaml +7 -0
  120. data/install_scripts/GEO/platforms/GPL273.yaml +7 -0
  121. data/install_scripts/GEO/platforms/GPL2763.yaml +7 -0
  122. data/install_scripts/GEO/platforms/GPL2824.yaml +7 -0
  123. data/install_scripts/GEO/platforms/GPL284.yaml +7 -0
  124. data/install_scripts/GEO/platforms/GPL287.yaml +4 -0
  125. data/install_scripts/GEO/platforms/GPL2872.yaml +7 -0
  126. data/install_scripts/GEO/platforms/GPL288.yaml +4 -0
  127. data/install_scripts/GEO/platforms/GPL2883.yaml +7 -0
  128. data/install_scripts/GEO/platforms/GPL289.yaml +4 -0
  129. data/install_scripts/GEO/platforms/GPL2895.yaml +4 -0
  130. data/install_scripts/GEO/platforms/GPL2897.yaml +7 -0
  131. data/install_scripts/GEO/platforms/GPL2902.yaml +7 -0
  132. data/install_scripts/GEO/platforms/GPL2987.yaml +4 -0
  133. data/install_scripts/GEO/platforms/GPL2995.yaml +7 -0
  134. data/install_scripts/GEO/platforms/GPL3039.yaml +4 -0
  135. data/install_scripts/GEO/platforms/GPL3050.yaml +7 -0
  136. data/install_scripts/GEO/platforms/GPL3084.yaml +7 -0
  137. data/install_scripts/GEO/platforms/GPL3113.yaml +7 -0
  138. data/install_scripts/GEO/platforms/GPL317.yaml +7 -0
  139. data/install_scripts/GEO/platforms/GPL319.yaml +7 -0
  140. data/install_scripts/GEO/platforms/GPL32.yaml +4 -0
  141. data/install_scripts/GEO/platforms/GPL3222.yaml +7 -0
  142. data/install_scripts/GEO/platforms/GPL3295.yaml +7 -0
  143. data/install_scripts/GEO/platforms/GPL3305.yaml +4 -0
  144. data/install_scripts/GEO/platforms/GPL3306.yaml +7 -0
  145. data/install_scripts/GEO/platforms/GPL3307.yaml +7 -0
  146. data/install_scripts/GEO/platforms/GPL333.yaml +4 -0
  147. data/install_scripts/GEO/platforms/GPL3341.yaml +7 -0
  148. data/install_scripts/GEO/platforms/GPL3349.yaml +7 -0
  149. data/install_scripts/GEO/platforms/GPL339.yaml +4 -0
  150. data/install_scripts/GEO/platforms/GPL340.yaml +4 -0
  151. data/install_scripts/GEO/platforms/GPL3408.yaml +7 -0
  152. data/install_scripts/GEO/platforms/GPL341.yaml +4 -0
  153. data/install_scripts/GEO/platforms/GPL3415.yaml +4 -0
  154. data/install_scripts/GEO/platforms/GPL3423.yaml +7 -0
  155. data/install_scripts/GEO/platforms/GPL3440.yaml +7 -0
  156. data/install_scripts/GEO/platforms/GPL3457.yaml +4 -0
  157. data/install_scripts/GEO/platforms/GPL3504.yaml +4 -0
  158. data/install_scripts/GEO/platforms/GPL3506.yaml +4 -0
  159. data/install_scripts/GEO/platforms/GPL355.yaml +7 -0
  160. data/install_scripts/GEO/platforms/GPL3558.yaml +7 -0
  161. data/install_scripts/GEO/platforms/GPL3607.yaml +7 -0
  162. data/install_scripts/GEO/platforms/GPL368.yaml +4 -0
  163. data/install_scripts/GEO/platforms/GPL3695.yaml +7 -0
  164. data/install_scripts/GEO/platforms/GPL371.yaml +7 -0
  165. data/install_scripts/GEO/platforms/GPL3834.yaml +4 -0
  166. data/install_scripts/GEO/platforms/GPL4006.yaml +7 -0
  167. data/install_scripts/GEO/platforms/GPL4055.yaml +7 -0
  168. data/install_scripts/GEO/platforms/GPL409.yaml +7 -0
  169. data/install_scripts/GEO/platforms/GPL4191.yaml +7 -0
  170. data/install_scripts/GEO/platforms/GPL4226.yaml +7 -0
  171. data/install_scripts/GEO/platforms/GPL4371.yaml +7 -0
  172. data/install_scripts/GEO/platforms/GPL4567.yaml +4 -0
  173. data/install_scripts/GEO/platforms/GPL4685.yaml +4 -0
  174. data/install_scripts/GEO/platforms/GPL483.yaml +7 -0
  175. data/install_scripts/GEO/platforms/GPL49.yaml +7 -0
  176. data/install_scripts/GEO/platforms/GPL50.yaml +7 -0
  177. data/install_scripts/GEO/platforms/GPL500.yaml +7 -0
  178. data/install_scripts/GEO/platforms/GPL507.yaml +4 -0
  179. data/install_scripts/GEO/platforms/GPL51.yaml +7 -0
  180. data/install_scripts/GEO/platforms/GPL513.yaml +7 -0
  181. data/install_scripts/GEO/platforms/GPL519.yaml +7 -0
  182. data/install_scripts/GEO/platforms/GPL52.yaml +7 -0
  183. data/install_scripts/GEO/platforms/GPL529.yaml +7 -0
  184. data/install_scripts/GEO/platforms/GPL53.yaml +7 -0
  185. data/install_scripts/GEO/platforms/GPL5356.yaml +7 -0
  186. data/install_scripts/GEO/platforms/GPL538.yaml +7 -0
  187. data/install_scripts/GEO/platforms/GPL54.yaml +7 -0
  188. data/install_scripts/GEO/platforms/GPL543.yaml +7 -0
  189. data/install_scripts/GEO/platforms/GPL544.yaml +7 -0
  190. data/install_scripts/GEO/platforms/GPL545.yaml +7 -0
  191. data/install_scripts/GEO/platforms/GPL546.yaml +7 -0
  192. data/install_scripts/GEO/platforms/GPL547.yaml +7 -0
  193. data/install_scripts/GEO/platforms/GPL549.yaml +7 -0
  194. data/install_scripts/GEO/platforms/GPL550.yaml +4 -0
  195. data/install_scripts/GEO/platforms/GPL56.yaml +7 -0
  196. data/install_scripts/GEO/platforms/GPL560.yaml +4 -0
  197. data/install_scripts/GEO/platforms/GPL564.yaml +7 -0
  198. data/install_scripts/GEO/platforms/GPL57.yaml +7 -0
  199. data/install_scripts/GEO/platforms/GPL570.yaml +4 -0
  200. data/install_scripts/GEO/platforms/GPL571.yaml +4 -0
  201. data/install_scripts/GEO/platforms/GPL576.yaml +7 -0
  202. data/install_scripts/GEO/platforms/GPL58.yaml +7 -0
  203. data/install_scripts/GEO/platforms/GPL5823.yaml +4 -0
  204. data/install_scripts/GEO/platforms/GPL59.yaml +7 -0
  205. data/install_scripts/GEO/platforms/GPL5915.yaml +4 -0
  206. data/install_scripts/GEO/platforms/GPL5947.yaml +7 -0
  207. data/install_scripts/GEO/platforms/GPL61.yaml +7 -0
  208. data/install_scripts/GEO/platforms/GPL64.yaml +7 -0
  209. data/install_scripts/GEO/platforms/GPL6419.yaml +7 -0
  210. data/install_scripts/GEO/platforms/GPL6424.yaml +7 -0
  211. data/install_scripts/GEO/platforms/GPL65.yaml +7 -0
  212. data/install_scripts/GEO/platforms/GPL6574.yaml +4 -0
  213. data/install_scripts/GEO/platforms/GPL6649.yaml +4 -0
  214. data/install_scripts/GEO/platforms/GPL67.yaml +7 -0
  215. data/install_scripts/GEO/platforms/GPL6720.yaml +7 -0
  216. data/install_scripts/GEO/platforms/GPL7054.yaml +4 -0
  217. data/install_scripts/GEO/platforms/GPL737.yaml +7 -0
  218. data/install_scripts/GEO/platforms/GPL738.yaml +7 -0
  219. data/install_scripts/GEO/platforms/GPL74.yaml +4 -0
  220. data/install_scripts/GEO/platforms/GPL75.yaml +4 -0
  221. data/install_scripts/GEO/platforms/GPL76.yaml +4 -0
  222. data/install_scripts/GEO/platforms/GPL764.yaml +7 -0
  223. data/install_scripts/GEO/platforms/GPL772.yaml +7 -0
  224. data/install_scripts/GEO/platforms/GPL782.yaml +7 -0
  225. data/install_scripts/GEO/platforms/GPL783.yaml +7 -0
  226. data/install_scripts/GEO/platforms/GPL784.yaml +7 -0
  227. data/install_scripts/GEO/platforms/GPL80.yaml +4 -0
  228. data/install_scripts/GEO/platforms/GPL81.yaml +4 -0
  229. data/install_scripts/GEO/platforms/GPL82.yaml +4 -0
  230. data/install_scripts/GEO/platforms/GPL83.yaml +4 -0
  231. data/install_scripts/GEO/platforms/GPL85.yaml +4 -0
  232. data/install_scripts/GEO/platforms/GPL86.yaml +4 -0
  233. data/install_scripts/GEO/platforms/GPL87.yaml +4 -0
  234. data/install_scripts/GEO/platforms/GPL870.yaml +7 -0
  235. data/install_scripts/GEO/platforms/GPL875.yaml +7 -0
  236. data/install_scripts/GEO/platforms/GPL884.yaml +7 -0
  237. data/install_scripts/GEO/platforms/GPL887.yaml +7 -0
  238. data/install_scripts/GEO/platforms/GPL89.yaml +4 -0
  239. data/install_scripts/GEO/platforms/GPL890.yaml +7 -0
  240. data/install_scripts/GEO/platforms/GPL891.yaml +7 -0
  241. data/install_scripts/GEO/platforms/GPL90.yaml +7 -0
  242. data/install_scripts/GEO/platforms/GPL91.yaml +4 -0
  243. data/install_scripts/GEO/platforms/GPL92.yaml +4 -0
  244. data/install_scripts/GEO/platforms/GPL920.yaml +7 -0
  245. data/install_scripts/GEO/platforms/GPL922.yaml +7 -0
  246. data/install_scripts/GEO/platforms/GPL924.yaml +7 -0
  247. data/install_scripts/GEO/platforms/GPL93.yaml +4 -0
  248. data/install_scripts/GEO/platforms/GPL96.yaml +4 -0
  249. data/install_scripts/GEO/platforms/GPL968.yaml +4 -0
  250. data/install_scripts/GEO/platforms/GPL97.yaml +4 -0
  251. data/install_scripts/GEO/platforms/GPL98.yaml +7 -0
  252. data/install_scripts/GEO/platforms/GPL981.yaml +7 -0
  253. data/install_scripts/GEO/platforms/GPL99.yaml +7 -0
  254. data/install_scripts/GEO/platforms/GPL999.yaml +7 -0
  255. data/install_scripts/GEO/series/GSE10018.yaml +61 -0
  256. data/install_scripts/GEO/series/GSE1002.yaml +135 -0
  257. data/install_scripts/GEO/series/GSE10066.yaml +31 -0
  258. data/install_scripts/GEO/series/GSE10073.yaml +19 -0
  259. data/install_scripts/GEO/series/GSE10091.yaml +15 -0
  260. data/install_scripts/GEO/series/GSE101.yaml +17 -0
  261. data/install_scripts/GEO/series/GSE10100.yaml +15 -0
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  267. data/install_scripts/GEO/series/GSE103.yaml +19 -0
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  270. data/install_scripts/GEO/series/GSE10521.yaml +56 -0
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  272. data/install_scripts/GEO/series/GSE1073.yaml +127 -0
  273. data/install_scripts/GEO/series/GSE10860.yaml +25 -0
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  300. data/install_scripts/GEO/series/GSE12104.yaml +10 -0
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  302. data/install_scripts/GEO/series/GSE12150.yaml +32 -0
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  305. data/install_scripts/GEO/series/GSE1365.yaml +14 -0
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  307. data/install_scripts/GEO/series/GSE1492.yaml +15 -0
  308. data/install_scripts/GEO/series/GSE15222.yaml +731 -0
  309. data/install_scripts/GEO/series/GSE1553.yaml +23 -0
  310. data/install_scripts/GEO/series/GSE1617.yaml +39 -0
  311. data/install_scripts/GEO/series/GSE1688.yaml +36 -0
  312. data/install_scripts/GEO/series/GSE1693.yaml +60 -0
  313. data/install_scripts/GEO/series/GSE1752.yaml +32 -0
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  319. data/install_scripts/GEO/series/GSE1763.yaml +19 -0
  320. data/install_scripts/GEO/series/GSE1915.yaml +39 -0
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@@ -0,0 +1,150 @@
1
+ require "rubygems"
2
+ require "rubygems/source_index"
3
+ require "rubygems/dependency_installer"
4
+ require "rubygems/uninstaller"
5
+ require "fileutils"
6
+ require File.join(File.dirname(__FILE__), "utils")
7
+ require File.join(File.dirname(__FILE__), "gem_ext")
8
+ require File.join(File.dirname(__FILE__), "ops")
9
+
10
+ $INSTALLING = []
11
+
12
+ module Merb
13
+
14
+ class Gem < Thor
15
+ extend ColorfulMessages
16
+
17
+ def initialize
18
+ dirs = [Dir.pwd, File.dirname(__FILE__) / ".."]
19
+ root = dirs.find {|d| File.file?(d / "config" / "dependencies.rb")}
20
+
21
+ if root
22
+ @depsrb = root / "config" / "dependencies.rb"
23
+ else
24
+ self.class.error "dependencies.rb was not found"
25
+ exit!
26
+ end
27
+
28
+ FileUtils.mkdir_p(Dir.pwd / "gems")
29
+
30
+ @list = Collector.collect(File.read(@depsrb))
31
+ @idx = ::Gem::SourceIndex.new.load_gems_in("gems/specifications")
32
+ end
33
+
34
+ def list
35
+ require "pp"
36
+ pp @list
37
+ end
38
+
39
+ desc "redeploy", "Syncs up gems/cache with gems/gems. All gems in the cache " \
40
+ "that are not already installed will be installed from the " \
41
+ "cache. All installed gems that are not in the cache will " \
42
+ "be uninstalled."
43
+ def redeploy
44
+ gem_dir = Dir.pwd / "gems" / "gems"
45
+ cache_dir = Dir.pwd / "gems" / "cache"
46
+
47
+ gems = Dir[gem_dir / "*"].map! {|n| File.basename(n)}
48
+ cache = Dir[cache_dir / "*.gem"].map! {|n| File.basename(n, ".gem")}
49
+ new_gems = cache - gems
50
+ outdated = gems - cache
51
+ idx = ::Gem::SourceIndex.new
52
+ idx.load_gems_in(Dir.pwd / "gems" / "specifications")
53
+
54
+ new_gems.each do |g|
55
+ installer = ::Gem::Installer.new(cache_dir / "#{g}.gem",
56
+ :bin_dir => Dir.pwd / "bin",
57
+ :install_dir => Dir.pwd / "gems",
58
+ :ignore_dependencies => true,
59
+ :user_install => false,
60
+ :wrappers => true,
61
+ :source_index => idx)
62
+
63
+ installer.install
64
+ end
65
+
66
+ outdated.each do |g|
67
+ /(.*)\-(.*)/ =~ g
68
+ name, version = $1, $2
69
+ uninstaller = ::Gem::Uninstaller.new(name,
70
+ :version => version,
71
+ :bin_dir => Dir.pwd / "bin",
72
+ :install_dir => Dir.pwd / "gems",
73
+ :ignore => true,
74
+ :executables => true
75
+ )
76
+ uninstaller.uninstall
77
+ end
78
+ end
79
+
80
+ desc "confirm", "Confirm the current setup. merb:gem:install will " \
81
+ "automatically run this task before committing the " \
82
+ "changes it makes."
83
+ def confirm(gems = @list)
84
+ ::Gem.path.replace([Dir.pwd / "gems"])
85
+ ::Gem.source_index.load_gems_in(Dir.pwd / "gems" / "specifications")
86
+
87
+ self.class.info "Confirming configuration..."
88
+
89
+ ::Gem.loaded_specs.clear
90
+
91
+ begin
92
+ gems.each do |name, versions|
93
+ versions ||= []
94
+ ::Gem.activate name, *versions
95
+ end
96
+ rescue ::Gem::LoadError => e
97
+ self.class.error "Configuration could not be confirmed: #{e.message}"
98
+ self.class.rollback_trans
99
+ end
100
+ self.class.info "Confirmed"
101
+ end
102
+
103
+ desc 'install', 'Sync up your bundled gems with the list in config/dependencies.rb'
104
+ def install(*gems)
105
+ if gems.empty?
106
+ gems = @list
107
+ else
108
+ gems = gems.map {|desc| name, *versions = desc.split(" ") }
109
+ end
110
+
111
+ $GEMS = gems
112
+
113
+ self.class.begin_trans
114
+
115
+ gems.each do |name, versions|
116
+ dep = ::Gem::Dependency.new(name, versions || [])
117
+ unless @idx.search(dep).empty?
118
+ next
119
+ end
120
+
121
+ rescue_failures do
122
+ $INSTALLING = dep
123
+ _install(dep)
124
+ end
125
+ end
126
+
127
+ gem_dir = Dir.pwd / "gems" / "gems"
128
+ installed_gems = Dir[gem_dir / "*"].map! {|n| File.basename(n)}
129
+
130
+ list = full_list.map {|x| x.full_name}.compact
131
+
132
+ (installed_gems - list).each do |g|
133
+ /^(.*)\-(.*)$/ =~ g
134
+ name, version = $1, $2
135
+ uninstaller = ::Gem::Uninstaller.new(name,
136
+ :version => version,
137
+ :bin_dir => (Dir.pwd / "bin").to_s,
138
+ :install_dir => (Dir.pwd / "gems").to_s,
139
+ :ignore => true,
140
+ :executables => true
141
+ )
142
+ uninstaller.uninstall
143
+ end
144
+
145
+ confirm(gems)
146
+
147
+ self.class.commit_trans
148
+ end
149
+ end
150
+ end
@@ -0,0 +1,93 @@
1
+ module Thor::Tasks
2
+ module Merb
3
+ class Collector
4
+ attr_reader :dependencies
5
+
6
+ def self.collect(str)
7
+ collector = new
8
+ collector.instance_eval(str)
9
+ collector.dependencies
10
+ end
11
+
12
+ def initialize
13
+ @dependencies = []
14
+ end
15
+
16
+ def dependency(name, *versions)
17
+ versions.pop if versions.last.is_a?(Hash)
18
+ @dependencies << [name, versions]
19
+ end
20
+ end
21
+
22
+ class Gem < Thor
23
+ def full_list
24
+ @idx.load_gems_in("gems/specifications")
25
+
26
+ @list.map do |name, versions|
27
+ dep = ::Gem::Dependency.new(name, versions)
28
+ spec = @idx.search(dep).last
29
+ unless spec
30
+ self.class.error "A required dependency #{dep} was not found"
31
+ self.class.rollback_trans
32
+ end
33
+ deps = spec.recursive_dependencies(dep, @idx)
34
+ [spec] + deps
35
+ end.flatten.uniq
36
+ end
37
+
38
+ def rescue_failures(error = StandardError, prc = nil)
39
+ begin
40
+ yield
41
+ rescue error => e
42
+ if prc
43
+ prc.call(e)
44
+ else
45
+ puts e.message
46
+ puts e.backtrace
47
+ end
48
+ self.class.rollback_trans
49
+ end
50
+ end
51
+
52
+ def self.begin_trans
53
+ note "Beginning transaction"
54
+ FileUtils.cp_r(Dir.pwd / "gems", Dir.pwd / ".original_gems")
55
+ end
56
+
57
+ def self.commit_trans
58
+ note "Committing transaction"
59
+ FileUtils.rm_rf(Dir.pwd / ".original_gems")
60
+ end
61
+
62
+ def self.rollback_trans
63
+ if File.exist?(Dir.pwd / ".original_gems")
64
+ note "Rolling back transaction"
65
+ FileUtils.rm_rf(Dir.pwd / "gems")
66
+ FileUtils.mv(Dir.pwd / ".original_gems", Dir.pwd / "gems")
67
+ end
68
+ exit!
69
+ end
70
+
71
+ private
72
+ def _install(dep)
73
+ @idx.load_gems_in("gems/specifications")
74
+ return if @idx.search(dep).last
75
+
76
+ installer = ::Gem::DependencyInstaller.new(
77
+ :bin_dir => Dir.pwd / "bin",
78
+ :install_dir => Dir.pwd / "gems",
79
+ :user_install => false)
80
+
81
+ begin
82
+ installer.install dep.name, dep.version_requirements
83
+ rescue ::Gem::GemNotFoundException => e
84
+ puts "Cannot find #{dep}"
85
+ rescue ::Gem::RemoteFetcher::FetchError => e
86
+ puts e.message
87
+ puts "Retrying..."
88
+ retry
89
+ end
90
+ end
91
+ end
92
+ end
93
+ end
@@ -0,0 +1,40 @@
1
+ class String
2
+ def /(other)
3
+ (Pathname.new(self) + other).to_s
4
+ end
5
+ end
6
+
7
+ module ColorfulMessages
8
+
9
+ # red
10
+ def error(*messages)
11
+ puts messages.map { |msg| "\033[1;31m#{msg}\033[0m" }
12
+ end
13
+
14
+ # yellow
15
+ def warning(*messages)
16
+ puts messages.map { |msg| "\033[1;33m#{msg}\033[0m" }
17
+ end
18
+
19
+ # green
20
+ def success(*messages)
21
+ puts messages.map { |msg| "\033[1;32m#{msg}\033[0m" }
22
+ end
23
+
24
+ alias_method :message, :success
25
+
26
+ # magenta
27
+ def note(*messages)
28
+ puts messages.map { |msg| "\033[1;35m#{msg}\033[0m" }
29
+ end
30
+
31
+ # blue
32
+ def info(*messages)
33
+ puts messages.map { |msg| "\033[1;34m#{msg}\033[0m" }
34
+ end
35
+
36
+ end
37
+
38
+ module ThorUI
39
+ extend ColorfulMessages
40
+ end
@@ -0,0 +1,21 @@
1
+ require 'MARQ'
2
+
3
+ $datadir = MARQ.datadir
4
+ $scriptdir = File.join(MARQ.rootdir, '/install_scripts')
5
+
6
+ task 'GEO' do |t|
7
+ directory = "#{$datadir}/GEO"
8
+ FileUtils.mkdir_p(directory)
9
+ %w(Rakefile series).each{|f|
10
+ FileUtils.cp_r File.join($scriptdir, "GEO/#{ f }"), directory
11
+ }
12
+ FileUtils.mkdir(File.join(directory, "platforms")) unless File.exist? File.join(directory, "platforms")
13
+ end
14
+
15
+ task 'CustomDS' do |t|
16
+ directory = "#{$datadir}/CustomDS"
17
+ FileUtils.mkdir_p(directory)
18
+ Dir.glob($scriptdir + '/CustomDS/*').each{|f|
19
+ FileUtils.cp_r f, directory
20
+ }
21
+ end
@@ -0,0 +1,167 @@
1
+ #!/usr/bin/ruby
2
+
3
+ require 'MARQ'
4
+ require 'MARQ/main'
5
+ require 'MARQ/annotations'
6
+ require 'simplews/jobs'
7
+ require 'zlib'
8
+ require 'zaml'
9
+
10
+ class MARQWS < SimpleWS::Jobs
11
+ class ArgumentError < Exception; end
12
+ class NotDone < Exception; end
13
+
14
+ helper :gzip do |string|
15
+ ostream = StringIO.new
16
+ begin
17
+ gz = Zlib::GzipWriter.new(ostream)
18
+ gz.write(string)
19
+ ostream.string
20
+ ensure
21
+ gz.close
22
+ end
23
+ end
24
+
25
+ helper :gunzip do |file|
26
+ begin
27
+ gz = Zlib::GzipReader.new(File.open(file))
28
+ gz.read
29
+ end
30
+ end
31
+
32
+ def logratios(dataset, comparison, genes)
33
+ path = MARQ.dataset_path(dataset)
34
+
35
+ position = File.open(path + '.experiments').collect{|l| l.chomp.strip}.index(comparison.chomp.strip)
36
+ raise ArgumentError, "Comparison #{ comparison.chomp.strip } not found" if position.nil?
37
+
38
+ `paste #{path + '.codes'} #{path + '.logratios'}| grep '#{genes.collect{|gene| "^#{ gene }[[:space:]]"}.join('\|')}'|cut -f1,#{position + 2}`
39
+ end
40
+
41
+ def ts(dataset, comparison, genes)
42
+ path = MARQ.dataset_path(dataset)
43
+ if comparison.match(/\[ratio\]/)
44
+ raise ArgumentError, "Comparison #{ comparison.chomp.strip } does not have a t value"
45
+ end
46
+
47
+ position = File.open(path + '.experiments').collect{|l| l.chomp.strip}.select{|name| !name.match(/\[ratio\]/)}.index(comparison.chomp.strip)
48
+ raise ArgumentError, "Comparison #{ comparison.chomp.strip } not found" if position.nil?
49
+
50
+ `paste #{path + '.codes'} #{path + '.t'}| grep '#{genes.collect{|gene| "^#{ gene }[[:space:]]"}.join('\|')}'|cut -f1,#{position + 2}`
51
+ end
52
+
53
+
54
+ task :annotations, %w(job type), {:job => :string, :type => :string}, ["annotations/{JOB}.yaml", "annotations/{JOB}_enriched.yaml"] do |job, type|
55
+ step(:scores, "Loading Scores")
56
+ scores = YAML::load(gunzip(File.join(workdir, "scores/#{job}.yaml.gz")))
57
+
58
+ step(:annotations, "Getting annotations")
59
+ annotations, terms = Annotations.annotations(scores, type, 0.05, :rank)
60
+
61
+ step(:saving, "Saving")
62
+
63
+ write("annotations/#{job_name}.yaml", gzip(ZAML.dump(annotations)))
64
+ write("annotations/#{job_name}_enriched.yaml", gzip(ZAML.dump(terms)))
65
+ end
66
+
67
+ task :match_platform, %w(platform up down), {:platform => :string, :up => :array, :down => :array},
68
+ ['scores/{JOB}.yaml.gz' ] do |platform, up, down|
69
+
70
+ up = up.collect{|gene| gene.strip if gene}
71
+ down = down.collect{|gene| gene.strip if gene}
72
+
73
+ info(:platform => platform,
74
+ :organism => MARQ.platform_organism(platform),
75
+ :up => up,
76
+ :down => down
77
+ )
78
+
79
+ raise ArgumentError, "No genes identified" if up.empty? && down.empty?
80
+ step(:matching, "Matching genes to platform #{ platform }, up: #{up.length}, down: #{down.length}")
81
+ scores = MARQ.platform_scores_up_down(platform, up, down)
82
+
83
+ raise ArgumentError, "No genes matched in platform #{ platform }, check that they are in the right format, automatic transalation is not performed in platform specific queries" if scores.keys.empty?
84
+
85
+ step(:saving, "Saving results")
86
+ write("scores/#{job_name}.yaml.gz", gzip(ZAML.dump(scores)))
87
+ end
88
+
89
+ task :match_organism, %w(organism up down), {:organism => :string, :up => :array, :down => :array},
90
+ ['scores/{JOB}.yaml.gz'] do |organism, up, down|
91
+ require 'MARQ/ID'
92
+
93
+ up = up.collect{|gene| gene.strip if gene}
94
+ down = down.collect{|gene| gene.strip if gene}
95
+
96
+ step(:translating, "Translating genes")
97
+
98
+ cross_platform_up = ID.translate(organism, up)
99
+ cross_platform_down = ID.translate(organism, down)
100
+
101
+ info(:organism => organism,
102
+ :up => up,
103
+ :down => down,
104
+ :cross_platform_up => cross_platform_up.collect{|n| n || "NO MATCH"},
105
+ :cross_platform_down => cross_platform_down.collect{|n| n || "NO MATCH"})
106
+
107
+ cross_platform_up = cross_platform_up.compact
108
+ cross_platform_down = cross_platform_down.compact
109
+
110
+ raise ArgumentError, "No genes identified" if cross_platform_up.empty? && cross_platform_down.empty?
111
+
112
+ step(:matching, "Matching genes to organism #{ organism }, up: #{cross_platform_up.length}, down: #{cross_platform_down.length}")
113
+
114
+ platforms = MARQ::organism_platforms(organism).select{|platform| MARQ.has_cross_platform? nil, platform }.collect{|platform| platform + "_cross_platform"}
115
+
116
+ scores = {}
117
+ step(:processing, "Procesing #{platforms.length} datasets")
118
+ platforms.each_with_index{|platform, i |
119
+ step(:processing, "Generating Scores for platform #{ platform } #{ i + 1 }/#{platforms.length}.")
120
+ scores = scores.merge(MARQ.platform_scores_up_down(platform, cross_platform_up, cross_platform_down))
121
+ }
122
+ step(:saving, "Saving results")
123
+ write("scores/#{job_name}.yaml.gz", gzip(ZAML.dump(scores)))
124
+ end
125
+
126
+
127
+
128
+ class Scheduler::Job
129
+ alias_method :old_step, :step
130
+ def step(status, message=nil)
131
+ puts "#{Time.now} => [#{ @name }]: #{ status }. #{ message }"
132
+ old_step(status, message)
133
+ end
134
+ end
135
+
136
+ def initialize(*args)
137
+ super(*args)
138
+ @soaplet.allow_content_encoding_gzip = true
139
+
140
+ serve :logratios, %w(dataset comparison genes), {:dataset => :string, :comparison => :string, :genes => :array, :return => :string}
141
+ serve :ts, %w(dataset comparison genes), {:dataset => :string, :comparison => :string, :genes => :array, :return => :string}
142
+ FileUtils.mkdir(File.join(workdir, 'scores')) unless File.exist?(File.join(workdir, 'scores'))
143
+ FileUtils.mkdir(File.join(workdir, 'annotations')) unless File.exist?(File.join(workdir, 'annotations'))
144
+ end
145
+
146
+
147
+ end
148
+
149
+ if __FILE__ == $0
150
+
151
+ puts "Starting WS"
152
+ host = ARGV[0] || `hostname`.chomp.strip + '.' + `hostname -d`.chomp.strip
153
+ port = ARGV[1] || '8282'
154
+
155
+ puts "Starting Server in #{ host }:#{ port }"
156
+ server = MARQWS.new("MARQ", "MARQ Web Server",host, port, File.join(MARQ.workdir,'webservice', 'jobs'))
157
+
158
+ FileUtils.mkdir_p File.join(MARQ.workdir, '/webservice', 'wsdl/') unless File.exist? File.join(MARQ.workdir, '/webservice', 'wsdl/')
159
+ File.open(File.join(MARQ.workdir, '/webservice', 'wsdl', 'MARQWS.wsdl'),'w'){|file| file.write server.wsdl}
160
+
161
+ trap('INT') { server.shutdown }
162
+ server.start
163
+
164
+ end
165
+
166
+
167
+