- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 3346: Create NGS peak calling section. Add MACS peak...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e9de35947c06 changeset: 3346:e9de35947c06 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Feb 05 16:06:27 2010 -0500 description: Create NGS peak calling section. Add MACS peak caller. Move GeneTrack to new section. Increment sam2interval tool version. diffstat: test-data/chipseq_enriched.bed.gz | 0 test-data/chipseq_input.bed.gz | 0 test-data/macs_test_1_out.bed | 1271 ++++++++++++++++++++ test-data/macs_test_2_neg_peaks_out.interval | 59 + test-data/macs_test_2_peaks_out.interval | 1289 +++++++++++++++++++++ tool_conf.xml.main | 6 +- tool_conf.xml.sample | 7 +- tools/genetrack/genetrack_indexer.py | 42 + tools/genetrack/genetrack_indexer.xml | 54 + tools/genetrack/genetrack_peak_prediction.py | 40 + tools/genetrack/genetrack_peak_prediction.xml | 59 + tools/peak_calling/macs_wrapper.py | 138 ++ tools/peak_calling/macs_wrapper.xml | 213 +++ tools/samtools/sam2interval.xml | 2 +- tools/visualization/genetrack_indexer.py | 39 - tools/visualization/genetrack_indexer.xml | 54 - tools/visualization/genetrack_peak_prediction.py | 40 - tools/visualization/genetrack_peak_prediction.xml | 59 - 18 files changed, 3176 insertions(+), 196 deletions(-) diffs (truncated from 3460 to 3000 lines): diff -r 49961332adb6 -r e9de35947c06 test-data/chipseq_enriched.bed.gz Binary file test-data/chipseq_enriched.bed.gz has changed diff -r 49961332adb6 -r e9de35947c06 test-data/chipseq_input.bed.gz Binary file test-data/chipseq_input.bed.gz has changed diff -r 49961332adb6 -r e9de35947c06 test-data/macs_test_1_out.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/macs_test_1_out.bed Fri Feb 05 16:06:27 2010 -0500 @@ -0,0 +1,1271 @@ +track name="MACS peaks for MACS_in_Galaxy" +chr1 3138857 3139271 MACS_peak_1 53.08 +chr1 4133899 4134700 MACS_peak_2 51.91 +chr1 4323670 4324367 MACS_peak_3 272.01 +chr1 4336486 4337946 MACS_peak_4 228.35 +chr1 4407086 4409120 MACS_peak_5 300.46 +chr1 4507832 4508710 MACS_peak_6 161.74 +chr1 4657704 4658572 MACS_peak_7 280.37 +chr1 4658705 4659021 MACS_peak_8 131.25 +chr1 4659147 4660581 MACS_peak_9 463.08 +chr1 4661156 4661317 MACS_peak_10 174.88 +chr1 4661505 4661617 MACS_peak_11 100.24 +chr1 4661790 4662463 MACS_peak_12 219.58 +chr1 4662710 4663434 MACS_peak_13 395.94 +chr1 4664135 4664430 MACS_peak_14 169.10 +chr1 4665001 4665113 MACS_peak_15 100.24 +chr1 4665839 4666425 MACS_peak_16 332.40 +chr1 4666581 4666693 MACS_peak_17 100.24 +chr1 4666840 4666981 MACS_peak_18 174.88 +chr1 4667600 4667712 MACS_peak_19 100.24 +chr1 4668711 4669005 MACS_peak_20 169.17 +chr1 4669126 4669238 MACS_peak_21 100.24 +chr1 4669537 4669752 MACS_peak_22 174.88 +chr1 4669936 4670048 MACS_peak_23 100.24 +chr1 4670216 4670449 MACS_peak_24 212.68 +chr1 4673856 4674051 MACS_peak_25 137.07 +chr1 4674349 4674478 MACS_peak_26 137.07 +chr1 4675027 4675152 MACS_peak_27 137.07 +chr1 4676227 4676339 MACS_peak_28 100.24 +chr1 4676511 4676623 MACS_peak_29 100.24 +chr1 4676954 4677151 MACS_peak_30 100.24 +chr1 4677646 4677758 MACS_peak_31 100.24 +chr1 4678360 4678472 MACS_peak_32 100.24 +chr1 4678659 4679136 MACS_peak_33 230.04 +chr1 4679439 4679551 MACS_peak_34 100.24 +chr1 4680106 4680523 MACS_peak_35 126.43 +chr1 4680822 4680934 MACS_peak_36 100.24 +chr1 4681075 4682050 MACS_peak_37 241.81 +chr1 4682229 4682387 MACS_peak_38 100.24 +chr1 4682594 4682706 MACS_peak_39 100.24 +chr1 4683158 4683270 MACS_peak_40 100.24 +chr1 4683473 4683585 MACS_peak_41 100.24 +chr1 4683832 4683944 MACS_peak_42 100.24 +chr1 4684591 4684775 MACS_peak_43 100.24 +chr1 4685292 4685404 MACS_peak_44 100.24 +chr1 4685810 4686198 MACS_peak_45 127.69 +chr1 4686493 4686605 MACS_peak_46 100.24 +chr1 4686818 4686930 MACS_peak_47 100.24 +chr1 4687387 4687499 MACS_peak_48 100.24 +chr1 4687692 4687902 MACS_peak_49 174.88 +chr1 4688181 4688790 MACS_peak_50 258.16 +chr1 4689101 4689557 MACS_peak_51 231.41 +chr1 4690039 4690151 MACS_peak_52 100.24 +chr1 4690290 4690402 MACS_peak_53 100.24 +chr1 4690780 4690907 MACS_peak_54 137.07 +chr1 4691478 4692335 MACS_peak_55 315.89 +chr1 4692464 4692768 MACS_peak_56 131.92 +chr1 4693243 4693751 MACS_peak_57 228.13 +chr1 4694306 4694418 MACS_peak_58 100.24 +chr1 4694738 4695016 MACS_peak_59 170.38 +chr1 4695207 4695378 MACS_peak_60 100.24 +chr1 4695503 4696600 MACS_peak_61 374.29 +chr1 4696903 4697015 MACS_peak_62 100.24 +chr1 4697569 4697912 MACS_peak_63 240.07 +chr1 4698224 4698395 MACS_peak_64 100.24 +chr1 4698790 4698904 MACS_peak_65 137.07 +chr1 4699223 4699430 MACS_peak_66 137.07 +chr1 4699642 4699754 MACS_peak_67 100.24 +chr1 4700457 4700569 MACS_peak_68 100.24 +chr1 4700853 4700965 MACS_peak_69 100.24 +chr1 4708474 4708898 MACS_peak_70 126.15 +chr1 4709426 4709741 MACS_peak_71 167.67 +chr1 4709925 4710127 MACS_peak_72 137.07 +chr1 4710465 4710577 MACS_peak_73 100.24 +chr1 4710812 4711277 MACS_peak_74 194.68 +chr1 4711462 4711762 MACS_peak_75 132.15 +chr1 4712202 4712479 MACS_peak_76 97.58 +chr1 4712673 4713163 MACS_peak_77 340.17 +chr1 4713659 4714656 MACS_peak_78 414.78 +chr1 4714840 4715470 MACS_peak_79 221.59 +chr1 4715671 4715783 MACS_peak_80 100.24 +chr1 4715908 4716811 MACS_peak_81 530.04 +chr1 4717318 4717430 MACS_peak_82 100.24 +chr1 4717789 4718230 MACS_peak_83 232.43 +chr1 4718990 4719236 MACS_peak_84 99.13 +chr1 4719718 4719830 MACS_peak_85 100.24 +chr1 4720276 4720388 MACS_peak_86 100.24 +chr1 4721061 4721173 MACS_peak_87 100.24 +chr1 4721620 4721782 MACS_peak_88 100.24 +chr1 4722229 4722341 MACS_peak_89 100.24 +chr1 4723262 4723374 MACS_peak_90 100.24 +chr1 4724496 4724608 MACS_peak_91 100.24 +chr1 4726179 4726291 MACS_peak_92 100.24 +chr1 4726472 4727091 MACS_peak_93 187.23 +chr1 4727268 4727705 MACS_peak_94 196.30 +chr1 4727871 4727983 MACS_peak_95 100.24 +chr1 4728976 4729088 MACS_peak_96 100.24 +chr1 4729473 4729611 MACS_peak_97 137.07 +chr1 4729954 4730093 MACS_peak_98 137.07 +chr1 4730636 4730805 MACS_peak_99 100.24 +chr1 4730936 4731305 MACS_peak_100 164.24 +chr1 4731799 4732585 MACS_peak_101 355.47 +chr1 4733192 4733304 MACS_peak_102 100.24 +chr1 4733710 4733831 MACS_peak_103 137.07 +chr1 4734062 4734891 MACS_peak_104 352.92 +chr1 4735075 4735290 MACS_peak_105 137.07 +chr1 4735523 4736190 MACS_peak_106 185.28 +chr1 4736399 4737184 MACS_peak_107 355.53 +chr1 4737395 4737601 MACS_peak_108 137.07 +chr1 4737973 4738425 MACS_peak_109 231.68 +chr1 4738796 4739212 MACS_peak_110 197.58 +chr1 4739379 4739491 MACS_peak_111 100.24 +chr1 4739612 4740720 MACS_peak_112 588.51 +chr1 4741405 4741655 MACS_peak_113 135.32 +chr1 4741998 4742300 MACS_peak_114 132.04 +chr1 4742829 4742952 MACS_peak_115 137.07 +chr1 4743079 4743327 MACS_peak_116 135.46 +chr1 4743612 4744566 MACS_peak_117 453.30 +chr1 4744719 4745224 MACS_peak_118 264.66 +chr1 4745398 4745786 MACS_peak_119 236.32 +chr1 4746034 4746316 MACS_peak_120 170.07 +chr1 4747206 4748408 MACS_peak_121 474.57 +chr1 4748814 4748926 MACS_peak_122 100.24 +chr1 4749222 4749334 MACS_peak_123 100.24 +chr1 4749686 4750054 MACS_peak_124 275.66 +chr1 4750335 4750697 MACS_peak_125 164.65 +chr1 4750863 4751682 MACS_peak_126 247.87 +chr1 4751853 4752428 MACS_peak_127 189.15 +chr1 4752581 4753611 MACS_peak_128 412.95 +chr1 4754241 4754864 MACS_peak_129 329.74 +chr1 4755088 4755200 MACS_peak_130 100.24 +chr1 4755722 4756029 MACS_peak_131 205.50 +chr1 4756768 4756880 MACS_peak_132 100.24 +chr1 4757199 4758615 MACS_peak_133 569.34 +chr1 4758753 4762214 MACS_peak_134 3100.00 +chr1 4763207 4763319 MACS_peak_135 100.24 +chr1 4763614 4763726 MACS_peak_136 100.24 +chr1 4763998 4764322 MACS_peak_137 358.13 +chr1 4764568 4764850 MACS_peak_138 133.23 +chr1 4765104 4765765 MACS_peak_139 291.01 +chr1 4765892 4766067 MACS_peak_140 100.24 +chr1 4766232 4766420 MACS_peak_141 100.24 +chr1 4766539 4767148 MACS_peak_142 367.65 +chr1 4767417 4767529 MACS_peak_143 100.24 +chr1 4768245 4768357 MACS_peak_144 100.24 +chr1 4768587 4768870 MACS_peak_145 170.00 +chr1 4768989 4769272 MACS_peak_146 133.17 +chr1 4769463 4769684 MACS_peak_147 174.88 +chr1 4769861 4770236 MACS_peak_148 200.29 +chr1 4770689 4771270 MACS_peak_149 224.05 +chr1 4771393 4772502 MACS_peak_150 1799.39 +chr1 4772633 4772916 MACS_peak_151 133.17 +chr1 4773121 4773284 MACS_peak_152 100.24 +chr1 4773476 4773614 MACS_peak_153 137.07 +chr1 4773827 4774279 MACS_peak_154 159.83 +chr1 4774510 4774622 MACS_peak_155 100.24 +chr1 4775041 4775694 MACS_peak_156 291.49 +chr1 4775832 4775944 MACS_peak_157 100.24 +chr1 4776166 4776310 MACS_peak_158 137.07 +chr1 4776506 4776851 MACS_peak_159 165.70 +chr1 4777100 4777321 MACS_peak_160 137.07 +chr1 4777505 4777617 MACS_peak_161 100.24 +chr1 4777764 4778298 MACS_peak_162 156.21 +chr1 4778680 4778792 MACS_peak_163 100.24 +chr1 4779265 4779377 MACS_peak_164 100.24 +chr1 4780814 4780926 MACS_peak_165 100.24 +chr1 4781238 4781436 MACS_peak_166 137.07 +chr1 4781600 4781712 MACS_peak_167 100.24 +chr1 4784249 4784487 MACS_peak_168 173.76 +chr1 4784800 4784912 MACS_peak_169 100.24 +chr1 4785500 4785612 MACS_peak_170 100.24 +chr1 4786820 4787357 MACS_peak_171 226.44 +chr1 4787570 4787682 MACS_peak_172 100.24 +chr1 4789440 4789978 MACS_peak_173 262.47 +chr1 4790257 4790424 MACS_peak_174 100.24 +chr1 4790723 4791308 MACS_peak_175 223.84 +chr1 4791871 4792641 MACS_peak_176 392.73 +chr1 4792756 4793323 MACS_peak_177 189.52 +chr1 4794493 4794929 MACS_peak_178 232.77 +chr1 4795046 4795357 MACS_peak_179 131.53 +chr1 4795495 4795607 MACS_peak_180 100.24 +chr1 4796218 4796432 MACS_peak_181 174.88 +chr1 4796841 4796953 MACS_peak_182 100.24 +chr1 4797267 4797499 MACS_peak_183 99.89 +chr1 4797910 4798022 MACS_peak_184 100.24 +chr1 4799151 4799263 MACS_peak_185 100.24 +chr1 4799518 4800266 MACS_peak_186 216.37 +chr1 4800415 4800527 MACS_peak_187 100.24 +chr1 4800989 4801101 MACS_peak_188 100.24 +chr1 4801344 4802288 MACS_peak_189 311.70 +chr1 4802600 4802712 MACS_peak_190 100.24 +chr1 4802944 4803056 MACS_peak_191 100.24 +chr1 4803408 4803520 MACS_peak_192 100.24 +chr1 4803899 4804011 MACS_peak_193 100.24 +chr1 4804278 4804390 MACS_peak_194 100.24 +chr1 4804716 4805427 MACS_peak_195 360.26 +chr1 4805843 4806018 MACS_peak_196 100.24 +chr1 4806294 4806406 MACS_peak_197 100.24 +chr1 4806523 4806849 MACS_peak_198 241.61 +chr1 4807024 4807205 MACS_peak_199 174.88 +chr1 4807520 4807740 MACS_peak_200 100.24 +chr1 4808021 4808133 MACS_peak_201 100.24 +chr1 4809641 4810406 MACS_peak_202 320.82 +chr1 4810853 4812088 MACS_peak_203 508.29 +chr1 4812253 4812665 MACS_peak_204 234.49 +chr1 4813090 4813202 MACS_peak_205 100.24 +chr1 4813466 4813836 MACS_peak_206 200.64 +chr1 4814068 4814180 MACS_peak_207 100.24 +chr1 4814343 4814700 MACS_peak_208 129.13 +chr1 4814902 4815014 MACS_peak_209 100.24 +chr1 4815190 4815343 MACS_peak_210 174.88 +chr1 4815570 4816098 MACS_peak_211 191.37 +chr1 4816683 4817303 MACS_peak_212 222.07 +chr1 4817449 4817735 MACS_peak_213 97.17 +chr1 4818299 4818411 MACS_peak_214 100.24 +chr1 4819699 4819870 MACS_peak_215 137.07 +chr1 4820406 4821178 MACS_peak_216 429.22 +chr1 4821318 4821821 MACS_peak_217 192.64 +chr1 4822130 4822242 MACS_peak_218 100.24 +chr1 4822509 4823010 MACS_peak_219 192.74 +chr1 4823526 4823638 MACS_peak_220 100.24 +chr1 4823838 4823996 MACS_peak_221 174.88 +chr1 4824146 4824258 MACS_peak_222 100.24 +chr1 4824694 4824806 MACS_peak_223 100.24 +chr1 4825207 4825319 MACS_peak_224 100.24 +chr1 4825494 4825606 MACS_peak_225 100.24 +chr1 4825793 4825905 MACS_peak_226 100.24 +chr1 4827008 4827120 MACS_peak_227 100.24 +chr1 4827550 4827866 MACS_peak_228 95.87 +chr1 4828619 4829306 MACS_peak_229 184.51 +chr1 4829921 4830483 MACS_peak_230 409.14 +chr1 4830656 4830878 MACS_peak_231 137.07 +chr1 4831394 4831506 MACS_peak_232 100.24 +chr1 4831844 4831956 MACS_peak_233 100.24 +chr1 4832109 4832299 MACS_peak_234 137.07 +chr1 4832653 4832765 MACS_peak_235 100.24 +chr1 4833194 4833306 MACS_peak_236 100.24 +chr1 4833562 4834290 MACS_peak_237 322.98 +chr1 4834418 4834761 MACS_peak_238 129.83 +chr1 4835007 4835561 MACS_peak_239 225.49 +chr1 4835772 4835884 MACS_peak_240 100.24 +chr1 4836111 4836342 MACS_peak_241 136.69 +chr1 4836700 4836872 MACS_peak_242 100.24 +chr1 4837011 4837326 MACS_peak_243 95.91 +chr1 4837787 4838061 MACS_peak_244 97.73 +chr1 4838509 4838621 MACS_peak_245 100.24 +chr1 4838750 4839072 MACS_peak_246 130.92 +chr1 4839375 4839615 MACS_peak_247 211.91 +chr1 4840334 4840446 MACS_peak_248 100.24 +chr1 4841036 4841160 MACS_peak_249 137.07 +chr1 4841416 4841762 MACS_peak_250 165.63 +chr1 4842486 4842598 MACS_peak_251 100.24 +chr1 4842727 4843432 MACS_peak_252 183.84 +chr1 4843856 4844363 MACS_peak_253 301.38 +chr1 4844645 4845031 MACS_peak_254 163.26 +chr1 4845512 4845972 MACS_peak_255 159.45 +chr1 4846211 4846346 MACS_peak_256 213.48 +chr1 4846821 4847168 MACS_peak_257 129.63 +chr1 4847291 4847699 MACS_peak_258 126.81 +chr1 4847873 4848128 MACS_peak_259 98.66 +chr1 4848823 4848969 MACS_peak_260 137.07 +chr1 4849335 4850291 MACS_peak_261 453.17 +chr1 4850534 4850878 MACS_peak_262 129.78 +chr1 4851485 4851770 MACS_peak_263 97.21 +chr1 4852224 4852336 MACS_peak_264 100.24 +chr1 4852629 4852893 MACS_peak_265 171.51 +chr1 4853247 4853359 MACS_peak_266 100.24 +chr1 4853500 4853612 MACS_peak_267 100.24 +chr1 4854342 4854454 MACS_peak_268 100.24 +chr1 4854696 4854915 MACS_peak_269 137.07 +chr1 4855160 4855749 MACS_peak_270 154.08 +chr1 4856482 4857364 MACS_peak_271 211.36 +chr1 4857573 4857697 MACS_peak_272 213.48 +chr1 4857830 4857942 MACS_peak_273 100.24 +chr1 4858204 4858599 MACS_peak_274 235.78 +chr1 4858812 4859245 MACS_peak_275 125.78 +chr1 4859843 4859955 MACS_peak_276 100.24 +chr1 4860077 4860209 MACS_peak_277 137.07 +chr1 4860573 4861449 MACS_peak_278 458.48 +chr1 4861747 4861976 MACS_peak_279 100.06 +chr1 4862268 4862651 MACS_peak_280 93.36 +chr1 4863414 4863526 MACS_peak_281 100.24 +chr1 4864845 4865021 MACS_peak_282 100.24 +chr1 4865297 4865766 MACS_peak_283 230.56 +chr1 4865923 4866035 MACS_peak_284 100.24 +chr1 4866382 4866494 MACS_peak_285 100.24 +chr1 4867682 4867807 MACS_peak_286 137.07 +chr1 4868654 4868766 MACS_peak_287 100.24 +chr1 4868930 4869268 MACS_peak_288 94.99 +chr1 4869676 4869788 MACS_peak_289 100.24 +chr1 4872133 4872544 MACS_peak_290 271.82 +chr1 4872662 4873337 MACS_peak_291 254.59 +chr1 4874062 4874473 MACS_peak_292 271.82 +chr1 4874975 4875211 MACS_peak_293 173.94 +chr1 4876698 4876810 MACS_peak_294 100.24 +chr1 4877028 4877284 MACS_peak_295 98.61 +chr1 4877427 4877588 MACS_peak_296 100.24 +chr1 4878177 4878289 MACS_peak_297 100.24 +chr1 4878676 4878788 MACS_peak_298 100.24 +chr1 4879245 4880188 MACS_peak_299 209.33 +chr1 4880427 4881235 MACS_peak_300 318.45 +chr1 4881879 4882060 MACS_peak_301 137.07 +chr1 4882471 4883064 MACS_peak_302 295.25 +chr1 4883301 4883864 MACS_peak_303 155.06 +chr1 4884407 4884593 MACS_peak_304 100.24 +chr1 4884796 4884908 MACS_peak_305 100.24 +chr1 4885346 4886192 MACS_peak_306 212.63 +chr1 4886722 4886834 MACS_peak_307 100.24 +chr1 4887003 4887328 MACS_peak_308 130.76 +chr1 4887618 4887730 MACS_peak_309 100.24 +chr1 4889449 4889763 MACS_peak_310 95.95 +chr1 4890020 4890132 MACS_peak_311 100.24 +chr1 4890331 4890463 MACS_peak_312 137.07 +chr1 4890662 4891095 MACS_peak_313 270.01 +chr1 4891457 4893061 MACS_peak_314 701.27 +chr1 4893216 4893887 MACS_peak_315 290.43 +chr1 4894234 4894346 MACS_peak_316 100.24 +chr1 4894464 4894730 MACS_peak_317 171.34 +chr1 4895365 4895858 MACS_peak_318 157.95 +chr1 4896603 4896715 MACS_peak_319 100.24 +chr1 4897044 4897793 MACS_peak_320 216.33 +chr1 4898184 4898296 MACS_peak_321 100.24 +chr1 4898589 4898701 MACS_peak_322 100.24 +chr1 4898838 4899317 MACS_peak_323 124.03 +chr1 4899461 4900031 MACS_peak_324 296.80 +chr1 4900244 4900356 MACS_peak_325 100.24 +chr1 4900490 4900638 MACS_peak_326 137.07 +chr1 4900927 4901039 MACS_peak_327 100.24 +chr1 4901371 4901558 MACS_peak_328 137.07 +chr1 4901767 4902496 MACS_peak_329 359.06 +chr1 4902621 4903202 MACS_peak_330 259.79 +chr1 4903396 4903692 MACS_peak_331 169.02 +chr1 4903871 4903983 MACS_peak_332 100.24 +chr1 4904596 4904708 MACS_peak_333 100.24 +chr1 4905302 4905414 MACS_peak_334 100.24 +chr1 4905612 4906211 MACS_peak_335 294.86 +chr1 4906407 4906662 MACS_peak_336 172.26 +chr1 4907188 4907339 MACS_peak_337 100.24 +chr1 4908299 4909216 MACS_peak_338 455.70 +chr1 4909542 4909654 MACS_peak_339 100.24 +chr1 4909952 4910103 MACS_peak_340 100.24 +chr1 4910247 4910755 MACS_peak_341 192.38 +chr1 4910931 4911043 MACS_peak_342 100.24 +chr1 4912153 4912290 MACS_peak_343 137.07 +chr1 4913430 4913601 MACS_peak_344 100.24 +chr1 4913916 4914526 MACS_peak_345 153.32 +chr1 4914785 4915085 MACS_peak_346 132.15 +chr1 4915254 4916101 MACS_peak_347 351.90 +chr1 4916248 4916612 MACS_peak_348 128.80 +chr1 4916731 4916898 MACS_peak_349 100.24 +chr1 4917041 4918520 MACS_peak_350 565.94 +chr1 4918971 4919511 MACS_peak_351 155.97 +chr1 4920143 4920281 MACS_peak_352 137.07 +chr1 4920830 4920976 MACS_peak_353 174.88 +chr1 4921156 4921616 MACS_peak_354 231.14 +chr1 4921783 4922072 MACS_peak_355 132.80 +chr1 4922200 4922312 MACS_peak_356 100.24 +chr1 4922698 4922810 MACS_peak_357 100.24 +chr1 4922952 4923064 MACS_peak_358 100.24 +chr1 4923711 4923825 MACS_peak_359 137.07 +chr1 4924847 4925134 MACS_peak_360 169.69 +chr1 4925374 4925521 MACS_peak_361 137.07 +chr1 4926127 4926628 MACS_peak_362 228.55 +chr1 4926755 4927616 MACS_peak_363 351.11 +chr1 4927845 4928143 MACS_peak_364 168.88 +chr1 4928391 4929764 MACS_peak_365 431.16 +chr1 4929891 4930203 MACS_peak_366 131.47 +chr1 4930358 4930563 MACS_peak_367 100.24 +chr1 4930982 4931172 MACS_peak_368 100.24 +chr1 4931361 4931660 MACS_peak_369 168.80 +chr1 4932382 4932963 MACS_peak_370 224.05 +chr1 4933440 4933552 MACS_peak_371 100.24 +chr1 4933681 4934002 MACS_peak_372 204.34 +chr1 4934226 4934700 MACS_peak_373 266.86 +chr1 4934820 4935023 MACS_peak_374 100.24 +chr1 4935896 4936217 MACS_peak_375 280.40 +chr1 4936341 4937067 MACS_peak_376 217.28 +chr1 4937317 4937429 MACS_peak_377 100.24 +chr1 4937921 4938033 MACS_peak_378 100.24 +chr1 4944882 4945123 MACS_peak_379 290.36 +chr1 4945522 4945861 MACS_peak_380 130.03 +chr1 4946020 4946166 MACS_peak_381 137.07 +chr1 4946436 4946584 MACS_peak_382 137.07 +chr1 4946710 4946822 MACS_peak_383 100.24 +chr1 4946951 4947336 MACS_peak_384 163.31 +chr1 4948023 4948135 MACS_peak_385 100.24 +chr1 4948535 4948658 MACS_peak_386 137.07 +chr1 4951023 4951135 MACS_peak_387 100.24 +chr1 4952397 4953059 MACS_peak_388 185.48 +chr1 4953377 4953609 MACS_peak_389 136.62 +chr1 4953840 4954681 MACS_peak_390 246.95 +chr1 4955012 4956131 MACS_peak_391 443.60 +chr1 4956418 4956838 MACS_peak_392 161.43 +chr1 4957163 4957694 MACS_peak_393 299.57 +chr1 4958356 4958529 MACS_peak_394 100.24 +chr1 4958823 4959148 MACS_peak_395 166.99 +chr1 4959772 4960322 MACS_peak_396 298.20 +chr1 4960576 4962064 MACS_peak_397 636.53 +chr1 4962737 4963409 MACS_peak_398 326.45 +chr1 4963700 4963974 MACS_peak_399 133.73 +chr1 4965851 4966062 MACS_peak_400 100.24 +chr1 4966437 4967281 MACS_peak_401 352.07 +chr1 4967476 4967641 MACS_peak_402 100.24 +chr1 4967813 4968456 MACS_peak_403 220.97 +chr1 4968607 4968752 MACS_peak_404 174.88 +chr1 4968965 4969286 MACS_peak_405 95.66 +chr1 4969410 4969822 MACS_peak_406 126.64 +chr1 4970372 4970484 MACS_peak_407 100.24 +chr1 4975200 4975343 MACS_peak_408 174.88 +chr1 4975521 4975633 MACS_peak_409 100.24 +chr1 4975762 4975980 MACS_peak_410 100.24 +chr1 4976829 4976941 MACS_peak_411 100.24 +chr1 4978309 4978421 MACS_peak_412 100.24 +chr1 4979774 4980223 MACS_peak_413 195.59 +chr1 4980423 4980535 MACS_peak_414 100.24 +chr1 4980817 4980991 MACS_peak_415 100.24 +chr1 4981234 4981537 MACS_peak_416 168.51 +chr1 4981655 4982010 MACS_peak_417 165.08 +chr1 4982893 4983037 MACS_peak_418 137.07 +chr1 4984463 4984708 MACS_peak_419 135.67 +chr1 4985269 4985381 MACS_peak_420 100.24 +chr1 4986003 4986204 MACS_peak_421 100.24 +chr1 4987600 4987712 MACS_peak_422 100.24 +chr1 4988896 4989008 MACS_peak_423 100.24 +chr1 4990354 4990466 MACS_peak_424 100.24 +chr1 4991245 4991357 MACS_peak_425 100.24 +chr1 4992001 4992258 MACS_peak_426 98.56 +chr1 4992834 4993305 MACS_peak_427 194.35 +chr1 4993542 4993654 MACS_peak_428 100.24 +chr1 4993878 4994124 MACS_peak_429 135.60 +chr1 4994717 4995335 MACS_peak_430 187.27 +chr1 4995469 4996377 MACS_peak_431 492.84 +chr1 4996497 4996609 MACS_peak_432 100.24 +chr1 4996828 4997058 MACS_peak_433 100.01 +chr1 4997280 4997406 MACS_peak_434 137.07 +chr1 4997521 4997646 MACS_peak_435 137.07 +chr1 4997838 4998328 MACS_peak_436 193.32 +chr1 4998584 4998978 MACS_peak_437 273.29 +chr1 4999395 4999507 MACS_peak_438 100.24 +chr1 5000025 5000145 MACS_peak_439 137.07 +chr1 5000445 5000681 MACS_peak_440 99.67 +chr1 5002097 5002492 MACS_peak_441 162.76 +chr1 5003083 5003284 MACS_peak_442 100.24 +chr1 5003661 5004017 MACS_peak_443 165.01 +chr1 5004225 5004846 MACS_peak_444 293.45 +chr1 5004962 5005074 MACS_peak_445 100.24 +chr1 5005414 5005526 MACS_peak_446 100.24 +chr1 5005899 5006531 MACS_peak_447 221.49 +chr1 5006687 5006799 MACS_peak_448 100.24 +chr1 5007121 5007233 MACS_peak_449 100.24 +chr1 5007621 5007888 MACS_peak_450 98.06 +chr1 5008386 5008804 MACS_peak_451 161.53 +chr1 5009297 5009455 MACS_peak_452 100.24 +chr1 5009800 5009919 MACS_peak_453 137.07 +chr1 5010164 5010383 MACS_peak_454 100.24 +chr1 5010702 5010814 MACS_peak_455 100.24 +chr1 5011318 5011430 MACS_peak_456 100.24 +chr1 5011570 5011904 MACS_peak_457 130.29 +chr1 5012040 5012172 MACS_peak_458 213.48 +chr1 5012312 5012452 MACS_peak_459 174.88 +chr1 5013118 5013359 MACS_peak_460 99.40 +chr1 5013518 5013658 MACS_peak_461 174.88 +chr1 5013881 5013993 MACS_peak_462 100.24 +chr1 5014248 5014742 MACS_peak_463 228.98 +chr1 5015114 5015226 MACS_peak_464 100.24 +chr1 5015801 5016141 MACS_peak_465 129.98 +chr1 5016467 5016756 MACS_peak_466 132.80 +chr1 5016937 5017049 MACS_peak_467 100.24 +chr1 5017244 5017888 MACS_peak_468 256.22 +chr1 5018361 5018825 MACS_peak_469 230.88 +chr1 5018988 5019283 MACS_peak_470 132.45 +chr1 5019483 5019735 MACS_peak_471 135.18 +chr1 5019878 5020096 MACS_peak_472 100.24 +chr1 5020521 5020633 MACS_peak_473 100.24 +chr1 5021108 5021423 MACS_peak_474 95.91 +chr1 5021637 5021749 MACS_peak_475 100.24 +chr1 5021983 5022543 MACS_peak_476 189.84 +chr1 5022857 5023545 MACS_peak_477 218.91 +chr1 5023746 5023858 MACS_peak_478 100.24 +chr1 5023989 5024146 MACS_peak_479 100.24 +chr1 5024463 5024752 MACS_peak_480 245.27 +chr1 5024980 5025092 MACS_peak_481 100.24 +chr1 5025520 5025734 MACS_peak_482 137.07 +chr1 5032611 5032723 MACS_peak_483 100.24 +chr1 5033023 5033254 MACS_peak_484 99.95 +chr1 5033681 5033793 MACS_peak_485 100.24 +chr1 5034513 5034625 MACS_peak_486 100.24 +chr1 5035054 5035185 MACS_peak_487 137.07 +chr1 5038790 5039022 MACS_peak_488 136.62 +chr1 5039491 5039790 MACS_peak_489 96.59 +chr1 5040037 5040149 MACS_peak_490 100.24 +chr1 5042044 5042156 MACS_peak_491 100.24 +chr1 5044343 5044455 MACS_peak_492 100.24 +chr1 5045148 5045303 MACS_peak_493 100.24 +chr1 5045444 5045580 MACS_peak_494 137.07 +chr1 5045759 5046137 MACS_peak_495 274.73 +chr1 5046459 5046932 MACS_peak_496 124.25 +chr1 5047196 5047790 MACS_peak_497 188.30 +chr1 5048329 5048441 MACS_peak_498 100.24 +chr1 5051379 5051491 MACS_peak_499 100.24 +chr1 5054182 5054620 MACS_peak_500 160.51 +chr1 5054821 5054933 MACS_peak_501 100.24 +chr1 5055158 5055270 MACS_peak_502 100.24 +chr1 5055388 5055791 MACS_peak_503 272.50 +chr1 5056110 5056222 MACS_peak_504 100.24 +chr1 5056524 5056951 MACS_peak_505 161.07 +chr1 5057086 5057694 MACS_peak_506 222.67 +chr1 5058767 5058879 MACS_peak_507 100.24 +chr1 5059021 5059659 MACS_peak_508 256.54 +chr1 5060172 5060284 MACS_peak_509 100.24 +chr1 5060462 5060574 MACS_peak_510 100.24 +chr1 5061165 5061359 MACS_peak_511 137.07 +chr1 5061551 5062254 MACS_peak_512 585.63 +chr1 5062414 5062526 MACS_peak_513 100.24 +chr1 5062713 5062989 MACS_peak_514 133.60 +chr1 5063187 5063299 MACS_peak_515 100.24 +chr1 5064348 5064562 MACS_peak_516 174.88 +chr1 5064956 5065068 MACS_peak_517 100.24 +chr1 5065226 5065447 MACS_peak_518 174.88 +chr1 5065611 5066438 MACS_peak_519 213.32 +chr1 5066845 5066957 MACS_peak_520 100.24 +chr1 5067268 5067380 MACS_peak_521 100.24 +chr1 5067511 5067627 MACS_peak_522 137.07 +chr1 5074120 5074316 MACS_peak_523 174.88 +chr1 5074836 5074948 MACS_peak_524 100.24 +chr1 5075666 5076224 MACS_peak_525 225.27 +chr1 5076921 5077525 MACS_peak_526 258.45 +chr1 5077697 5079141 MACS_peak_527 428.10 +chr1 5079395 5079507 MACS_peak_528 100.24 +chr1 5079650 5079862 MACS_peak_529 100.24 +chr1 5081683 5081832 MACS_peak_530 137.07 +chr1 5081976 5082088 MACS_peak_531 100.24 +chr1 5082876 5083204 MACS_peak_532 95.38 +chr1 5083349 5083507 MACS_peak_533 100.24 +chr1 5083630 5083769 MACS_peak_534 137.07 +chr1 5084103 5084215 MACS_peak_535 100.24 +chr1 5084548 5084886 MACS_peak_536 130.08 +chr1 5085651 5085824 MACS_peak_537 137.07 +chr1 5086191 5086343 MACS_peak_538 100.24 +chr1 5086595 5087134 MACS_peak_539 190.83 +chr1 5087415 5087527 MACS_peak_540 100.24 +chr1 5087866 5088086 MACS_peak_541 137.07 +chr1 5088244 5088578 MACS_peak_542 203.30 +chr1 5089007 5089195 MACS_peak_543 137.07 +chr1 5089715 5089831 MACS_peak_544 137.07 +chr1 5090015 5090353 MACS_peak_545 130.08 +chr1 5090497 5090609 MACS_peak_546 100.24 +chr1 5091306 5091577 MACS_peak_547 133.92 +chr1 5091972 5092130 MACS_peak_548 100.24 +chr1 5092602 5092857 MACS_peak_549 172.26 +chr1 5093070 5093254 MACS_peak_550 100.24 +chr1 5093580 5094069 MACS_peak_551 158.12 +chr1 5094211 5094776 MACS_peak_552 485.14 +chr1 5094935 5095339 MACS_peak_553 272.42 +chr1 5095631 5095955 MACS_peak_554 130.82 +chr1 5096075 5096386 MACS_peak_555 131.53 +chr1 5097061 5097359 MACS_peak_556 96.63 +chr1 5097863 5098163 MACS_peak_557 206.10 +chr1 5098989 5099101 MACS_peak_558 100.24 +chr1 5099702 5099814 MACS_peak_559 100.24 +chr1 5100443 5100725 MACS_peak_560 97.35 +chr1 5105969 5106193 MACS_peak_561 174.88 +chr1 5106329 5106441 MACS_peak_562 100.24 +chr1 5106565 5106677 MACS_peak_563 100.24 +chr1 5106814 5107170 MACS_peak_564 238.93 +chr1 5107427 5107660 MACS_peak_565 136.54 +chr1 5107833 5108160 MACS_peak_566 95.42 +chr1 5108453 5108565 MACS_peak_567 100.24 +chr1 5108705 5108860 MACS_peak_568 100.24 +chr1 5109105 5109217 MACS_peak_569 100.24 +chr1 5109576 5109688 MACS_peak_570 100.24 +chr1 5110000 5110112 MACS_peak_571 100.24 +chr1 5110475 5111286 MACS_peak_572 213.91 +chr1 5111879 5112070 MACS_peak_573 100.24 +chr1 5112186 5112435 MACS_peak_574 135.39 +chr1 5112580 5112692 MACS_peak_575 100.24 +chr1 5113545 5113657 MACS_peak_576 100.24 +chr1 5114104 5114508 MACS_peak_577 310.25 +chr1 5115038 5115191 MACS_peak_578 100.24 +chr1 5115640 5115752 MACS_peak_579 100.24 +chr1 5116113 5116531 MACS_peak_580 161.53 +chr1 5116969 5117081 MACS_peak_581 100.24 +chr1 5118784 5118914 MACS_peak_582 213.48 +chr1 5119112 5119565 MACS_peak_583 125.00 +chr1 5119931 5120133 MACS_peak_584 100.24 +chr1 5120509 5120783 MACS_peak_585 97.73 +chr1 5122513 5123111 MACS_peak_586 331.52 +chr1 5124258 5124546 MACS_peak_587 132.86 +chr1 5125243 5125355 MACS_peak_588 100.24 +chr1 5125474 5126301 MACS_peak_589 247.53 +chr1 5126879 5127188 MACS_peak_590 96.16 +chr1 5127510 5127622 MACS_peak_591 100.24 +chr1 5128418 5128797 MACS_peak_592 200.01 +chr1 5129100 5129423 MACS_peak_593 130.87 +chr1 5129639 5130227 MACS_peak_594 295.59 +chr1 5130392 5130670 MACS_peak_595 208.08 +chr1 5131190 5131730 MACS_peak_596 226.27 +chr1 5131882 5132669 MACS_peak_597 428.13 +chr1 5133036 5133148 MACS_peak_598 100.24 +chr1 5133406 5133811 MACS_peak_599 162.22 +chr1 5134265 5134418 MACS_peak_600 100.24 +chr1 5134545 5135189 MACS_peak_601 220.92 +chr1 5135648 5135760 MACS_peak_602 100.24 +chr1 5135922 5136197 MACS_peak_603 133.66 +chr1 5137176 5137712 MACS_peak_604 190.98 +chr1 5138380 5138492 MACS_peak_605 100.24 +chr1 5138673 5138785 MACS_peak_606 100.24 +chr1 5139178 5139447 MACS_peak_607 171.10 +chr1 5140390 5140502 MACS_peak_608 100.24 +chr1 5141274 5141386 MACS_peak_609 100.24 +chr1 5141930 5142225 MACS_peak_610 96.76 +chr1 5142569 5143225 MACS_peak_611 220.36 +chr1 5143538 5143758 MACS_peak_612 137.07 +chr1 5144459 5144571 MACS_peak_613 100.24 +chr1 5145367 5145546 MACS_peak_614 137.07 +chr1 5146746 5146858 MACS_peak_615 100.24 +chr1 5147216 5147328 MACS_peak_616 100.24 +chr1 5148439 5148925 MACS_peak_617 193.53 +chr1 5149170 5149620 MACS_peak_618 195.54 +chr1 5149975 5150169 MACS_peak_619 137.07 +chr1 5150944 5151056 MACS_peak_620 100.24 +chr1 5151214 5151612 MACS_peak_621 235.55 +chr1 5151849 5152235 MACS_peak_622 163.26 +chr1 5152352 5152662 MACS_peak_623 131.58 +chr1 5152894 5153006 MACS_peak_624 100.24 +chr1 5153179 5153550 MACS_peak_625 128.46 +chr1 5153683 5154461 MACS_peak_626 249.65 +chr1 5154978 5155690 MACS_peak_627 217.87 +chr1 5156139 5156251 MACS_peak_628 100.24 +chr1 5157081 5157193 MACS_peak_629 100.24 +chr1 5159033 5159145 MACS_peak_630 100.24 +chr1 5159942 5160260 MACS_peak_631 95.79 +chr1 5160427 5160539 MACS_peak_632 100.24 +chr1 5161207 5161319 MACS_peak_633 100.24 +chr1 5161624 5161843 MACS_peak_634 100.24 +chr1 5162094 5162256 MACS_peak_635 100.24 +chr1 5162373 5162485 MACS_peak_636 100.24 +chr1 5164184 5164730 MACS_peak_637 225.94 +chr1 5165964 5166076 MACS_peak_638 100.24 +chr1 5166208 5166320 MACS_peak_639 100.24 +chr1 5166857 5167382 MACS_peak_640 227.13 +chr1 5167811 5167961 MACS_peak_641 252.75 +chr1 5168164 5168628 MACS_peak_642 230.88 +chr1 5168852 5168964 MACS_peak_643 100.24 +chr1 5169149 5169385 MACS_peak_644 136.32 +chr1 5170312 5170424 MACS_peak_645 100.24 +chr1 5170892 5171004 MACS_peak_646 100.24 +chr1 5171504 5171624 MACS_peak_647 137.07 +chr1 5172575 5172847 MACS_peak_648 97.82 +chr1 5173299 5173617 MACS_peak_649 131.14 +chr1 5174320 5175248 MACS_peak_650 677.53 +chr1 5176172 5176514 MACS_peak_651 202.69 +chr1 5176705 5177327 MACS_peak_652 403.86 +chr1 5177495 5178136 MACS_peak_653 292.21 +chr1 5178335 5178447 MACS_peak_654 100.24 +chr1 5178577 5179078 MACS_peak_655 264.94 +chr1 5179327 5179439 MACS_peak_656 100.24 +chr1 5179573 5179930 MACS_peak_657 201.57 +chr1 5180202 5180486 MACS_peak_658 133.11 +chr1 5187026 5187438 MACS_peak_659 126.64 +chr1 5189520 5189632 MACS_peak_660 100.24 +chr1 5190641 5190753 MACS_peak_661 100.24 +chr1 5193903 5194083 MACS_peak_662 137.07 +chr1 5194313 5194507 MACS_peak_663 100.24 +chr1 5194886 5195134 MACS_peak_664 211.06 +chr1 5195426 5195539 MACS_peak_665 174.88 +chr1 5195775 5195951 MACS_peak_666 137.07 +chr1 5196298 5197058 MACS_peak_667 215.89 +chr1 5197469 5197637 MACS_peak_668 100.24 +chr1 5197796 5198864 MACS_peak_669 591.38 +chr1 5199145 5199310 MACS_peak_670 174.88 +chr1 5199643 5199824 MACS_peak_671 137.07 +chr1 5200158 5200523 MACS_peak_672 93.99 +chr1 5200710 5201367 MACS_peak_673 185.68 +chr1 5201497 5202378 MACS_peak_674 531.75 +chr1 5202917 5203141 MACS_peak_675 213.48 +chr1 5203327 5203439 MACS_peak_676 100.24 +chr1 5204084 5204196 MACS_peak_677 100.24 +chr1 5204570 5204682 MACS_peak_678 100.24 +chr1 5205197 5205309 MACS_peak_679 100.24 +chr1 5205592 5205787 MACS_peak_680 137.07 +chr1 5205929 5206041 MACS_peak_681 100.24 +chr1 5206900 5207012 MACS_peak_682 100.24 +chr1 5207183 5207396 MACS_peak_683 137.07 +chr1 5207524 5207736 MACS_peak_684 137.07 +chr1 5207873 5209950 MACS_peak_685 746.37 +chr1 5210089 5210201 MACS_peak_686 100.24 +chr1 5210451 5210563 MACS_peak_687 100.24 +chr1 5211018 5211130 MACS_peak_688 100.24 +chr1 5211276 5211388 MACS_peak_689 100.24 +chr1 5211564 5211734 MACS_peak_690 100.24 +chr1 5212067 5212435 MACS_peak_691 275.66 +chr1 5212594 5212753 MACS_peak_692 100.24 +chr1 5212901 5213013 MACS_peak_693 100.24 +chr1 5213338 5213697 MACS_peak_694 201.42 +chr1 5214024 5214232 MACS_peak_695 137.07 +chr1 5214383 5214747 MACS_peak_696 128.80 +chr1 5214900 5215012 MACS_peak_697 100.24 +chr1 5215554 5215666 MACS_peak_698 100.24 +chr1 5216098 5216421 MACS_peak_699 95.58 +chr1 5216849 5217112 MACS_peak_700 171.59 +chr1 5217261 5217531 MACS_peak_701 208.84 +chr1 5217649 5217761 MACS_peak_702 100.24 +chr1 5218122 5218337 MACS_peak_703 137.07 +chr1 5218836 5219185 MACS_peak_704 165.45 +chr1 5219969 5220835 MACS_peak_705 350.84 +chr1 5220968 5221934 MACS_peak_706 416.57 +chr1 5222619 5223011 MACS_peak_707 127.51 +chr1 5223269 5223882 MACS_peak_708 257.93 +chr1 5224180 5225221 MACS_peak_709 483.94 +chr1 5225717 5226312 MACS_peak_710 223.32 +chr1 5226601 5226880 MACS_peak_711 97.49 +chr1 5227642 5227754 MACS_peak_712 100.24 +chr1 5229513 5229625 MACS_peak_713 100.24 +chr1 5229772 5230341 MACS_peak_714 260.52 +chr1 5230857 5231047 MACS_peak_715 137.07 +chr1 5231309 5231610 MACS_peak_716 96.50 +chr1 5232430 5232542 MACS_peak_717 100.24 +chr1 5232868 5233105 MACS_peak_718 136.25 +chr1 5234222 5234548 MACS_peak_719 130.71 +chr1 5234732 5234930 MACS_peak_720 137.07 +chr1 5235612 5236082 MACS_peak_721 158.98 +chr1 5236311 5236423 MACS_peak_722 100.24 +chr1 5236609 5236721 MACS_peak_723 100.24 +chr1 5237018 5237130 MACS_peak_724 100.24 +chr1 5237454 5237566 MACS_peak_725 100.24 +chr1 5238037 5238329 MACS_peak_726 132.62 +chr1 5239958 5240439 MACS_peak_727 229.79 +chr1 5240929 5241239 MACS_peak_728 168.02 +chr1 5247940 5248227 MACS_peak_729 132.92 +chr1 5248801 5249638 MACS_peak_730 179.37 +chr1 5249894 5250597 MACS_peak_731 434.51 +chr1 5250980 5251895 MACS_peak_732 278.31 +chr1 5253201 5253499 MACS_peak_733 206.27 +chr1 5253899 5254138 MACS_peak_734 136.10 +chr1 5254545 5254925 MACS_peak_735 199.94 +chr1 5255688 5255800 MACS_peak_736 100.24 +chr1 5256047 5256432 MACS_peak_737 199.60 +chr1 5256609 5256721 MACS_peak_738 100.24 +chr1 5257206 5257318 MACS_peak_739 100.24 +chr1 5257448 5257698 MACS_peak_740 135.32 +chr1 5257987 5258099 MACS_peak_741 100.24 +chr1 5264494 5264931 MACS_peak_742 160.56 +chr1 5265092 5265455 MACS_peak_743 164.59 +chr1 5266250 5266425 MACS_peak_744 100.24 +chr1 5267306 5268160 MACS_peak_745 351.50 +chr1 5269815 5269927 MACS_peak_746 100.24 +chr1 5270319 5270873 MACS_peak_747 372.17 +chr1 5271490 5271846 MACS_peak_748 129.18 +chr1 5272438 5272660 MACS_peak_749 100.24 +chr1 5272916 5273028 MACS_peak_750 100.24 +chr1 5273367 5273479 MACS_peak_751 100.24 +chr1 5273651 5273916 MACS_peak_752 171.42 +chr1 5274301 5274503 MACS_peak_753 100.24 +chr1 5274805 5274917 MACS_peak_754 100.24 +chr1 5275154 5275487 MACS_peak_755 166.46 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5292542 MACS_peak_779 194.29 +chr1 5292725 5293056 MACS_peak_780 166.60 +chr1 5293630 5293742 MACS_peak_781 100.24 +chr1 5294389 5294501 MACS_peak_782 100.24 +chr1 5295225 5295496 MACS_peak_783 170.94 +chr1 5295638 5296068 MACS_peak_784 160.91 +chr1 5296664 5296893 MACS_peak_785 100.06 +chr1 5297035 5297147 MACS_peak_786 100.24 +chr1 5297414 5297652 MACS_peak_787 173.76 +chr1 5298093 5298205 MACS_peak_788 100.24 +chr1 5298450 5298562 MACS_peak_789 100.24 +chr1 5298836 5298948 MACS_peak_790 100.24 +chr1 5299179 5299291 MACS_peak_791 100.24 +chr1 5301534 5302030 MACS_peak_792 123.42 +chr1 5302355 5302467 MACS_peak_793 100.24 +chr1 5303486 5303988 MACS_peak_794 192.69 +chr1 5304193 5304415 MACS_peak_795 100.24 +chr1 5304910 5305054 MACS_peak_796 137.07 +chr1 5305212 5305561 MACS_peak_797 277.50 +chr1 5305849 5305961 MACS_peak_798 100.24 +chr1 5306358 5307242 MACS_peak_799 421.57 +chr1 5307503 5307615 MACS_peak_800 100.24 +chr1 5307966 5308078 MACS_peak_801 100.24 +chr1 5308356 5308796 MACS_peak_802 160.42 +chr1 5308937 5309049 MACS_peak_803 100.24 +chr1 5309978 5310174 MACS_peak_804 213.48 +chr1 5310859 5311560 MACS_peak_805 360.93 +chr1 5312430 5312542 MACS_peak_806 100.24 +chr1 5312774 5313432 MACS_peak_807 220.26 +chr1 5313660 5313837 MACS_peak_808 137.07 +chr1 5314653 5314836 MACS_peak_809 174.88 +chr1 5315019 5315195 MACS_peak_810 137.07 +chr1 5315769 5315897 MACS_peak_811 137.07 +chr1 5316584 5316696 MACS_peak_812 100.24 +chr1 5316832 5316963 MACS_peak_813 137.07 +chr1 5317136 5317248 MACS_peak_814 100.24 +chr1 5317391 5317503 MACS_peak_815 100.24 +chr1 5317762 5317960 MACS_peak_816 137.07 +chr1 5318214 5318326 MACS_peak_817 100.24 +chr1 5318467 5318579 MACS_peak_818 100.24 +chr1 5319598 5319710 MACS_peak_819 100.24 +chr1 5323467 5323847 MACS_peak_820 163.60 +chr1 5324049 5324358 MACS_peak_821 96.16 +chr1 5324608 5325155 MACS_peak_822 225.88 +chr1 5325488 5325600 MACS_peak_823 100.24 +chr1 5325740 5325852 MACS_peak_824 100.24 +chr1 5326235 5326358 MACS_peak_825 137.07 +chr1 5326624 5326736 MACS_peak_826 100.24 +chr1 5327281 5327573 MACS_peak_827 132.62 +chr1 5327763 5327875 MACS_peak_828 100.24 +chr1 5328183 5328407 MACS_peak_829 137.07 +chr1 5328841 5329232 MACS_peak_830 127.55 +chr1 5329875 5330189 MACS_peak_831 95.95 +chr1 5330659 5330843 MACS_peak_832 137.07 +chr1 5331227 5331644 MACS_peak_833 126.43 +chr1 5332229 5332997 MACS_peak_834 148.32 +chr1 5333621 5333919 MACS_peak_835 96.63 +chr1 5336159 5336284 MACS_peak_836 137.07 +chr1 5336624 5336736 MACS_peak_837 100.24 +chr1 5338469 5338837 MACS_peak_838 128.61 +chr1 5341114 5341226 MACS_peak_839 100.24 +chr1 5348682 5349065 MACS_peak_840 199.74 +chr1 5351411 5351523 MACS_peak_841 100.24 +chr1 5353817 5354635 MACS_peak_842 213.65 +chr1 5354853 5354965 MACS_peak_843 100.24 +chr1 5355226 5355738 MACS_peak_844 122.87 +chr1 5356031 5356587 MACS_peak_845 190.03 +chr1 5356826 5356938 MACS_peak_846 100.24 +chr1 5358473 5358620 MACS_peak_847 137.07 +chr1 5359262 5359374 MACS_peak_848 100.24 +chr1 5359830 5360056 MACS_peak_849 100.24 +chr1 5360690 5360802 MACS_peak_850 100.24 +chr1 5361077 5361237 MACS_peak_851 100.24 +chr1 5361530 5361845 MACS_peak_852 131.31 +chr1 5362114 5362226 MACS_peak_853 100.24 +chr1 5362446 5362765 MACS_peak_854 131.09 +chr1 5363772 5363884 MACS_peak_855 100.24 +chr1 5364061 5364281 MACS_peak_856 137.07 +chr1 5364765 5365453 MACS_peak_857 289.45 +chr1 5369402 5369522 MACS_peak_858 137.07 +chr1 5369724 5370212 MACS_peak_859 158.17 +chr1 5370537 5370922 MACS_peak_860 199.60 +chr1 5371214 5371326 MACS_peak_861 100.24 +chr1 5371623 5371735 MACS_peak_862 100.24 +chr1 5372053 5372738 MACS_peak_863 184.59 +chr1 5372983 5373095 MACS_peak_864 100.24 +chr1 5373677 5373936 MACS_peak_865 134.71 +chr1 5374110 5374317 MACS_peak_866 100.24 +chr1 5374621 5374787 MACS_peak_867 100.24 +chr1 5375015 5375148 MACS_peak_868 137.07 +chr1 5375692 5375804 MACS_peak_869 100.24 +chr1 5376645 5376921 MACS_peak_870 97.63 +chr1 5377193 5377305 MACS_peak_871 100.24 +chr1 5377627 5377739 MACS_peak_872 100.24 +chr1 5378171 5378283 MACS_peak_873 100.24 +chr1 5378780 5378892 MACS_peak_874 100.24 +chr1 5379864 5379976 MACS_peak_875 100.24 +chr1 5380338 5380497 MACS_peak_876 100.24 +chr1 5381362 5381897 MACS_peak_877 156.17 +chr1 5382544 5382739 MACS_peak_878 137.07 +chr1 5383063 5383175 MACS_peak_879 100.24 +chr1 5384104 5384571 MACS_peak_880 267.38 +chr1 5384899 5385011 MACS_peak_881 100.24 +chr1 5385907 5386019 MACS_peak_882 100.24 +chr1 5386152 5386562 MACS_peak_883 161.95 +chr1 5386780 5387026 MACS_peak_884 250.17 +chr1 5387186 5387298 MACS_peak_885 100.24 +chr1 5387430 5387542 MACS_peak_886 100.24 +chr1 5388238 5388350 MACS_peak_887 100.24 +chr1 5388677 5388789 MACS_peak_888 100.24 +chr1 5389752 5389864 MACS_peak_889 100.24 +chr1 5390871 5390983 MACS_peak_890 100.24 +chr1 5391768 5391880 MACS_peak_891 100.24 +chr1 5392107 5392219 MACS_peak_892 100.24 +chr1 5392575 5392687 MACS_peak_893 100.24 +chr1 5392911 5393023 MACS_peak_894 100.24 +chr1 5393487 5393599 MACS_peak_895 100.24 +chr1 5393950 5394062 MACS_peak_896 100.24 +chr1 5394309 5394421 MACS_peak_897 100.24 +chr1 5394907 5395019 MACS_peak_898 100.24 +chr1 5395147 5395259 MACS_peak_899 100.24 +chr1 5395472 5395733 MACS_peak_900 134.57 +chr1 5396464 5396791 MACS_peak_901 166.86 +chr1 5397126 5397238 MACS_peak_902 100.24 +chr1 5397681 5397793 MACS_peak_903 100.24 +chr1 5398165 5398319 MACS_peak_904 100.24 +chr1 5399619 5399760 MACS_peak_905 137.07 +chr1 5400650 5401142 MACS_peak_906 265.57 +chr1 5401404 5401516 MACS_peak_907 100.24 +chr1 5401643 5401755 MACS_peak_908 100.24 +chr1 5402151 5402415 MACS_peak_909 98.21 +chr1 5402963 5403143 MACS_peak_910 100.24 +chr1 5403907 5404247 MACS_peak_911 129.98 +chr1 5405321 5405433 MACS_peak_912 100.24 +chr1 5405744 5405856 MACS_peak_913 100.24 +chr1 5407339 5407836 MACS_peak_914 157.77 +chr1 5408061 5408173 MACS_peak_915 100.24 +chr1 5408557 5408669 MACS_peak_916 100.24 +chr1 5408846 5409368 MACS_peak_917 191.67 +chr1 5409651 5409882 MACS_peak_918 174.41 +chr1 5410205 5410317 MACS_peak_919 100.24 +chr1 5410454 5410566 MACS_peak_920 100.24 +chr1 5410745 5410915 MACS_peak_921 100.24 +chr1 5411515 5411627 MACS_peak_922 100.24 +chr1 5411988 5412276 MACS_peak_923 207.16 +chr1 5412450 5412739 MACS_peak_924 169.54 +chr1 5412903 5413063 MACS_peak_925 100.24 +chr1 5413539 5413651 MACS_peak_926 100.24 +chr1 5414865 5414977 MACS_peak_927 100.24 +chr1 5420860 5421109 MACS_peak_928 135.39 +chr1 5428000 5428519 MACS_peak_929 122.63 +chr1 5429035 5429300 MACS_peak_930 134.31 +chr1 5429474 5430067 MACS_peak_931 331.88 +chr1 5430868 5430980 MACS_peak_932 100.24 +chr1 5431368 5431603 MACS_peak_933 99.73 +chr1 5431763 5432040 MACS_peak_934 133.54 +chr1 5432590 5433045 MACS_peak_935 124.92 +chr1 5433978 5434479 MACS_peak_936 123.25 +chr1 5436699 5436811 MACS_peak_937 100.24 +chr1 5439583 5439762 MACS_peak_938 100.24 +chr1 5439969 5440081 MACS_peak_939 100.24 +chr1 5440202 5440466 MACS_peak_940 134.37 +chr1 5442066 5442392 MACS_peak_941 241.61 +chr1 5442655 5442900 MACS_peak_942 135.67 +chr1 5443104 5443663 MACS_peak_943 155.22 +chr1 5444022 5444134 MACS_peak_944 100.24 +chr1 5444854 5444966 MACS_peak_945 100.24 +chr1 5446233 5446411 MACS_peak_946 100.24 +chr1 5446923 5447035 MACS_peak_947 100.24 +chr1 5447953 5448404 MACS_peak_948 268.59 +chr1 5448527 5448801 MACS_peak_949 97.73 +chr1 5448936 5449234 MACS_peak_950 96.63 +chr1 5451111 5451223 MACS_peak_951 100.24 +chr1 5451833 5451945 MACS_peak_952 100.24 +chr1 5452089 5452282 MACS_peak_953 100.24 +chr1 5452539 5452780 MACS_peak_954 135.96 +chr1 5453277 5453389 MACS_peak_955 100.24 +chr1 5453504 5454001 MACS_peak_956 228.79 +chr1 5454325 5454437 MACS_peak_957 100.24 +chr1 5454758 5455004 MACS_peak_958 99.13 +chr1 5455134 5455246 MACS_peak_959 100.24 +chr1 5455945 5456161 MACS_peak_960 174.88 +chr1 5456297 5456409 MACS_peak_961 100.24 +chr1 5456864 5457147 MACS_peak_962 97.31 +chr1 5457642 5457754 MACS_peak_963 100.24 +chr1 5458103 5458215 MACS_peak_964 100.24 +chr1 5460540 5460652 MACS_peak_965 100.24 +chr1 5461820 5461932 MACS_peak_966 100.24 +chr1 5462911 5463023 MACS_peak_967 100.24 +chr1 5470721 5470985 MACS_peak_968 134.37 +chr1 5472485 5472597 MACS_peak_969 100.24 +chr1 5475515 5475779 MACS_peak_970 209.43 +chr1 5476676 5476818 MACS_peak_971 137.07 +chr1 5478224 5478336 MACS_peak_972 100.24 +chr1 5478474 5478586 MACS_peak_973 100.24 +chr1 5478817 5478929 MACS_peak_974 100.24 +chr1 5480909 5481021 MACS_peak_975 100.24 +chr1 5481599 5481711 MACS_peak_976 100.24 +chr1 5482077 5482189 MACS_peak_977 100.24 +chr1 5483535 5483720 MACS_peak_978 137.07 +chr1 5484900 5485245 MACS_peak_979 129.73 +chr1 5485374 5485486 MACS_peak_980 100.24 +chr1 5486127 5486239 MACS_peak_981 100.24 +chr1 5486825 5486937 MACS_peak_982 100.24 +chr1 5487580 5487748 MACS_peak_983 100.24 +chr1 5487864 5488141 MACS_peak_984 170.46 +chr1 5488854 5488966 MACS_peak_985 100.24 +chr1 5492731 5492846 MACS_peak_986 137.07 +chr1 5493221 5493333 MACS_peak_987 100.24 +chr1 5493915 5494069 MACS_peak_988 100.24 +chr1 5496103 5496419 MACS_peak_989 131.25 +chr1 5496817 5497009 MACS_peak_990 137.07 +chr1 5497128 5497240 MACS_peak_991 100.24 +chr1 5497499 5497611 MACS_peak_992 100.24 +chr1 5497727 5498173 MACS_peak_993 160.12 +chr1 5498588 5498967 MACS_peak_994 128.09 +chr1 5501839 5501951 MACS_peak_995 100.24 +chr1 5502127 5502441 MACS_peak_996 95.95 +chr1 5502702 5502889 MACS_peak_997 100.24 +chr1 5503139 5503251 MACS_peak_998 100.24 +chr1 5503416 5503932 MACS_peak_999 122.74 +chr1 5504222 5504334 MACS_peak_1000 100.24 +chr1 5504630 5504773 MACS_peak_1001 137.07 +chr1 5505091 5505493 MACS_peak_1002 127.07 +chr1 5505842 5506053 MACS_peak_1003 100.24 +chr1 5506187 5506366 MACS_peak_1004 137.07 +chr1 5506700 5506812 MACS_peak_1005 100.24 +chr1 5507137 5508211 MACS_peak_1006 205.38 +chr1 5508512 5508959 MACS_peak_1007 160.07 +chr1 5509346 5509458 MACS_peak_1008 100.24 +chr1 5509588 5509700 MACS_peak_1009 100.24 +chr1 5510449 5511245 MACS_peak_1010 427.49 +chr1 5511937 5512049 MACS_peak_1011 100.24 +chr1 5512408 5512787 MACS_peak_1012 237.03 +chr1 5514476 5514635 MACS_peak_1013 100.24 +chr1 5514751 5515081 MACS_peak_1014 130.50 +chr1 5515212 5515324 MACS_peak_1015 100.24 +chr1 5515589 5515853 MACS_peak_1016 134.37 +chr1 5516182 5516294 MACS_peak_1017 100.24 +chr1 5516448 5516560 MACS_peak_1018 100.24 +chr1 5522530 5522642 MACS_peak_1019 100.24 +chr1 5522808 5523114 MACS_peak_1020 96.29 +chr1 5523747 5523859 MACS_peak_1021 100.24 +chr1 5524091 5524648 MACS_peak_1022 155.30 +chr1 5525817 5525929 MACS_peak_1023 100.24 +chr1 5526129 5526352 MACS_peak_1024 100.24 +chr1 5526994 5527106 MACS_peak_1025 100.24 +chr1 5527307 5527419 MACS_peak_1026 100.24 +chr1 5527948 5528060 MACS_peak_1027 100.24 +chr1 5528479 5528591 MACS_peak_1028 100.24 +chr1 5528843 5528955 MACS_peak_1029 100.24 +chr1 5529535 5529795 MACS_peak_1030 98.41 +chr1 5530073 5530501 MACS_peak_1031 125.98 +chr1 5530662 5530801 MACS_peak_1032 137.07 +chr1 5530933 5531145 MACS_peak_1033 100.24 +chr1 5532316 5532575 MACS_peak_1034 209.93 +chr1 5532814 5533414 MACS_peak_1035 223.07 +chr1 5533683 5534046 MACS_peak_1036 238.34 +chr1 5534750 5534862 MACS_peak_1037 100.24 +chr1 5535654 5536031 MACS_peak_1038 128.19 +chr1 5539337 5539449 MACS_peak_1039 100.24 +chr1 5539958 5540105 MACS_peak_1040 174.88 +chr1 5540372 5540520 MACS_peak_1041 137.07 +chr1 5540857 5541254 MACS_peak_1042 162.65 +chr1 5541543 5541655 MACS_peak_1043 100.24 +chr1 5547312 5547424 MACS_peak_1044 100.24 +chr1 5548151 5548263 MACS_peak_1045 100.24 +chr1 5548760 5549292 MACS_peak_1046 226.73 +chr1 5549828 5549972 MACS_peak_1047 137.07 +chr1 5550175 5550306 MACS_peak_1048 137.07 +chr1 5550522 5550679 MACS_peak_1049 100.24 +chr1 5550864 5551382 MACS_peak_1050 156.87 +chr1 5552871 5552983 MACS_peak_1051 100.24 +chr1 5555738 5555850 MACS_peak_1052 100.24 +chr1 5559490 5559602 MACS_peak_1053 100.24 +chr1 5560846 5560958 MACS_peak_1054 100.24 +chr1 5561340 5561521 MACS_peak_1055 100.24 +chr1 5563505 5563769 MACS_peak_1056 98.21 +chr1 5564533 5564700 MACS_peak_1057 100.24 +chr1 5564912 5565024 MACS_peak_1058 100.24 +chr1 5565259 5565371 MACS_peak_1059 100.24 +chr1 5568363 5568657 MACS_peak_1060 283.46 +chr1 5569291 5570044 MACS_peak_1061 216.17 +chr1 5570260 5570902 MACS_peak_1062 292.15 +chr1 5571279 5571615 MACS_peak_1063 130.19 +chr1 5571758 5572146 MACS_peak_1064 236.32 +chr1 5572441 5572553 MACS_peak_1065 100.24 +chr1 5572747 5572859 MACS_peak_1066 100.24 +chr1 5573400 5573512 MACS_peak_1067 100.24 +chr1 5576223 5576419 MACS_peak_1068 100.24 +chr1 5576544 5576662 MACS_peak_1069 137.07 +chr1 5576892 5577241 MACS_peak_1070 129.53 +chr1 5577515 5578153 MACS_peak_1071 256.54 +chr1 5578298 5578410 MACS_peak_1072 100.24 +chr1 5578808 5578920 MACS_peak_1073 100.24 +chr1 5579210 5579554 MACS_peak_1074 129.78 +chr1 5579672 5580062 MACS_peak_1075 199.26 +chr1 5580481 5580593 MACS_peak_1076 100.24 +chr1 5580882 5580994 MACS_peak_1077 100.24 +chr1 5581303 5581626 MACS_peak_1078 241.89 +chr1 5581877 5581989 MACS_peak_1079 100.24 +chr1 5582232 5582417 MACS_peak_1080 100.24 +chr1 5582575 5583094 MACS_peak_1081 122.63 +chr1 5583521 5583633 MACS_peak_1082 100.24 +chr1 5583818 5583930 MACS_peak_1083 100.24 +chr1 5584211 5584323 MACS_peak_1084 100.24 +chr1 5584502 5584788 MACS_peak_1085 97.17 +chr1 5585486 5585847 MACS_peak_1086 164.71 +chr1 5586024 5586188 MACS_peak_1087 174.88 +chr1 5586310 5586426 MACS_peak_1088 137.07 +chr1 5586843 5586955 MACS_peak_1089 100.24 +chr1 5587182 5587294 MACS_peak_1090 100.24 +chr1 5587715 5588020 MACS_peak_1091 131.87 +chr1 5588165 5588277 MACS_peak_1092 100.24 +chr1 5588680 5588894 MACS_peak_1093 174.88 +chr1 5589048 5589314 MACS_peak_1094 98.11 +chr1 5589639 5589751 MACS_peak_1095 100.24 +chr1 5589901 5590358 MACS_peak_1096 231.34 +chr1 5591315 5591427 MACS_peak_1097 100.24 +chr1 5591562 5591674 MACS_peak_1098 100.24 +chr1 5591879 5591991 MACS_peak_1099 100.24 +chr1 5592196 5592429 MACS_peak_1100 99.84 +chr1 5593248 5594359 MACS_peak_1101 588.30 +chr1 5594491 5594708 MACS_peak_1102 174.88 +chr1 5595151 5595263 MACS_peak_1103 100.24 +chr1 5595498 5595820 MACS_peak_1104 130.92 +chr1 5596027 5596139 MACS_peak_1105 100.24 +chr1 5596276 5596388 MACS_peak_1106 100.24 +chr1 5596667 5596945 MACS_peak_1107 208.08 +chr1 5597235 5597476 MACS_peak_1108 99.40 +chr1 5598124 5598263 MACS_peak_1109 137.07 +chr1 5598532 5598644 MACS_peak_1110 100.24 +chr1 5598989 5599453 MACS_peak_1111 159.26 +chr1 5599963 5600126 MACS_peak_1112 174.88 +chr1 5600438 5600611 MACS_peak_1113 100.24 +chr1 5601284 5601731 MACS_peak_1114 125.23 +chr1 5602492 5602639 MACS_peak_1115 137.07 +chr1 5603011 5603123 MACS_peak_1116 100.24 +chr1 5603421 5603960 MACS_peak_1117 156.01 +chr1 5604580 5604898 MACS_peak_1118 95.79 +chr1 5605109 5605221 MACS_peak_1119 100.24 +chr1 5605645 5605886 MACS_peak_1120 99.40 +chr1 5606332 5606831 MACS_peak_1121 192.84 +chr1 5607289 5607401 MACS_peak_1122 100.24 +chr1 5607640 5607752 MACS_peak_1123 100.24 +chr1 5608156 5608359 MACS_peak_1124 100.24 +chr1 5609092 5609220 MACS_peak_1125 137.07 +chr1 5609679 5609791 MACS_peak_1126 100.24 +chr1 5610548 5610660 MACS_peak_1127 100.24 +chr1 5610980 5611132 MACS_peak_1128 100.24 +chr1 5611284 5611396 MACS_peak_1129 100.24 +chr1 5611566 5611772 MACS_peak_1130 100.24 +chr1 5611896 5612157 MACS_peak_1131 98.36 +chr1 5612291 5612403 MACS_peak_1132 100.24 +chr1 5612549 5612718 MACS_peak_1133 174.88 +chr1 5612859 5613143 MACS_peak_1134 133.11 +chr1 5613560 5613672 MACS_peak_1135 100.24 +chr1 5614561 5615373 MACS_peak_1136 282.97 +chr1 5615704 5615816 MACS_peak_1137 100.24 +chr1 5616141 5616253 MACS_peak_1138 100.24 +chr1 5616372 5616484 MACS_peak_1139 100.24 +chr1 5616668 5617219 MACS_peak_1140 335.07 +chr1 5617497 5617795 MACS_peak_1141 96.63 +chr1 5619893 5620086 MACS_peak_1142 100.24 +chr1 5620435 5620547 MACS_peak_1143 100.24 +chr1 5621379 5622034 MACS_peak_1144 220.40 +chr1 5624571 5624683 MACS_peak_1145 100.24 +chr1 5625232 5625344 MACS_peak_1146 100.24 +chr1 5627078 5627190 MACS_peak_1147 100.24 +chr1 5632017 5632129 MACS_peak_1148 100.24 +chr1 5632376 5632652 MACS_peak_1149 170.54 +chr1 5633321 5633535 MACS_peak_1150 137.07 +chr1 5633696 5633881 MACS_peak_1151 100.24 +chr1 5634469 5634687 MACS_peak_1152 100.24 +chr1 5635062 5635329 MACS_peak_1153 98.06 +chr1 5635461 5635573 MACS_peak_1154 100.24 +chr1 5635728 5635840 MACS_peak_1155 100.24 +chr1 5636596 5636789 MACS_peak_1156 100.24 +chr1 5637075 5637187 MACS_peak_1157 100.24 +chr1 5637607 5637719 MACS_peak_1158 100.24 +chr1 5640953 5641065 MACS_peak_1159 100.24 +chr1 5643184 5643361 MACS_peak_1160 100.24 +chr1 5644450 5644562 MACS_peak_1161 100.24 +chr1 5646326 5646650 MACS_peak_1162 130.82 +chr1 5646766 5647194 MACS_peak_1163 125.98 +chr1 5647474 5647766 MACS_peak_1164 132.62 +chr1 5648437 5649089 MACS_peak_1165 364.39 +chr1 5649411 5650167 MACS_peak_1166 467.44 +chr1 5650744 5650944 MACS_peak_1167 137.07 +chr1 5651395 5651820 MACS_peak_1168 197.02 +chr1 5652003 5652323 MACS_peak_1169 167.33 +chr1 5652795 5653010 MACS_peak_1170 137.07 +chr1 5653365 5653689 MACS_peak_1171 318.88 +chr1 5653877 5653989 MACS_peak_1172 100.24 +chr1 5654231 5654343 MACS_peak_1173 100.24 +chr1 5654571 5654866 MACS_peak_1174 96.76 +chr1 5655769 5656176 MACS_peak_1175 198.15 +chr1 5656312 5656424 MACS_peak_1176 100.24 +chr1 5657271 5657383 MACS_peak_1177 100.24 +chr1 5657651 5657988 MACS_peak_1178 166.21 +chr1 5658525 5658637 MACS_peak_1179 100.24 +chr1 5659194 5659308 MACS_peak_1180 137.07 +chr1 5660375 5660575 MACS_peak_1181 137.07 +chr1 5660781 5660893 MACS_peak_1182 100.24 +chr1 5661327 5661439 MACS_peak_1183 100.24 +chr1 5662504 5662697 MACS_peak_1184 137.07 +chr1 5663691 5663885 MACS_peak_1185 137.07 +chr1 5664582 5664750 MACS_peak_1186 100.24 +chr1 5665076 5665188 MACS_peak_1187 100.24 +chr1 5665895 5666007 MACS_peak_1188 100.24 +chr1 5666448 5666930 MACS_peak_1189 193.75 +chr1 5667751 5667934 MACS_peak_1190 100.24 +chr1 5674057 5674169 MACS_peak_1191 100.24 +chr1 5675063 5675175 MACS_peak_1192 100.24 +chr1 5676274 5676386 MACS_peak_1193 100.24 +chr1 5676599 5676711 MACS_peak_1194 100.24 +chr1 5677228 5677340 MACS_peak_1195 100.24 +chr1 5677740 5677852 MACS_peak_1196 100.24 +chr1 5679022 5679667 MACS_peak_1197 291.97 +chr1 5680026 5681034 MACS_peak_1198 240.66 +chr1 5682911 5683023 MACS_peak_1199 100.24 +chr1 5688032 5688144 MACS_peak_1200 100.24 +chr1 5688335 5688657 MACS_peak_1201 130.92 +chr1 5688801 5688913 MACS_peak_1202 100.24 +chr1 5689087 5689348 MACS_peak_1203 98.36 +chr1 5689475 5689587 MACS_peak_1204 100.24 +chr1 5689771 5689883 MACS_peak_1205 100.24 +chr1 5690261 5690373 MACS_peak_1206 100.24 +chr1 5690750 5690873 MACS_peak_1207 137.07 +chr1 5694742 5695180 MACS_peak_1208 160.51 +chr1 5695333 5695675 MACS_peak_1209 129.88 +chr1 5696080 5696192 MACS_peak_1210 100.24 +chr1 5696612 5697345 MACS_peak_1211 251.72 +chr1 5697961 5698073 MACS_peak_1212 100.24 +chr1 5698235 5698383 MACS_peak_1213 137.07 +chr1 5698832 5699021 MACS_peak_1214 100.24 +chr1 5699479 5699591 MACS_peak_1215 100.24 +chr1 5700029 5700141 MACS_peak_1216 100.24 +chr1 5700387 5700503 MACS_peak_1217 137.07 +chr1 5703736 5703848 MACS_peak_1218 100.24 +chr1 5704571 5704683 MACS_peak_1219 100.24 +chr1 5704979 5705219 MACS_peak_1220 136.03 +chr1 5705728 5705840 MACS_peak_1221 100.24 +chr1 5706213 5706482 MACS_peak_1222 247.45 +chr1 5706879 5706991 MACS_peak_1223 100.24 +chr1 5707211 5707414 MACS_peak_1224 100.24 +chr1 5707733 5707955 MACS_peak_1225 100.24 +chr1 5708418 5708530 MACS_peak_1226 100.24 +chr1 5708711 5708823 MACS_peak_1227 100.24 +chr1 5709009 5709168 MACS_peak_1228 100.24 +chr1 5709626 5709738 MACS_peak_1229 100.24 +chr1 5710175 5710287 MACS_peak_1230 100.24 +chr1 5711491 5711603 MACS_peak_1231 100.24 +chr1 5712452 5712913 MACS_peak_1232 159.40 +chr1 5713590 5713702 MACS_peak_1233 100.24 +chr1 5714277 5714835 MACS_peak_1234 189.93 +chr1 5715628 5715793 MACS_peak_1235 100.24 +chr1 5715919 5716031 MACS_peak_1236 100.24 +chr1 5716150 5716384 MACS_peak_1237 174.12 +chr1 5717000 5717112 MACS_peak_1238 100.24 +chr1 5717383 5717774 MACS_peak_1239 127.55 +chr1 5718298 5718531 MACS_peak_1240 136.54 +chr1 5718754 5719002 MACS_peak_1241 172.86 +chr1 5719627 5719739 MACS_peak_1242 100.24 +chr1 5720578 5720690 MACS_peak_1243 100.24 +chr1 5721523 5721843 MACS_peak_1244 95.71 +chr1 5722221 5722388 MACS_peak_1245 100.24 +chr1 5722739 5722851 MACS_peak_1246 100.24 +chr1 5723148 5723403 MACS_peak_1247 134.98 +chr1 5724342 5724566 MACS_peak_1248 100.24 +chr1 5725453 5725597 MACS_peak_1249 137.07 +chr1 5725942 5726075 MACS_peak_1250 137.07 +chr1 5726202 5726647 MACS_peak_1251 306.48 +chr1 5726801 5726913 MACS_peak_1252 100.24 +chr1 5727303 5727415 MACS_peak_1253 100.24 +chr1 5727541 5727720 MACS_peak_1254 213.48 +chr1 5728015 5728127 MACS_peak_1255 100.24 +chr1 5728661 5728922 MACS_peak_1256 98.36 +chr1 5729591 5729703 MACS_peak_1257 100.24 +chr1 5729971 5730118 MACS_peak_1258 137.07 +chr1 5735097 5735209 MACS_peak_1259 100.24 +chr1 5738165 5738277 MACS_peak_1260 100.24 +chr1 5741886 5742013 MACS_peak_1261 137.07 +chr1 5742222 5742493 MACS_peak_1262 133.92 +chr1 5742624 5742892 MACS_peak_1263 98.02 +chr1 5743479 5743591 MACS_peak_1264 100.24 +chr1 5743802 5743943 MACS_peak_1265 137.07 +chr1 5744327 5745001 MACS_peak_1266 185.01 +chr1 5745544 5746174 MACS_peak_1267 221.59 +chr1 5746482 5747182 MACS_peak_1268 218.38 +chr1 5747751 5747863 MACS_peak_1269 100.24 +chr1 5749480 5749592 MACS_peak_1270 100.24 diff -r 49961332adb6 -r e9de35947c06 test-data/macs_test_2_neg_peaks_out.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/macs_test_2_neg_peaks_out.interval Fri Feb 05 16:06:27 2010 -0500 @@ -0,0 +1,59 @@ +#negative peaks file +#chr start end length summit tags -10*log10(pvalue) fold_enrichment +chr1 3012338 3012474 136 69 3 79.72 265.54 +chr1 3012631 3012751 120 61 3 79.72 265.54 +chr1 3055826 3056120 294 96 9 59.49 18.22 +chr1 3066934 3067568 634 101 10 53.35 18.44 +chr1 3076059 3076339 280 112 6 58.24 29.50 +chr1 3092687 3093270 583 344 11 50.81 10.32 +chr1 3114123 3114523 400 107 10 51.47 11.06 +chr1 3125324 3126255 931 573 13 65.69 12.07 +chr1 3126473 3127174 701 249 11 65.43 13.28 +chr1 3127353 3127879 526 265 14 110.59 22.13 +chr1 3195224 3195844 620 395 13 56.61 13.28 +chr1 3228283 3228748 465 388 6 50.25 26.55 +chr1 3275975 3276467 492 404 9 55.17 15.39 +chr1 3285007 3286005 998 891 18 66.19 11.06 +chr1 3312699 3313743 1044 204 21 60.12 11.06 +chr1 3446632 3447508 876 176 14 61.26 14.75 +chr1 3468402 3469436 1034 109 18 50.75 7.08 +chr1 3474772 3476374 1602 960 22 66.92 12.29 +chr1 3514508 3515086 578 110 13 59.90 11.06 +chr1 3517009 3518094 1085 84 14 50.75 11.80 +chr1 3599829 3601141 1312 109 19 65.77 10.41 +chr1 3605828 3605951 123 62 4 52.20 18.63 +chr1 3606596 3607433 837 548 10 66.22 27.23 +chr1 3613851 3614116 265 103 6 57.63 34.04 +chr1 3614432 3615882 1450 85 15 63.55 13.28 +chr1 3617465 3617784 319 211 9 51.03 11.06 +chr1 3640315 3641949 1634 273 32 81.39 10.68 +chr1 3647349 3648562 1213 411 19 67.14 9.83 +chr1 3735801 3736852 1051 878 17 73.61 14.75 +chr1 3796005 3796544 539 65 5 54.89 44.26 +chr1 3797371 3797763 392 70 6 54.44 26.55 +chr1 3835421 3835673 252 171 6 53.74 22.13 +chr1 3856581 3857561 980 110 19 52.84 9.48 +chr1 3968246 3968621 375 85 7 60.72 34.04 +chr1 3970428 3970718 290 69 5 56.15 50.58 +chr1 4034953 4036094 1141 465 15 66.64 18.44 +chr1 4051823 4055268 3445 669 46 119.08 9.32 +chr1 4099917 4100882 965 256 18 84.48 11.39 +chr1 4112353 4113269 916 72 15 53.99 9.32 +chr1 4139620 4140296 676 399 14 71.23 11.06 +chr1 4191034 4191488 454 386 9 51.16 15.81 +chr1 4191774 4192345 571 102 10 51.50 12.64 +chr1 4201259 4202176 917 651 13 64.28 19.24 +chr1 4218597 4219458 861 460 16 53.64 5.77 +chr1 4223608 4224231 623 472 14 78.93 14.75 +chr1 4238528 4239382 854 90 14 54.69 15.12 +chr1 4283406 4284196 790 400 11 60.42 22.13 +chr1 4368609 4369824 1215 504 19 72.89 10.75 +chr1 4382657 4385390 2733 1297 36 97.80 12.10 +chr1 4439048 4440167 1119 927 19 80.31 13.83 +chr1 4447108 4448669 1561 1375 31 62.31 7.54 +chr1 4462162 4466719 4557 4366 75 90.49 8.30 +chr1 4479282 4480091 809 700 19 60.40 10.33 +chr1 4568704 4569556 852 319 25 69.71 8.62 +chr1 4596926 4597745 819 449 17 51.74 9.48 +chr1 4636007 4637827 1820 110 30 51.27 8.57 +chr1 4646136 4647867 1731 101 28 53.47 7.38 diff -r 49961332adb6 -r e9de35947c06 test-data/macs_test_2_peaks_out.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/macs_test_2_peaks_out.interval Fri Feb 05 16:06:27 2010 -0500 @@ -0,0 +1,1289 @@ +#peaks file +# This file is generated by MACS +# ARGUMENTS LIST: +# name = MACS_in_Galaxy +# format = BED +# ChIP-seq file = /galaxy/home/dan/central/database/files/000/dataset_404.dat +# control file = /galaxy/home/dan/central/database/files/000/dataset_405.dat +# effective genome size = 2.70e+09 +# tag size = 36 +# band width = 300 +# model fold = 13 +# pvalue cutoff = 1.00e-05 +# Ranges for calculating regional lambda are : peak_region,1000,5000,10000 +# unique tags in treatment: 9898 +# total tags in treatment: 10000 +# unique tags in control: 9896 +# total tags in control: 10000 +# d = 113 +#chr start end length summit tags -10*log10(pvalue) fold_enrichment FDR(%) +chr1 3138857 3139271 414 95 6 53.08 35.39 3.55 +chr1 4133899 4134700 801 157 27 51.91 9.92 3.70 +chr1 4323670 4324367 697 306 49 272.01 29.81 0.00 +chr1 4336486 4337946 1460 1216 65 228.35 32.00 0.00 +chr1 4407086 4409120 2034 1133 105 300.46 29.27 0.00 +chr1 4507832 4508710 878 245 44 161.74 18.90 0.00 +chr1 4657704 4658572 868 775 9 280.37 7242.01 0.00 +chr1 4658705 4659021 316 110 4 131.25 4828.01 0.00 +chr1 4659147 4660581 1434 844 15 463.08 7242.01 0.00 +chr1 4661156 4661317 161 81 4 174.88 9656.01 0.00 +chr1 4661505 4661617 112 57 2 100.24 4828.01 0.17 +chr1 4661790 4662463 673 287 7 219.58 4828.01 0.00 +chr1 4662710 4663434 724 623 12 395.94 9656.01 0.00 +chr1 4664135 4664430 295 64 5 169.10 7242.01 0.00 +chr1 4665001 4665113 112 57 2 100.24 4828.01 0.17 +chr1 4665839 4666425 586 475 10 332.40 12070.02 0.00 +chr1 4666581 4666693 112 57 2 100.24 4828.01 0.17 +chr1 4666840 4666981 141 71 4 174.88 9656.01 0.00 +chr1 4667600 4667712 112 57 2 100.24 4828.01 0.17 +chr1 4668711 4669005 294 75 5 169.17 7242.01 0.00 +chr1 4669126 4669238 112 57 2 100.24 4828.01 0.17 +chr1 4669537 4669752 215 108 5 174.88 12070.02 0.00 +chr1 4669936 4670048 112 57 2 100.24 4828.01 0.17 +chr1 4670216 4670449 233 97 6 212.68 12070.02 0.00 +chr1 4673856 4674051 195 98 4 137.07 9656.01 0.00 +chr1 4674349 4674478 129 65 3 137.07 7242.01 0.00 +chr1 4675027 4675152 125 63 3 137.07 7242.01 0.00 +chr1 4676227 4676339 112 57 2 100.24 4828.01 0.17 +chr1 4676511 4676623 112 57 2 100.24 4828.01 0.17 +chr1 4676954 4677151 197 99 3 100.24 7242.01 0.17 +chr1 4677646 4677758 112 57 2 100.24 4828.01 0.17 +chr1 4678360 4678472 112 57 2 100.24 4828.01 0.17 +chr1 4678659 4679136 477 307 7 230.04 7242.01 0.00 +chr1 4679439 4679551 112 57 2 100.24 4828.01 0.17 +chr1 4680106 4680523 417 103 5 126.43 4828.01 0.00 +chr1 4680822 4680934 112 57 2 100.24 4828.01 0.17 +chr1 4681075 4682050 975 104 8 241.81 4828.01 0.00 +chr1 4682229 4682387 158 80 3 100.24 7242.01 0.17 +chr1 4682594 4682706 112 57 2 100.24 4828.01 0.17 +chr1 4683158 4683270 112 57 2 100.24 4828.01 0.17 +chr1 4683473 4683585 112 57 2 100.24 4828.01 0.17 +chr1 4683832 4683944 112 57 2 100.24 4828.01 0.17 +chr1 4684591 4684775 184 93 3 100.24 7242.01 0.17 +chr1 4685292 4685404 112 57 2 100.24 4828.01 0.17 +chr1 4685810 4686198 388 75 4 127.69 4828.01 0.00 +chr1 4686493 4686605 112 57 2 100.24 4828.01 0.17 +chr1 4686818 4686930 112 57 2 100.24 4828.01 0.17 +chr1 4687387 4687499 112 57 2 100.24 4828.01 0.17 +chr1 4687692 4687902 210 106 5 174.88 12070.02 0.00 +chr1 4688181 4688790 609 96 8 258.16 9656.01 0.00 +chr1 4689101 4689557 456 250 7 231.41 9656.01 0.00 +chr1 4690039 4690151 112 57 2 100.24 4828.01 0.17 +chr1 4690290 4690402 112 57 2 100.24 4828.01 0.17 +chr1 4690780 4690907 127 64 3 137.07 7242.01 0.00 +chr1 4691478 4692335 857 509 10 315.89 7242.01 0.00 +chr1 4692464 4692768 304 67 4 131.92 7242.01 0.00 +chr1 4693243 4693751 508 307 7 228.13 9656.01 0.00 +chr1 4694306 4694418 112 57 2 100.24 4828.01 0.17 +chr1 4694738 4695016 278 75 5 170.38 9656.01 0.00 +chr1 4695207 4695378 171 86 3 100.24 7242.01 0.17 +chr1 4695503 4696600 1097 535 12 374.29 7242.01 0.00 +chr1 4696903 4697015 112 57 2 100.24 4828.01 0.17 +chr1 4697569 4697912 343 106 7 240.07 12070.02 0.00 +chr1 4698224 4698395 171 86 3 100.24 7242.01 0.17 +chr1 4698790 4698904 114 58 3 137.07 7242.01 0.00 +chr1 4699223 4699430 207 104 4 137.07 9656.01 0.00 +chr1 4699642 4699754 112 57 2 100.24 4828.01 0.17 +chr1 4700457 4700569 112 57 2 100.24 4828.01 0.17 +chr1 4700853 4700965 112 57 2 100.24 4828.01 0.17 +chr1 4708474 4708898 424 57 4 126.15 4828.01 0.00 +chr1 4709426 4709741 315 102 5 167.67 9656.01 0.00 +chr1 4709925 4710127 202 102 4 137.07 9656.01 0.00 +chr1 4710465 4710577 112 57 2 100.24 4828.01 0.17 +chr1 4710812 4711277 465 111 6 194.68 7242.01 0.00 +chr1 4711462 4711762 300 102 4 132.15 4828.01 0.00 +chr1 4712202 4712479 277 57 3 97.58 4828.01 0.24 +chr1 4712673 4713163 490 111 10 340.17 9656.01 0.00 +chr1 4713659 4714656 997 230 13 414.78 7242.01 0.00 +chr1 4714840 4715470 630 83 7 221.59 7242.01 0.00 +chr1 4715671 4715783 112 57 2 100.24 4828.01 0.17 +chr1 4715908 4716811 903 824 16 530.04 12070.02 0.00 +chr1 4717318 4717430 112 57 2 100.24 4828.01 0.17 +chr1 4717789 4718230 441 103 7 232.43 12070.02 0.00 +chr1 4718990 4719236 246 57 3 99.13 4828.01 0.16 +chr1 4719718 4719830 112 57 2 100.24 4828.01 0.17 +chr1 4720276 4720388 112 57 2 100.24 4828.01 0.17 +chr1 4721061 4721173 112 57 2 100.24 4828.01 0.17 +chr1 4721620 4721782 162 82 3 100.24 7242.01 0.17 +chr1 4722229 4722341 112 57 2 100.24 4828.01 0.17 +chr1 4723262 4723374 112 57 2 100.24 4828.01 0.17 +chr1 4724496 4724608 112 57 2 100.24 4828.01 0.17 +chr1 4726179 4726291 112 57 2 100.24 4828.01 0.17 +chr1 4726472 4727091 619 82 6 187.23 7242.01 0.00 +chr1 4727268 4727705 437 66 6 196.30 7242.01 0.00 +chr1 4727871 4727983 112 57 2 100.24 4828.01 0.17 +chr1 4728976 4729088 112 57 2 100.24 4828.01 0.17 +chr1 4729473 4729611 138 70 3 137.07 7242.01 0.00 +chr1 4729954 4730093 139 70 3 137.07 7242.01 0.00 +chr1 4730636 4730805 169 85 3 100.24 7242.01 0.17 +chr1 4730936 4731305 369 111 5 164.24 9656.01 0.00 +chr1 4731799 4732585 786 443 11 355.47 7242.01 0.00 +chr1 4733192 4733304 112 57 2 100.24 4828.01 0.17 +chr1 4733710 4733831 121 61 3 137.07 7242.01 0.00 +chr1 4734062 4734891 829 75 11 352.92 9656.01 0.00 +chr1 4735075 4735290 215 108 4 137.07 9656.01 0.00 +chr1 4735523 4736190 667 236 7 185.28 4828.01 0.00 +chr1 4736399 4737184 785 80 11 355.53 9656.01 0.00 +chr1 4737395 4737601 206 104 4 137.07 9656.01 0.00 +chr1 4737973 4738425 452 188 7 231.68 7242.01 0.00 +chr1 4738796 4739212 416 311 6 197.58 7242.01 0.00 +chr1 4739379 4739491 112 57 2 100.24 4828.01 0.17 +chr1 4739612 4740720 1108 105 18 588.51 9656.01 0.00 +chr1 4741405 4741655 250 80 4 135.32 7242.01 0.00 +chr1 4741998 4742300 302 79 4 132.04 4828.01 0.00 +chr1 4742829 4742952 123 62 3 137.07 7242.01 0.00 +chr1 4743079 4743327 248 101 4 135.46 4828.01 0.00 +chr1 4743612 4744566 954 97 14 453.30 12070.02 0.00 +chr1 4744719 4745224 505 260 8 264.66 7242.01 0.00 +chr1 4745398 4745786 388 301 8 236.32 9656.01 0.00 +chr1 4746034 4746316 282 112 5 170.07 9656.01 0.00 +chr1 4747206 4748408 1202 316 15 474.57 9656.01 0.00 +chr1 4748814 4748926 112 57 2 100.24 4828.01 0.17 +chr1 4749222 4749334 112 57 2 100.24 4828.01 0.17 +chr1 4749686 4750054 368 97 8 275.66 12070.02 0.00 +chr1 4750335 4750697 362 79 5 164.65 7242.01 0.00 +chr1 4750863 4751682 819 109 8 247.87 4828.01 0.00 +chr1 4751853 4752428 575 78 6 189.15 7242.01 0.00 +chr1 4752581 4753611 1030 565 13 412.95 9656.01 0.00 +chr1 4754241 4754864 623 233 10 329.74 9656.01 0.00 +chr1 4755088 4755200 112 57 2 100.24 4828.01 0.17 +chr1 4755722 4756029 307 100 6 205.50 12070.02 0.00 +chr1 4756768 4756880 112 57 2 100.24 4828.01 0.17 +chr1 4757199 4758615 1416 753 18 569.34 7242.01 0.00 +chr1 4758753 4762214 3461 1125 247 3100.00 217260.30 0.00 +chr1 4763207 4763319 112 57 2 100.24 4828.01 0.17 +chr1 4763614 4763726 112 57 2 100.24 4828.01 0.17 +chr1 4763998 4764322 324 233 10 358.13 14484.02 0.00 +chr1 4764568 4764850 282 62 4 133.23 7242.01 0.00 +chr1 4765104 4765765 661 112 9 291.01 12070.02 0.00 +chr1 4765892 4766067 175 88 3 100.24 7242.01 0.17 +chr1 4766232 4766420 188 95 3 100.24 7242.01 0.17 +chr1 4766539 4767148 609 171 11 367.65 14484.02 0.00 +chr1 4767417 4767529 112 57 2 100.24 4828.01 0.17 +chr1 4768245 4768357 112 57 2 100.24 4828.01 0.17 +chr1 4768587 4768870 283 99 5 170.00 9656.01 0.00 +chr1 4768989 4769272 283 104 4 133.17 4828.01 0.00 +chr1 4769463 4769684 221 111 5 174.88 12070.02 0.00 +chr1 4769861 4770236 375 287 6 200.29 7242.01 0.00 +chr1 4770689 4771270 581 256 7 224.05 7242.01 0.00 +chr1 4771393 4772502 1109 197 49 1799.39 57936.08 0.00 +chr1 4772633 4772916 283 95 4 133.17 7242.01 0.00 +chr1 4773121 4773284 163 82 3 100.24 7242.01 0.17 +chr1 4773476 4773614 138 70 3 137.07 7242.01 0.00 +chr1 4773827 4774279 452 84 5 159.83 7242.01 0.00 +chr1 4774510 4774622 112 57 2 100.24 4828.01 0.17 +chr1 4775041 4775694 653 100 9 291.49 12070.02 0.00 +chr1 4775832 4775944 112 57 2 100.24 4828.01 0.17 +chr1 4776166 4776310 144 73 3 137.07 7242.01 0.00 +chr1 4776506 4776851 345 276 5 165.70 7242.01 0.00 +chr1 4777100 4777321 221 111 4 137.07 9656.01 0.00 +chr1 4777505 4777617 112 57 2 100.24 4828.01 0.17 +chr1 4777764 4778298 534 84 5 156.21 4828.01 0.00 +chr1 4778680 4778792 112 57 2 100.24 4828.01 0.17 +chr1 4779265 4779377 112 57 2 100.24 4828.01 0.17 +chr1 4780814 4780926 112 57 2 100.24 4828.01 0.17 +chr1 4781238 4781436 198 100 4 137.07 9656.01 0.00 +chr1 4781600 4781712 112 57 2 100.24 4828.01 0.17 +chr1 4784249 4784487 238 164 5 173.76 7242.01 0.00 +chr1 4784800 4784912 112 57 2 100.24 4828.01 0.17 +chr1 4785500 4785612 112 57 2 100.24 4828.01 0.17 +chr1 4786820 4787357 537 358 7 226.44 4828.01 0.00 +chr1 4787570 4787682 112 57 2 100.24 4828.01 0.17 +chr1 4789440 4789978 538 100 8 262.47 7242.01 0.00 +chr1 4790257 4790424 167 84 3 100.24 7242.01 0.17 +chr1 4790723 4791308 585 104 7 223.84 12070.02 0.00 +chr1 4791871 4792641 770 664 12 392.73 14484.02 0.00 +chr1 4792756 4793323 567 109 6 189.52 7242.01 0.00 +chr1 4794493 4794929 436 254 7 232.77 9656.01 0.00 +chr1 4795046 4795357 311 89 4 131.53 4828.01 0.00 +chr1 4795495 4795607 112 57 2 100.24 4828.01 0.17 +chr1 4796218 4796432 214 108 5 174.88 12070.02 0.00 +chr1 4796841 4796953 112 57 2 100.24 4828.01 0.17 +chr1 4797267 4797499 232 57 3 99.89 4828.01 0.17 +chr1 4797910 4798022 112 57 2 100.24 4828.01 0.17 +chr1 4799151 4799263 112 57 2 100.24 4828.01 0.17 +chr1 4799518 4800266 748 108 8 216.37 7242.01 0.00 +chr1 4800415 4800527 112 57 2 100.24 4828.01 0.17 +chr1 4800989 4801101 112 57 2 100.24 4828.01 0.17 +chr1 4801344 4802288 944 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+chr1 5718754 5719002 248 96 5 172.86 9656.01 0.00 +chr1 5719627 5719739 112 57 2 100.24 4828.01 0.17 +chr1 5720578 5720690 112 57 2 100.24 4828.01 0.17 +chr1 5721523 5721843 320 57 3 95.71 4828.01 0.24 +chr1 5722221 5722388 167 84 3 100.24 7242.01 0.17 +chr1 5722739 5722851 112 57 2 100.24 4828.01 0.17 +chr1 5723148 5723403 255 105 4 134.98 4828.01 0.00 +chr1 5724342 5724566 224 57 3 100.24 4828.01 0.17 +chr1 5725453 5725597 144 73 3 137.07 7242.01 0.00 +chr1 5725942 5726075 133 67 3 137.07 7242.01 0.00 +chr1 5726202 5726647 445 349 9 306.48 12070.02 0.00 +chr1 5726801 5726913 112 57 2 100.24 4828.01 0.17 +chr1 5727303 5727415 112 57 2 100.24 4828.01 0.17 +chr1 5727541 5727720 179 90 5 213.48 12070.02 0.00 +chr1 5728015 5728127 112 57 2 100.24 4828.01 0.17 +chr1 5728661 5728922 261 57 3 98.36 4828.01 0.16 +chr1 5729591 5729703 112 57 2 100.24 4828.01 0.17 +chr1 5729971 5730118 147 74 3 137.07 7242.01 0.00 +chr1 5735097 5735209 112 57 2 100.24 4828.01 0.17 +chr1 5738165 5738277 112 57 2 100.24 4828.01 0.17 +chr1 5741886 5742013 127 64 3 137.07 7242.01 0.00 +chr1 5742222 5742493 271 85 4 133.92 7242.01 0.00 +chr1 5742624 5742892 268 57 3 98.02 4828.01 0.16 +chr1 5743479 5743591 112 57 2 100.24 4828.01 0.17 +chr1 5743802 5743943 141 71 3 137.07 7242.01 0.00 +chr1 5744327 5745001 674 99 6 185.01 4828.01 0.00 +chr1 5745544 5746174 630 291 7 221.59 4828.01 0.00 +chr1 5746482 5747182 700 89 7 218.38 9656.01 0.00 +chr1 5747751 5747863 112 57 2 100.24 4828.01 0.17 +chr1 5749480 5749592 112 57 2 100.24 4828.01 0.17 diff -r 49961332adb6 -r e9de35947c06 tool_conf.xml.main --- a/tool_conf.xml.main Fri Feb 05 15:51:01 2010 -0500 +++ b/tool_conf.xml.main Fri Feb 05 16:06:27 2010 -0500 @@ -298,5 +298,9 @@ <tool file="samtools/pileup_parser.xml" /> <tool file="samtools/pileup_interval.xml" /> </section> - + <section name="NGS: Peak Calling" id="peak_calling"> + <tool file="peak_calling/macs_wrapper.xml" /> + <tool file="genetrack/genetrack_indexer.xml" /> + <tool file="genetrack/genetrack_peak_prediction.xml" /> + </section> </toolbox> diff -r 49961332adb6 -r e9de35947c06 tool_conf.xml.sample --- a/tool_conf.xml.sample Fri Feb 05 15:51:01 2010 -0500 +++ b/tool_conf.xml.sample Fri Feb 05 16:06:27 2010 -0500 @@ -129,8 +129,6 @@ <tool file="visualization/GMAJ.xml" /> <tool file="visualization/LAJ.xml" /> <tool file="visualization/build_ucsc_custom_track.xml" /> - <tool file="visualization/genetrack_indexer.xml" /> - <tool file="visualization/genetrack_peak_prediction.xml" /> </section> <section name="Regional Variation" id="regVar"> <tool file="regVariation/windowSplitter.xml" /> @@ -207,6 +205,11 @@ <tool file="samtools/pileup_parser.xml" /> <tool file="samtools/pileup_interval.xml" /> </section> + <section name="NGS: Peak Calling" id="peak_calling"> + <tool file="peak_calling/macs_wrapper.xml" /> + <tool file="genetrack/genetrack_indexer.xml" /> + <tool file="genetrack/genetrack_peak_prediction.xml" /> + </section> <section name="Rg Data" id="rgData1"> <tool file="rgenetics/rgenetics_import.xml"/> <tool file="rgenetics/rgLpedPbed.xml"/> diff -r 49961332adb6 -r e9de35947c06 tools/genetrack/genetrack_indexer.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/genetrack/genetrack_indexer.py Fri Feb 05 16:06:27 2010 -0500 @@ -0,0 +1,42 @@ +#!/usr/bin/env python + +""" +Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy. + +usage: %prog input output shift +""" + +import sys, shutil, os +from galaxy import eggs +import pkg_resources +pkg_resources.require( "GeneTrack" ) + +from genetrack.scripts import tabs2genetrack +from genetrack import logger + +if __name__ == "__main__": + import os + os.environ[ 'LC_ALL' ] = 'C' + #os.system( 'export' ) + + parser = tabs2genetrack.option_parser() + + options, args = parser.parse_args() + + # uppercase the format + options.format = options.format.upper() + + if options.format not in ('BED', 'GFF'): + sys.stdout = sys.stderr + parser.print_help() + sys.exit(-1) + + logger.disable(options.verbosity) + + # missing file names + if not (options.inpname and options.outname and options.format): + parser.print_help() + sys.exit(-1) + else: + tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\ + format=options.format, shift=options.shift, index=options.index, options=options) diff -r 49961332adb6 -r e9de35947c06 tools/genetrack/genetrack_indexer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/genetrack/genetrack_indexer.xml Fri Feb 05 16:06:27 2010 -0500 @@ -0,0 +1,54 @@ +<tool id="bed2genetrack" name="GeneTrack indexer"> + + <description>on a BED file</description> + + <command interpreter="python"> + genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x + </command> + + <inputs> + + <param format="bed" name="input" type="data" help="Input data"> + <label>Select input bed file</label> + </param> + + <param name="shift" size="4" type="integer" value="0" help="distance in basepairs"> + <label>Shift at 5' end</label> + </param> + +  + + </inputs> + + <outputs> + <data format="genetrack" name="output" /> + </outputs> + +<help> +**Help** + +This tool will create a visualization of the bed file that is selected. + +**Parameters** + +- **Shift at 5' end** should be used when the location of interest is at a fixed distance from + the 5' end for **all sequenced fragments**! + + For example if the sequenced sample consists + mono-nucleosomal DNA (146bp) we should expect that + each nucleosome midpoint is located at 73 bp from the 5' end of the fragment. + Therefore we would enter 73 as the shift parameter. Once corrected the reads + on each strand will coincide and indicate the actual midpoints + of the nucleosomes. + + When shifting the averaging process in GeneTrack is able correct for longer or shorter + than expected fragment sizes as long as the errors are reasonably random. + +</help> + +</tool> diff -r 49961332adb6 -r e9de35947c06 tools/genetrack/genetrack_peak_prediction.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/genetrack/genetrack_peak_prediction.py Fri Feb 05 16:06:27 2010 -0500 @@ -0,0 +1,40 @@ +#!/usr/bin/env python + +""" +Wraps genetrack.scripts.peakpred so the tool can be executed from Galaxy. + +usage: %prog input output level sigma mode exclusion strand +""" + +import sys +from galaxy import eggs +import pkg_resources +pkg_resources.require( "GeneTrack" ) + +from genetrack.scripts import peakpred +from genetrack import logger + +if __name__ == "__main__": + + parser = peakpred.option_parser() + + options, args = parser.parse_args() + + logger.disable(options.verbosity) + + from genetrack import conf + + # trigger test mode + if options.test: + options.inpname = conf.testdata('test-hdflib-input.gtrack') + options.outname = conf.testdata('predictions.bed') + + # missing input file name + if not options.inpname and not options.outname: + parser.print_help() + else: + print 'Sigma = %s' % options.sigma + print 'Minimum peak = %s' % options.level + print 'Peak-to-peak = %s' % options.exclude + + peakpred.predict(options.inpname, options.outname, options) diff -r 49961332adb6 -r e9de35947c06 tools/genetrack/genetrack_peak_prediction.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/genetrack/genetrack_peak_prediction.xml Fri Feb 05 16:06:27 2010 -0500 @@ -0,0 +1,59 @@ +<tool id="predict2genetrack" name="Peak predictor"> + + <description>on GeneTrack index</description> + + <command interpreter="python"> + genetrack_peak_prediction.py -i $input -o $output --level=$level --sigma=$sigma --mode=$mode --exclusion=$exclusion --strand=$strand -v 0 -x + </command> + + <inputs> + + <param format="genetrack" name="input" type="data" help="Input data" label="Select input data"/> + + <param name="method" type="select" label="Smoothing method" help="The function used to average nearby read values"> + <option value="gauss">Gaussian kernel</option> +  + </param> + + <param name="sigma" size="4" type="integer" value="10" label="Smoothing factor" help="The interval over which each read is averaged" /> + + + <param name="mode" type="select" label="Peak prediction" help="Peak prediction method"> + <option value="nolap">Maximal non-overlapping</option> +  + <option value="all">All peaks</option> + </param> + + <param name="exclusion" type="integer" size="4" value="0" help="The minimal distance between peaks" label="Peak-to-peak distance"> + </param> + + <param name="level" size="4" type="float" value="1" label="Threshold" help="Return only peaks above this value" /> + + <param name="strand" type="select" label="Strands" help="Combine strand data or predict on each strand separately"> + <option value="all">Merge strands</option> +  + <option value="two">Separate strands</option> + </param> + + </inputs> + + <outputs> + <data format="bed" name="output" /> + </outputs> + +<help> +**Help** + +This tool will generate genome wide peak prediction from an index file. + +**Parameters** + +- **Smoothing method** the function used to average nearby values + +- **Smoothing value** the factor used in the method + +- **Prediction method** the function used to average nearby values + +</help> + +</tool> diff -r 49961332adb6 -r e9de35947c06 tools/peak_calling/macs_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/peak_calling/macs_wrapper.py Fri Feb 05 16:06:27 2010 -0500 @@ -0,0 +1,138 @@ +import sys, subprocess, tempfile, shutil, glob, os, os.path, gzip +from galaxy import eggs +import pkg_resources +pkg_resources.require( "simplejson" ) +import simplejson + +CHUNK_SIZE = 1024 +ERROR_LINES = [ 'ERROR', 'command not found' ] #'Fatal' errors that should be passed back to stderr +WARNING_LINE_START = 'WARNING @' + +def gunzip_cat_glob_path( glob_path, target_filename, delete = False ): + out = open( target_filename, 'wb' ) + for filename in glob.glob( glob_path ): + fh = gzip.open( filename, 'rb' ) + while True: + data = fh.read( CHUNK_SIZE ) + if data: + out.write( data ) + else: + break + fh.close() + if delete: + os.unlink( filename ) + out.close() + +def xls_to_interval( xls_file, interval_file, header = None ): + out = open( interval_file, 'wb' ) + if header: + out.write( '#%s\n' % header ) + wrote_header = False + #From macs readme: Coordinates in XLS is 1-based which is different with BED format. + for line in open( xls_file ): + #keep all existing comment lines + if line.startswith( '#' ): + out.write( line ) + elif not wrote_header: + out.write( '#%s' % line ) + wrote_header = True + else: + fields = line.split( '\t' ) + if len( fields ) > 1: + fields[1] = str( int( fields[1] ) - 1 ) + out.write( '\t'.join( fields ) ) + out.close() + +def main(): + options = simplejson.load( open( sys.argv[1] ) ) + output_bed = sys.argv[2] + output_extra_html = sys.argv[3] + output_extra_path = sys.argv[4] + + experiment_name = '_'.join( options['experiment_name'].split() ) #save experiment name here, it will be used by macs for filenames (gzip of wig files will fail with spaces - macs doesn't properly escape them)..need to replace all whitespace, split makes this easier + cmdline = "macs -t %s" % ",".join( options['input_chipseq'] ) + if options['input_control']: + cmdline = "%s -c %s" % ( cmdline, ",".join( options['input_control'] ) ) + cmdline = "%s --format='%s' --name='%s' --gsize='%s' --tsize='%s' --bw='%s' --pvalue='%s' --mfold='%s' %s --lambdaset='%s' %s" % ( cmdline, options['format'], experiment_name, options['gsize'], options['tsize'], options['bw'], options['pvalue'], options['mfold'], options['nolambda'], options['lambdaset'], options['futurefdr'] ) + if 'wig' in options: + wigextend = int( options['wig']['wigextend'] ) + if wigextend >= 0: + wigextend = "--wigextend='%s'" % wigextend + else: + wigextend = '' + cmdline = "%s --wig %s --space='%s'" % ( cmdline, wigextend, options['wig']['space'] ) + if 'nomodel' in options: + cmdline = "%s --nomodel --shiftsize='%s'" % ( cmdline, options['nomodel'] ) + if 'diag' in options: + cmdline = "%s --diag --fe-min='%s' --fe-max='%s' --fe-step='%s'" % ( cmdline, options['diag']['fe-min'], options['diag']['fe-max'], options['diag']['fe-step'] ) + + tmp_dir = tempfile.mkdtemp() #macs makes very messy output, need to contain it into a temp dir, then provide to user + stderr_name = tempfile.NamedTemporaryFile().name # redirect stderr here, macs provides lots of info via stderr, make it into a report + proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) ) + proc.wait() + + #Need to lightly parse stderr file to see if there is a fatal error (e.g. macs is not installed on system) + #We don't want to set tool run to error state if only warnings or info, e.g. mfold needs to be decreased, rather create empty outputs, but let user view macs log + for line in open( stderr_name ): + for err_text in ERROR_LINES: + if err_text in line: + #print error, but don't quit, allow cleanup to occur at end + print >> sys.stderr, line.rstrip( '\n\r' ) + if line.startswith( WARNING_LINE_START ): + #print warnings so they are viewable from info + print line.split( ':' )[-1].strip() + + #run R to create pdf from model script + if os.path.exists( os.path.join( tmp_dir, "%s_model.r" % experiment_name ) ): + cmdline = 'R --vanilla --slave < "%s_model.r" > "%s_model.r.log"' % ( experiment_name, experiment_name ) + proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir ) + proc.wait() + + + #move bed out to proper output file + created_bed_name = os.path.join( tmp_dir, "%s_peaks.bed" % experiment_name ) + if os.path.exists( created_bed_name ): + shutil.move( created_bed_name, output_bed ) + + #parse xls files to interval files as needed + if options['xls_to_interval']: + create_peak_xls_file = os.path.join( tmp_dir, '%s_peaks.xls' % experiment_name ) + if os.path.exists( create_peak_xls_file ): + xls_to_interval( create_peak_xls_file, options['xls_to_interval']['peaks_file'], header = 'peaks file' ) + create_peak_xls_file = os.path.join( tmp_dir, '%s_negative_peaks.xls' % experiment_name ) + if os.path.exists( create_peak_xls_file ): + xls_to_interval( create_peak_xls_file, options['xls_to_interval']['negative_peaks_file'], header = 'negative peaks file' ) + + #merge and move wig files as needed, delete gz'd files and remove emptied dirs + if 'wig' in options: + wig_base_dir = os.path.join( tmp_dir, "%s_MACS_wiggle" % experiment_name ) + if os.path.exists( wig_base_dir ): + #treatment + treatment_dir = os.path.join( wig_base_dir, "treat" ) + if os.path.exists( treatment_dir ):

1 0

[hg] galaxy 3345: Data library UI cleanup and improvements. Wid...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/49961332adb6 changeset: 3345:49961332adb6 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Feb 05 15:51:01 2010 -0500 description: Data library UI cleanup and improvements. Widgets are now displayed for the currently selected tempalte when adding one to a library item. diffstat: lib/galaxy/web/controllers/library_common.py | 41 +++++++++++- templates/library/common/browse_library.mako | 10 +- templates/library/common/common.mako | 36 +++++++--- templates/library/common/ldda_info.mako | 28 ++++---- templates/library/common/library_info.mako | 57 +++++++++++++++-- templates/library/common/select_info_template.mako | 70 +++++++++++++++++---- test/base/twilltestcase.py | 5 +- test/functional/test_security_and_libraries.py | 2 +- 8 files changed, 190 insertions(+), 59 deletions(-) diffs (435 lines): diff -r e3af9317e829 -r 49961332adb6 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Fri Feb 05 15:29:22 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Fri Feb 05 15:51:01 2010 -0500 @@ -1,4 +1,4 @@ -import os, os.path, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile +import os, os.path, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile, copy from galaxy.web.base.controller import * from galaxy import util, jobs from galaxy.datatypes import sniff @@ -6,6 +6,7 @@ from galaxy.util.json import to_json_string from galaxy.tools.actions import upload_common from galaxy.web.controllers.forms import get_all_forms +from galaxy.web.form_builder import SelectField from galaxy.model.orm import * from galaxy.util.streamball import StreamBall import logging, tempfile, zipfile, tarfile, os, sys @@ -1314,7 +1315,7 @@ action = 'ldda_edit_info' id = ldda_id if params.get( 'add_info_template_button', False ): - form = trans.sa_session.query( trans.app.model.FormDefinition ).get( int( params.form_id ) ) + form = trans.sa_session.query( trans.app.model.FormDefinition ).get( trans.security.decode_id( params.form_id ) ) form_values = trans.app.model.FormValues( form, [] ) trans.sa_session.add( form_values ) trans.sa_session.flush() @@ -1326,7 +1327,7 @@ assoc = trans.app.model.LibraryDatasetDatasetInfoAssociation( item, form, form_values ) trans.sa_session.add( assoc ) trans.sa_session.flush() - msg = 'An information template based on the form "%s" has been added to this %s.' % ( form.name, library_item_desc ) + msg = 'A template based on the form "%s" has been added to this %s.' % ( form.name, library_item_desc ) trans.response.send_redirect( web.url_for( controller='library_common', action=action, cntrller=cntrller, @@ -1336,6 +1337,36 @@ show_deleted=show_deleted, msg=msg, messagetype='done' ) ) + def generate_template_stuff( trans, forms, form_id ): + # Returns the following: + # - a list of template ids + # - a list of dictionaries whose keys are template ids and whose values are templates widgets. + # The dictionary built using the received forms param + # - a select list whose options are templates + template_ids = [ 'none' ] + widgets = [] + for form in forms: + template_ids.append( trans.security.encode_id( form.id ) ) + template_select_list = SelectField( 'form_id', + refresh_on_change=True, + refresh_on_change_values=template_ids[1:] ) + if form_id == 'none': + template_select_list.add_option( 'Select one', 'none', selected=True ) + decoded_form_id = None + else: + template_select_list.add_option( 'Select one', 'none' ) + decoded_form_id = trans.security.decode_id( form_id ) + for form in forms: + if decoded_form_id and decoded_form_id == form.id: + template_select_list.add_option( form.name, trans.security.encode_id( form.id ), selected=True ) + widgets = form.get_widgets( trans.user ) + else: + template_select_list.add_option( form.name, trans.security.encode_id( form.id ) ) + return template_ids, widgets, template_select_list + if params.get( 'refresh', False ): + template_ids, widgets, template_select_list = generate_template_stuff( trans, forms, kwd.get( 'form_id' ) ) + else: + template_ids, widgets, template_select_list = generate_template_stuff( trans, forms, 'none' ) return trans.fill_template( '/library/common/select_info_template.mako', cntrller=cntrller, library_item_name=item.name, @@ -1344,7 +1375,9 @@ library_id=library_id, folder_id=folder_id, ldda_id=ldda_id, - forms=forms, + template_ids=template_ids, + widgets=widgets, + template_select_list=template_select_list, show_deleted=show_deleted, msg=msg, messagetype=messagetype ) diff -r e3af9317e829 -r 49961332adb6 templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako Fri Feb 05 15:29:22 2010 -0500 +++ b/templates/library/common/browse_library.mako Fri Feb 05 15:51:01 2010 -0500 @@ -17,8 +17,6 @@ <% if cntrller in [ 'library', 'requests' ]: can_add = trans.app.security_agent.can_add_library_item( current_user_roles, library ) - if can_add: - info_association, inherited = library.get_info_association() can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, library ) can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, library ) info_association, inherited = library.get_info_association() @@ -277,7 +275,7 @@ %if folder.deleted: <span class="libraryItem-error"> %endif - ${folder.name} + <a href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=library_id, show_deleted=show_deleted )}">${folder.name}</a> %if folder.description: <i>- ${folder.description}</i> %endif @@ -372,7 +370,7 @@ <tr class="libraryTitle"> %if cntrller == 'library_admin' or can_add or can_modify or can_manage: <th style="padding-left: 42px;"> - ${library.name} + <a href="${h.url_for( controller='library_common', action='library_info', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}"><b>${library.name[:50]}</b></a> <a id="library-${library.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="library-${library.id}-popup"> %if not library.deleted: @@ -406,7 +404,9 @@ </div> </th> %else: - <th style="padding-left: 42px;">${library.name}</th> + <th style="padding-left: 42px;"> + <a href="${h.url_for( controller='library_common', action='library_info', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}"><b>${library.name[:50]}</b></a> + </th> %endif <th>Information</th> <th>Uploaded By</th> diff -r e3af9317e829 -r 49961332adb6 templates/library/common/common.mako --- a/templates/library/common/common.mako Fri Feb 05 15:29:22 2010 -0500 +++ b/templates/library/common/common.mako Fri Feb 05 15:51:01 2010 -0500 @@ -1,23 +1,20 @@ <%def name="render_template_info( cntrller, item_type, library_id, widgets, folder_id=None, ldda_id=None, editable=True )"> <% if item_type == 'library': - item_desc = 'library' item = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) elif item_type == 'folder': - item_desc = 'folder' item = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) ) elif item_type == 'ldda': - item_desc = 'dataset' item = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) ) if cntrller == 'library': current_user_roles = trans.get_current_user_roles() %> %if widgets: - <p/> - <div class="toolForm"> - <div class="toolFormTitle">Other information about ${item_desc} ${item.name}</div> - <div class="toolFormBody"> - %if editable and ( cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( current_user_roles, item ) ): + %if editable and ( cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( current_user_roles, item ) ): + <p/> + <div class="toolForm"> + <div class="toolFormTitle">Other information about ${item.name}</div> + <div class="toolFormBody"> <form name="edit_info" action="${h.url_for( controller='library_common', action='edit_template_info', cntrller=cntrller, item_type=item_type, library_id=library_id, num_widgets=len( widgets ), folder_id=folder_id, ldda_id=ldda_id, show_deleted=show_deleted )}" method="post"> %for i, field in enumerate( widgets ): <div class="form-row"> @@ -33,7 +30,22 @@ <input type="submit" name="edit_info_button" value="Save"/> </div> </form> - %else: + </div> + </div> + %else: + <% contents = False %> + %for i, field in enumerate( widgets ): + %if field[ 'widget' ].value: + <% + contents = True + break + %> + %endif + %endfor + %if contents: + <div class="toolForm"> + <div class="toolFormTitle">Other information about ${item.name}</div> + <div class="toolFormBody"> %for i, field in enumerate( widgets ): %if field[ 'widget' ].value: <div class="form-row"> @@ -46,9 +58,9 @@ </div> %endif %endfor - %endif - </div> - </div> + </div> + %endif + %endif %endif </%def> diff -r e3af9317e829 -r 49961332adb6 templates/library/common/ldda_info.mako --- a/templates/library/common/ldda_info.mako Fri Feb 05 15:29:22 2010 -0500 +++ b/templates/library/common/ldda_info.mako Fri Feb 05 15:51:01 2010 -0500 @@ -98,18 +98,18 @@ </div> %endif </div> - %if widgets: - ${render_template_info( cntrller=cntrller, item_type='ldda', library_id=library_id, widgets=widgets, folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), ldda_id=trans.security.encode_id( ldda.id ), editable=False )} +</div> +%if widgets: + ${render_template_info( cntrller=cntrller, item_type='ldda', library_id=library_id, widgets=widgets, folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), ldda_id=trans.security.encode_id( ldda.id ), editable=False )} +%endif +%if current_version: + <% expired_lddas = [ e_ldda for e_ldda in ldda.library_dataset.expired_datasets ] %> + %if expired_lddas: + <div class="toolFormTitle">Expired versions of ${ldda.name}</div> + %for expired_ldda in expired_lddas: + <div class="form-row"> + <a href="${h.url_for( controller='library_common', action='ldda_display_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( expired_ldda.library_dataset.folder.id ), id=trans.security.encode_id( expired_ldda.id ), show_deleted=show_deleted )}">${expired_ldda.name}</a> + </div> + %endfor %endif - %if current_version: - <% expired_lddas = [ e_ldda for e_ldda in ldda.library_dataset.expired_datasets ] %> - %if expired_lddas: - <div class="toolFormTitle">Expired versions of ${ldda.name}</div> - %for expired_ldda in expired_lddas: - <div class="form-row"> - <a href="${h.url_for( controller='library_common', action='ldda_display_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( expired_ldda.library_dataset.folder.id ), id=trans.security.encode_id( expired_ldda.id ), show_deleted=show_deleted )}">${expired_ldda.name}</a> - </div> - %endfor - %endif - %endif -</div> +%endif diff -r e3af9317e829 -r 49961332adb6 templates/library/common/library_info.mako --- a/templates/library/common/library_info.mako Fri Feb 05 15:29:22 2010 -0500 +++ b/templates/library/common/library_info.mako Fri Feb 05 15:51:01 2010 -0500 @@ -2,6 +2,14 @@ <%namespace file="/message.mako" import="render_msg" /> <%namespace file="/library/common/common.mako" import="render_template_info" /> +<% + if cntrller in [ 'library', 'requests' ]: + can_add = trans.app.security_agent.can_add_library_item( current_user_roles, library ) + can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, library ) + can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, library ) + info_association, inherited = library.get_info_association() +%> + <br/><br/> <ul class="manage-table-actions"> <li> @@ -13,7 +21,7 @@ ${render_msg( msg, messagetype )} %endif -%if cntrller == 'library_admin' or trans.app.security_agent.can_modify_library_item( current_user_roles, library ): +%if cntrller == 'library_admin' or can_modify: <div class="toolForm"> <div class="toolFormTitle">Change library name and description</div> <div class="toolFormBody"> @@ -32,21 +40,56 @@ </div> <div style="clear: both"></div> </div> - <input type="submit" name="rename_library_button" value="Save"/> + <div class="form-row"> + <input type="submit" name="rename_library_button" value="Save"/> + </div> </form> </div> </div> <p/> %else: <div class="toolForm"> - <div class="toolFormTitle">View information about ${library.name}</div> + <div class="toolFormTitle"> + %if cntrller == 'library_admin' or can_add or can_manage: + <th style="padding-left: 42px;"> + <a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}"><b>${library.name[:50]}</b></a> + <a id="library-${library.id}-popup" class="popup-arrow" style="display: none;">▼</a> + <div popupmenu="library-${library.id}-popup"> + %if not library.deleted: + %if ( cntrller == 'library_admin' or can_add ) and not library.info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='add_info_template', cntrller=cntrller, item_type='library', library_id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}">Add template</a> + %endif + %if cntrller == 'library_admin' and info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='delete_info_template', cntrller=cntrller, item_type='library', library_id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}">Delete template</a> + %endif + %if cntrller == 'library_admin' or can_manage: + <a class="action-button" href="${h.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}">Edit permissions</a> + %endif + %if cntrller == 'library_admin': + <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=trans.security.encode_id( library.id ), library_item_id=trans.security.encode_id( library.id ), library_item_type='library' )}">Delete this data library and its contents</a> + %endif + %elif cntrller == 'library_admin' and not library.purged: + <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=trans.security.encode_id( library.id ), library_item_id=trans.security.encode_id( library.id ), library_item_type='library' )}">Undelete this data library</a> + %endif + </div> + </th> + %else: + <th style="padding-left: 42px;"> + <a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}"><b>${library.name[:50]}</b></a> + </th> + %endif + </div> <div class="toolFormBody"> <div class="form-row"> - <b>Name:</b> ${library.name} - <div style="clear: both"></div> - <b>Description:</b> ${library.description} - <div style="clear: both"></div> + <label>Name:</label> + ${library.name} </div> + <div style="clear: both"></div> + <div class="form-row"> + <label>Description:</label> + ${library.description} + </div> + <div style="clear: both"></div> </div> </div> %endif diff -r e3af9317e829 -r 49961332adb6 templates/library/common/select_info_template.mako --- a/templates/library/common/select_info_template.mako Fri Feb 05 15:29:22 2010 -0500 +++ b/templates/library/common/select_info_template.mako Fri Feb 05 15:51:01 2010 -0500 @@ -1,6 +1,31 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> +<script type="text/javascript"> +$( function() { + $( "select[refresh_on_change='true']").change( function() { + var refresh = false; + var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) + if ( refresh_on_change_values ) { + refresh_on_change_values = refresh_on_change_values.value.split( ',' ); + var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); + for( i= 0; i < refresh_on_change_values.length; i++ ) { + if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ + refresh = true; + break; + } + } + } + else { + refresh = true; + } + if ( refresh ){ + $( "#select_info_template" ).submit(); + } + }); +}); +</script> + <br/><br/> <ul class="manage-table-actions"> <li> @@ -13,21 +38,38 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Select a form on which to base the template for the ${library_item_desc} '${library_item_name}'</div> - <form name="new_info_template" action="${h.url_for( controller='library_common', action='add_info_template', cntrller=cntrller, item_type=item_type, library_id=library_id, folder_id=folder_id, ldda_id=ldda_id, show_deleted=show_deleted )}" method="post" > + <div class="toolFormTitle">Select a template for the ${library_item_desc} '${library_item_name}'</div> + <form id="select_info_template" name="select_info_template" action="${h.url_for( controller='library_common', action='add_info_template', cntrller=cntrller, item_type=item_type, library_id=library_id, folder_id=folder_id, ldda_id=ldda_id, show_deleted=show_deleted )}" method="post" > <div class="toolFormBody"> - <div class="form-row"> - <label>Template:</label> - <select name="form_id"> - %for form in forms: - <option value="${form.id}">${form.name}</option> - %endfor - </select> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <input type="submit" name="add_info_template_button" value="Add template to ${library_item_desc}"/> - </div> + <table class="grid"> + <tr> + <div class="form-row"> + <td> + <input type="hidden" name="refresh" value="true" size="40"/> + <label>Template:</label> + ${template_select_list.get_html()} + </td> + <td> + <input type="submit" name="add_info_template_button" value="Add template to ${library_item_desc}"/> + </td> + </div> + </tr> + </table> + %if template_select_list.get_selected() != ('Select one', 'none'): + <div style="clear: both"></div> + <div class="form-row"> + %for i, field in enumerate( widgets ): + <div class="form-row"> + <label>${field[ 'label' ]}</label> + ${field[ 'widget' ].get_html()} + <div class="toolParamHelp" style="clear: both;"> + ${field[ 'helptext' ]} + </div> + <div style="clear: both"></div> + </div> + %endfor + </div> + %endif </div> </form> </div> diff -r e3af9317e829 -r 49961332adb6 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Fri Feb 05 15:29:22 2010 -0500 +++ b/test/base/twilltestcase.py Fri Feb 05 15:51:01 2010 -0500 @@ -1403,9 +1403,10 @@ elif item_type == 'ldda': url = "%s/library_common/add_info_template?cntrller=%s&item_type=%s&library_id=%s&folder_id=%s&ldda_id=%s" % ( self.url, cntrller, item_type, library_id, folder_id, ldda_id ) self.visit_url( url ) - self.check_page_for_string ( "Select a form on which to base the template" ) + self.check_page_for_string ( "Select a template for the" ) + tc.fv( '1', 'form_id', form_id ) tc.submit( 'add_info_template_button' ) - self.check_page_for_string = 'An information template based on the form "%s" has been added to this' % form_name + self.check_page_for_string = 'A template based on the form "%s" has been added to this' % form_name self.home() def library_info( self, library_id, library_name, ele_1_field_name, ele_1_contents, ele_2_field_name, ele_2_contents, controller='library_admin' ): """Add information to a library using an existing template with 2 elements""" diff -r e3af9317e829 -r 49961332adb6 test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Fri Feb 05 15:29:22 2010 -0500 +++ b/test/functional/test_security_and_libraries.py Fri Feb 05 15:51:01 2010 -0500 @@ -582,7 +582,7 @@ self.add_info_template( 'library_admin', 'library', self.security.encode_id( library_one.id ), - str( form_one.id ), + self.security.encode_id( form_one.id ), form_one.name ) # Make sure the template fields are displayed on the library information page field_dict = form_one.fields[ 0 ]

1 0

[hg] galaxy 3344: Merge.
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e3af9317e829 changeset: 3344:e3af9317e829 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Feb 05 15:29:22 2010 -0500 description: Merge. diffstat: buildbot_setup.sh | 9 +++++++++ 1 files changed, 9 insertions(+), 0 deletions(-) diffs (19 lines): diff -r 952795dbbe74 -r e3af9317e829 buildbot_setup.sh --- a/buildbot_setup.sh Fri Feb 05 15:29:01 2010 -0500 +++ b/buildbot_setup.sh Fri Feb 05 15:29:22 2010 -0500 @@ -10,6 +10,15 @@ kernel=`uname -r | cut -f1,2 -d.` HYPHY="/galaxy/software/linux$kernel-$HOSTTYPE/hyphy" ;; + darwin*) + this_minor=`uname -r | awk -F. '{print ($1-4)}'` + machine=`machine` + for minor in `jot - 3 $this_minor 1`; do + HYPHY="/galaxy/software/macosx10.$minor-$machine/hyphy" + [ -d "$HYPHY" ] && break + done + [ ! -d "$HYPHY" ] && unset HYPHY + ;; esac LINKS="

1 0

[hg] galaxy 3343: Pack script.
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/952795dbbe74 changeset: 3343:952795dbbe74 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Feb 05 15:29:01 2010 -0500 description: Pack script. diffstat: static/scripts/packed/galaxy.base.js | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (8 lines): diff -r 207298b5ea39 -r 952795dbbe74 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js Fri Feb 05 15:28:03 2010 -0500 +++ b/static/scripts/packed/galaxy.base.js Fri Feb 05 15:29:01 2010 -0500 @@ -1,1 +1,1 @@ -$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});make_popup_menus()});function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",t op:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ensure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></ul>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}var array_length=function(a){if(a.length){return a.length}var b=0;for(element in a){b++}return b};var replace_dbkey_select=function(){var c=$("select[name=dbkey]");var d=c.attr("value");if(c.length!=0){var e=$("<input id='dbkey-input' type='text'></input>");e.attr("size",40);e.attr("name",c.attr("name"));e.click(function(){var g=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",g);$(this).select()});var b=new Array();var a=new Object();c.children("option").each(function(){var h=$(this).text();var g=$(this).attr("value");if(g=="?"){return}b.push(h);a[h]=g;if(g==d){e.attr("value",h)}});if(e.attr("value")==""){e.attr("value","Click to Search or Select Build")}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};e.autocomplete(b,f);c.replaceWith(e);$("form").submit(function(){var i=$("#dbkey-input");if(i.length!=0){var h=i.attr("value");var g=a[h];if(g!=null&&g!=undefined){i.attr("value",g)}else{if(d!=""){i.attr("value",d)}else{i. attr("value","?")}}}})}};function async_save_text(d,f,e,a,c,h,i,g,b){if(c==null){c=30}if(i==null){i=4}$("#"+d).click(function(){var k=$("#"+f).text();if(h){var j=$("<textarea rows='"+i+"' cols='"+c+"'>"+k+"</textarea>")}else{var j=$("<input type='text' value='"+k+"' size='"+c+"'></input>")}j.blur(function(){$(this).remove();$("#"+f).show();if(b!=null){b(j)}});j.keyup(function(m){if(m.keyCode==27){$(this).trigger("blur")}else{if(m.keyCode==13){new_text=this.value;$(this).trigger("blur");var l=new Object();l[a]=new_text;$.ajax({url:e,data:l,error:function(){alert("Text editing for elt "+f+" failed")},success:function(){$("#"+f).text(new_text);if(b!=null){b(j)}}})}}});if(g!=null){g(j)}$("#"+f).hide();j.insertAfter($("#"+f));j.focus();j.select();return false})}; \ No newline at end of file +$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});make_popup_menus()});function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",t op:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ensure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></ul>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}var array_length=function(a){if(a.length){return a.length}var b=0;for(element in a){b++}return b};var replace_dbkey_select=function(){var c=$("select[name=dbkey]");var d=c.attr("value");if(c.length!=0){var e=$("<input id='dbkey-input' type='text'></input>");e.attr("size",40);e.attr("name",c.attr("name"));e.click(function(){var g=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",g);$(this).select()});var b=new Array();var a=new Object();c.children("option").each(function(){var h=$(this).text();var g=$(this).attr("value");if(g=="?"){return}b.push(h);a[h]=g;if(g==d){e.attr("value",h)}});if(e.attr("value")==""){e.attr("value","Click to Search or Select Build")}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};e.autocomplete(b,f);c.replaceWith(e);$("form").submit(function(){var i=$("#dbkey-input");if(i.length!=0){var h=i.attr("value");var g=a[h];if(g!=null&&g!=undefined){i.attr("value",g)}else{if(d!=""){i.attr("value",d)}else{i. attr("value","?")}}}})}};function async_save_text(d,f,e,a,c,h,i,g,b){if(c==null){c=30}if(i==null){i=4}$("#"+d).click(function(){var k=$("#"+f).text();if(h){var j=$("<textarea rows='"+i+"' cols='"+c+"'>"+k+"</textarea>")}else{var j=$("<input type='text' value='"+k+"' size='"+c+"'></input>")}j.blur(function(){$(this).remove();$("#"+f).show();if(b!=null){b(j)}});j.keyup(function(m){if(m.keyCode==27){$(this).trigger("blur")}else{if(m.keyCode==13){new_text=this.value;$(this).trigger("blur");var l=new Object();l[a]=new_text;$.ajax({url:e,data:l,error:function(){alert("Text editing for elt "+f+" failed")},success:function(n){$("#"+f).text(n);if(b!=null){b(j)}}})}}});if(g!=null){g(j)}$("#"+f).hide();j.insertAfter($("#"+f));j.focus();j.select();return false})}; \ No newline at end of file

1 0

[hg] galaxy 3342: Sanitize HTML in annotations and update annota...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/207298b5ea39 changeset: 3342:207298b5ea39 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Feb 05 15:28:03 2010 -0500 description: Sanitize HTML in annotations and update annotations via ajax to show sanitation results. diffstat: lib/galaxy/web/controllers/history.py | 8 +++++--- lib/galaxy/web/controllers/root.py | 5 ++++- lib/galaxy/web/controllers/workflow.py | 19 ++++++++++--------- static/scripts/galaxy.base.js | 4 ++-- 4 files changed, 21 insertions(+), 15 deletions(-) diffs (128 lines): diff -r 12789b4ba919 -r 207298b5ea39 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Fri Feb 05 14:25:38 2010 -0500 +++ b/lib/galaxy/web/controllers/history.py Fri Feb 05 15:28:03 2010 -0500 @@ -4,6 +4,7 @@ from galaxy.model.mapping import desc from galaxy.model.orm import * from galaxy.util.json import * +from galaxy.util.sanitize_html import sanitize_html from galaxy.tags.tag_handler import TagHandler from sqlalchemy.sql.expression import ClauseElement import webhelpers, logging, operator @@ -355,17 +356,18 @@ history.name = new_name trans.sa_session.add( history ) trans.sa_session.flush() + return history.name @web.expose @web.require_login( "use Galaxy histories" ) def annotate_async( self, trans, id, new_annotation=None, **kwargs ): history = self.get_history( trans, id ) if new_annotation: + # Sanitize annotation before adding it. + new_annotation = sanitize_html( new_annotation, 'utf-8', 'text/html' ) self.add_item_annotation( trans, history, new_annotation ) trans.sa_session.flush() - return - else: - return "failed" + return new_annotation @web.expose @web.json diff -r 12789b4ba919 -r 207298b5ea39 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Fri Feb 05 14:25:38 2010 -0500 +++ b/lib/galaxy/web/controllers/root.py Fri Feb 05 15:28:03 2010 -0500 @@ -5,6 +5,7 @@ from cgi import escape, FieldStorage from galaxy import util, datatypes, jobs, web, util from galaxy.web.base.controller import * +from galaxy.util.sanitize_html import sanitize_html from galaxy.model.orm import * log = logging.getLogger( __name__ ) @@ -305,7 +306,9 @@ else: setattr( data.metadata, name, spec.unwrap( params.get (name, None) ) ) data.datatype.after_setting_metadata( data ) - self.add_item_annotation( trans, data, params.annotation ) + # Sanitize annotation before adding it. + annotation = sanitize_html( params.annotation, 'utf-8', 'text/html' ) + self.add_item_annotation( trans, data, annotation ) else: msg = ' (Metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata.)' trans.sa_session.flush() diff -r 12789b4ba919 -r 207298b5ea39 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Fri Feb 05 14:25:38 2010 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Fri Feb 05 15:28:03 2010 -0500 @@ -11,6 +11,7 @@ from galaxy.datatypes.data import Data from galaxy.util.odict import odict from galaxy.util.bunch import Bunch +from galaxy.util.sanitize_html import sanitize_html from galaxy.util.topsort import topsort, topsort_levels, CycleError from galaxy.workflow.modules import * from galaxy.model.mapping import desc @@ -317,8 +318,9 @@ # Rename workflow. stored.name = kwargs[ 'name' ] if 'annotation' in kwargs: - # Set workflow annotation. - self.add_item_annotation( trans, stored, kwargs[ 'annotation' ] ) + # Set workflow annotation; sanitize annotation before adding it. + annotation = sanitize_html( kwargs[ 'annotation' ], 'utf-8', 'text/html' ) + self.add_item_annotation( trans, stored, annotation ) trans.sa_session.flush() return trans.fill_template( 'workflow/edit_attributes.mako', @@ -350,20 +352,18 @@ if new_name: stored.name = new_name trans.sa_session.flush() - return - else: - return "failed" + return stored.name @web.expose @web.require_login( "use Galaxy workflows" ) def annotate_async( self, trans, id, new_annotation=None, **kwargs ): stored = get_stored_workflow( trans, id ) if new_annotation: + # Sanitize annotation before adding it. + new_annotation = sanitize_html( new_annotation, 'utf-8', 'text/html' ) self.add_item_annotation( trans, stored, new_annotation ) trans.sa_session.flush() - return - else: - return "failed" + return new_annotation @web.expose @web.require_login( "use Galaxy workflows" ) @@ -643,7 +643,8 @@ step.temp_input_connections = step_dict['input_connections'] # Save step annotation. - self.add_item_annotation( trans, step, step_dict[ 'annotation' ] ) + annotation = sanitize_html( step_dict[ 'annotation' ], 'utf-8', 'text/html' ) + self.add_item_annotation( trans, step, annotation ) # Second pass to deal with connections between steps for step in steps: # Input connections diff -r 12789b4ba919 -r 207298b5ea39 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Fri Feb 05 14:25:38 2010 -0500 +++ b/static/scripts/galaxy.base.js Fri Feb 05 15:28:03 2010 -0500 @@ -249,9 +249,9 @@ alert( "Text editing for elt " + text_elt_id + " failed" ); // TODO: call finish or no? For now, let's not because error occurred. }, - success: function() { + success: function(processed_text) { // Set new text and call finish method. - $("#" + text_elt_id).text( new_text ); + $("#" + text_elt_id).text( processed_text ); if (on_finish != null) on_finish(t); }

1 0

[hg] galaxy 3341: Add path to OS X HYPHY for buildbot
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/30c0d321bcbd changeset: 3341:30c0d321bcbd user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Feb 05 15:27:38 2010 -0500 description: Add path to OS X HYPHY for buildbot diffstat: buildbot_setup.sh | 9 +++++++++ 1 files changed, 9 insertions(+), 0 deletions(-) diffs (19 lines): diff -r 12789b4ba919 -r 30c0d321bcbd buildbot_setup.sh --- a/buildbot_setup.sh Fri Feb 05 14:25:38 2010 -0500 +++ b/buildbot_setup.sh Fri Feb 05 15:27:38 2010 -0500 @@ -10,6 +10,15 @@ kernel=`uname -r | cut -f1,2 -d.` HYPHY="/galaxy/software/linux$kernel-$HOSTTYPE/hyphy" ;; + darwin*) + this_minor=`uname -r | awk -F. '{print ($1-4)}'` + machine=`machine` + for minor in `jot - 3 $this_minor 1`; do + HYPHY="/galaxy/software/macosx10.$minor-$machine/hyphy" + [ -d "$HYPHY" ] && break + done + [ ! -d "$HYPHY" ] && unset HYPHY + ;; esac LINKS="

1 0

[hg] galaxy 3340: Forms UI improvements
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/12789b4ba919 changeset: 3340:12789b4ba919 user: rc date: Fri Feb 05 14:25:38 2010 -0500 description: Forms UI improvements diffstat: lib/galaxy/web/controllers/forms.py | 8 +++++--- templates/display_common.mako | 34 +++++++++++++++++++--------------- 2 files changed, 24 insertions(+), 18 deletions(-) diffs (76 lines): diff -r 9e2ba4cf4494 -r 12789b4ba919 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Fri Feb 05 14:18:37 2010 -0500 +++ b/lib/galaxy/web/controllers/forms.py Fri Feb 05 14:25:38 2010 -0500 @@ -135,7 +135,9 @@ return trans.response.send_redirect( web.url_for( controller='forms', action='new', msg=msg, - messagetype='error' ) ) + messagetype='error', + name=util.restore_text( params.get( 'name', '' ) ), + description=util.restore_text( params.get( 'description', '' ) ) ) ) self.__get_saved_form( fd ) if self.__imported_from_file: return trans.response.send_redirect( web.url_for( controller='forms', @@ -151,8 +153,8 @@ name=fd.name, description=fd.desc, form_type_selectbox=fd.type ) ) - inputs = [ ( 'Name', TextField( 'name', 40, 'New Form' ) ), - ( 'Description', TextField( 'description', 40, '' ) ), + inputs = [ ( 'Name', TextField( 'name', 40, util.restore_text( params.get( 'name', '' ) ) ) ), + ( 'Description', TextField( 'description', 40, util.restore_text( params.get( 'description', '' ) ) ) ), ( 'Type', self.__form_types_widget(trans, selected=params.get( 'form_type', 'none' )) ), ( 'Import from csv file (Optional)', FileField( 'file_data', 40, '' ) ) ] return trans.fill_template( '/admin/forms/create_form.mako', diff -r 9e2ba4cf4494 -r 12789b4ba919 templates/display_common.mako --- a/templates/display_common.mako Fri Feb 05 14:18:37 2010 -0500 +++ b/templates/display_common.mako Fri Feb 05 14:25:38 2010 -0500 @@ -30,6 +30,8 @@ ## Start with exceptions, end with default. if a_class is model.History: return "Histories" + elif a_class is model.FormDefinitionCurrent: + return "Forms" else: return get_class_display_name( a_class ) + "s" %> @@ -55,21 +57,23 @@ ## Get plural term for class. <%def name="get_class_plural( a_class )"> - <% - if a_class == model.History: - class_plural = "Histories" - elif a_class == model.StoredWorkflow: - class_plural = "Workflows" - elif a_class == model.Page: - class_plural = "Pages" - elif a_class == model.Library: - class_plural = "Libraries" - elif a_class == model.HistoryDatasetAssociation: - class_plural = "Datasets" - else: - class_plural = a_class.__name__ + "s" - return class_plural - %> +<% + if a_class == model.History: + class_plural = "Histories" + elif a_class == model.StoredWorkflow: + class_plural = "Workflows" + elif a_class == model.Page: + class_plural = "Pages" + elif a_class == model.Library: + class_plural = "Libraries" + elif a_class == model.HistoryDatasetAssociation: + class_plural = "Datasets" + elif a_class == model.FormDefinitionCurrent: + class_plural = "Forms" + else: + class_plural = a_class.__name__ + "s" + return class_plural +%> </%def> ## Returns the controller name for an item based on its class.

1 0

[hg] galaxy 3339: UI improvements for history panel and tags: (1...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/9e2ba4cf4494 changeset: 3339:9e2ba4cf4494 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Feb 05 14:18:37 2010 -0500 description: UI improvements for history panel and tags: (1) added icons for tags, annotations; (2) added tooltips for editable text; (3) added tooltips for tags. diffstat: static/images/sticky-note-text.png | 0 static/images/tag-label.png | 0 static/june_2007_style/base.css.tmpl | 47 ++++++++++++++++++- static/june_2007_style/blue/base.css | 9 +++- static/scripts/galaxy.base.js | 13 +++- static/scripts/packed/galaxy.base.js | 2 +- templates/root/history.mako | 88 ++++++++++++++++++++-------------- templates/tagging_common.mako | 23 +++++--- 8 files changed, 129 insertions(+), 53 deletions(-) diffs (266 lines): diff -r 7163a2128267 -r 9e2ba4cf4494 static/images/sticky-note-text.png Binary file static/images/sticky-note-text.png has changed diff -r 7163a2128267 -r 9e2ba4cf4494 static/images/tag-label.png Binary file static/images/tag-label.png has changed diff -r 7163a2128267 -r 9e2ba4cf4494 static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Fri Feb 05 11:53:06 2010 -0500 +++ b/static/june_2007_style/base.css.tmpl Fri Feb 05 14:18:37 2010 -0500 @@ -697,4 +697,49 @@ .icon-button.edit:hover { -sprite-group: history-buttons; -sprite-image: pencil_icon_dark.png; -} \ No newline at end of file +} + +.icon-button.tag { + background-image:url(/static/images/tag-label.png); + background-repeat:no-repeat; + background-position:center; + padding: 0px 0px 0px 0px; +} + +.icon-button.annotate { + background-image:url(/static/images/sticky-note-text.png); + background-repeat:no-repeat; + background-position:center; + padding: 0px 0px 0px 0px; +} + +.tooltip { + position: relative; + cursor: pointer; +} + +.tooltip span.tip { + display: none +} + +.tooltip:hover span.tip { + font-size: 90%; + display: block; + position: absolute; + right:2em;top:-1.75em; + width: inherit; + background-color: black; + color: white; + text-align: center; + padding: 0.25em 0.5em; +} + +.editable-text { + cursor:pointer; +} + +.editable-text:hover{ + background-image:url(); + background-repeat:no-repeat; + background-position:right; +} diff -r 7163a2128267 -r 9e2ba4cf4494 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Fri Feb 05 11:53:06 2010 -0500 +++ b/static/june_2007_style/blue/base.css Fri Feb 05 14:18:37 2010 -0500 @@ -116,4 +116,11 @@ .icon-button.display{background:url(history-buttons.png) no-repeat 0px -0px;} .icon-button.display:hover{background:url(history-buttons.png) no-repeat 0px -26px;} .icon-button.delete{background:url(history-buttons.png) no-repeat 0px -104px;} -.icon-button.delete:hover{background:url(history-buttons.png) no-repeat 0px -130px;} \ No newline at end of file +.icon-button.delete:hover{background:url(history-buttons.png) no-repeat 0px -130px;} +.icon-button.tag{background-image:url(/static/images/tag-label.png);background-repeat:no-repeat;background-position:center;padding: 0px 0px 0px 0px;} +.icon-button.annotate{background-image:url(/static/images/sticky-note-text.png);background-repeat:no-repeat;background-position:center;padding: 0px 0px 0px 0px;} +.tooltip {position: relative; cursor: pointer} +.tooltip span.tip{display: none;} +.tooltip:hover span.tip{font-size: 90%; display: block;position: absolute;right:2em;top:-1.75em; width: inherit; background-color: black;color: white;text-align: center;padding: 0.25em 0.5em;} +.editable-text{cursor:pointer} +.editable-text:hover{background-image:url();background-repeat:no-repeat;background-position:right} \ No newline at end of file diff -r 7163a2128267 -r 9e2ba4cf4494 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Fri Feb 05 11:53:06 2010 -0500 +++ b/static/scripts/galaxy.base.js Fri Feb 05 14:18:37 2010 -0500 @@ -211,14 +211,21 @@ // // Edit and save text asynchronously. // -function async_save_text(click_to_edit_elt, text_elt_id, save_url, text_parm_name, use_textarea, num_rows, on_start, on_finish) +function async_save_text(click_to_edit_elt, text_elt_id, save_url, text_parm_name, num_cols, use_textarea, num_rows, on_start, on_finish) { + // Set defaults if necessary. + if (num_cols == null) + num_cols = 30; + if (num_rows == null) + num_rows = 4 + + // Set up input element. $("#" + click_to_edit_elt).click( function() { var old_text = $("#" + text_elt_id).text() if (use_textarea) - var t = $("<textarea rows='" + num_rows + "'>" + old_text + "</textarea>" ); + var t = $("<textarea rows='" + num_rows + "' cols='" + num_cols + "'>" + old_text + "</textarea>" ); else - var t = $("<input type='text' value='" + old_text + "'></input>" ); + var t = $("<input type='text' value='" + old_text + "' size='" + num_cols + "'></input>" ); t.blur( function() { $(this).remove(); $("#" + text_elt_id).show(); diff -r 7163a2128267 -r 9e2ba4cf4494 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js Fri Feb 05 11:53:06 2010 -0500 +++ b/static/scripts/packed/galaxy.base.js Fri Feb 05 14:18:37 2010 -0500 @@ -1,1 +1,1 @@ -$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});make_popup_menus()});function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",t op:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ensure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></ul>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}var array_length=function(a){if(a.length){return a.length}var b=0;for(element in a){b++}return b};var replace_dbkey_select=function(){var c=$("select[name=dbkey]");var d=c.attr("value");if(c.length!=0){var e=$("<input id='dbkey-input' type='text'></input>");e.attr("size",40);e.attr("name",c.attr("name"));e.click(function(){var g=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",g);$(this).select()});var b=new Array();var a=new Object();c.children("option").each(function(){var h=$(this).text();var g=$(this).attr("value");if(g=="?"){return}b.push(h);a[h]=g;if(g==d){e.attr("value",h)}});if(e.attr("value")==""){e.attr("value","Click to Search or Select Build")}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};e.autocomplete(b,f);c.replaceWith(e);$("form").submit(function(){var i=$("#dbkey-input");if(i.length!=0){var h=i.attr("value");var g=a[h];if(g!=null&&g!=undefined){i.attr("value",g)}else{if(d!=""){i.attr("value",d)}else{i. attr("value","?")}}}})}};function async_save_text(d,c,a,e,f,b){$("#"+d).click(function(){var h=$("#"+c).text();if(f){var g=$("<textarea rows='"+b+"'>"+h+"</textarea>")}else{var g=$("<input type='text' value='"+h+"'></input>")}g.blur(function(){$(this).remove();$("#"+c).show()});g.keyup(function(j){if(j.keyCode==27){$(this).trigger("blur")}else{if(j.keyCode==13){new_text=this.value;$(this).trigger("blur");var i=new Object();i[e]=new_text;$.ajax({url:a,data:i,error:function(){alert("Text editing for elt "+c+" failed")},success:function(){$("#"+c).text(new_text)}})}}});$("#"+c).hide();g.insertAfter($("#"+c));g.focus();g.select();return false})}; \ No newline at end of file +$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});make_popup_menus()});function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",t op:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ensure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></ul>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}var array_length=function(a){if(a.length){return a.length}var b=0;for(element in a){b++}return b};var replace_dbkey_select=function(){var c=$("select[name=dbkey]");var d=c.attr("value");if(c.length!=0){var e=$("<input id='dbkey-input' type='text'></input>");e.attr("size",40);e.attr("name",c.attr("name"));e.click(function(){var g=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",g);$(this).select()});var b=new Array();var a=new Object();c.children("option").each(function(){var h=$(this).text();var g=$(this).attr("value");if(g=="?"){return}b.push(h);a[h]=g;if(g==d){e.attr("value",h)}});if(e.attr("value")==""){e.attr("value","Click to Search or Select Build")}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};e.autocomplete(b,f);c.replaceWith(e);$("form").submit(function(){var i=$("#dbkey-input");if(i.length!=0){var h=i.attr("value");var g=a[h];if(g!=null&&g!=undefined){i.attr("value",g)}else{if(d!=""){i.attr("value",d)}else{i. attr("value","?")}}}})}};function async_save_text(d,f,e,a,c,h,i,g,b){if(c==null){c=30}if(i==null){i=4}$("#"+d).click(function(){var k=$("#"+f).text();if(h){var j=$("<textarea rows='"+i+"' cols='"+c+"'>"+k+"</textarea>")}else{var j=$("<input type='text' value='"+k+"' size='"+c+"'></input>")}j.blur(function(){$(this).remove();$("#"+f).show();if(b!=null){b(j)}});j.keyup(function(m){if(m.keyCode==27){$(this).trigger("blur")}else{if(m.keyCode==13){new_text=this.value;$(this).trigger("blur");var l=new Object();l[a]=new_text;$.ajax({url:e,data:l,error:function(){alert("Text editing for elt "+f+" failed")},success:function(){$("#"+f).text(new_text);if(b!=null){b(j)}}})}}});if(g!=null){g(j)}$("#"+f).hide();j.insertAfter($("#"+f));j.focus();j.select();return false})}; \ No newline at end of file diff -r 7163a2128267 -r 9e2ba4cf4494 templates/root/history.mako --- a/templates/root/history.mako Fri Feb 05 11:53:06 2010 -0500 +++ b/templates/root/history.mako Fri Feb 05 14:18:37 2010 -0500 @@ -42,19 +42,22 @@ $.jStore.remove("history_expand_state"); })); - // Rename async. - async_save_text("history-rename", "history-name", "${h.url_for( controller="/history", action="rename_async", id=trans.security.encode_id(history.id) )}", "new_name"); + // Rename management. + async_save_text("history-name", "history-name", "${h.url_for( controller="/history", action="rename_async", id=trans.security.encode_id(history.id) )}", "new_name", 18); - // Annotation async. - // Tag async. Simply have the workflow tag element generate a click on the tag element to activate tagging. - $('#workflow-tag').click( function() + // Tag management. + $('#history-tag').click( function() { - $('.tag-area').click(); + $('#history-tag-area').toggle("fast"); return false; }); - - // Annotate async. - async_save_text("history-annotate", "history-annotation", "${h.url_for( controller="/history", action="annotate_async", id=trans.security.encode_id(history.id) )}", "new_annotation", true, 4); + + // Annotation management. + $('#history-annotate').click( function() { + $('#history-annotation-area').toggle("fast"); + return false; + }); + async_save_text("history-annotation", "history-annotation", "${h.url_for( controller="/history", action="annotate_async", id=trans.security.encode_id(history.id) )}", "new_annotation", 18, true, 4); // Updater updater({ @@ -273,10 +276,24 @@ | <a href="${h.url_for('history', show_deleted=False)}">${_('hide deleted')}</a> %endif </div> - + <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold;"> - <div style="float: right"><a id="history-rename" title="Rename" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='history', action='rename' )}"></a></div> - <div id="history-name">${history.get_display_name() | h}</div> + <table width="100%" cellpadding="0" cellspacing="0"> + <tr> + <td align="left"> + <div id="history-name-container" class="editable-text tooltip"> + <span id="history-name">${history.get_display_name() | h}</span> + <span class="tip">Click to edit</span></a> + </div> + </td> + <td align="right"> + <div style="float: right"> + <a id="history-tag" title="Tag" class="icon-button tag tooltip" target="galaxy_main" href="${h.url_for( controller='history', action='tag' )}"></a> + <a id="history-annotate" title="Annotate" class="icon-button annotate" target="galaxy_main" href="${h.url_for( controller='history', action='annotate' )}"></a> + </div> + </td> + </tr> + </table> </div> %if history.deleted: @@ -291,33 +308,30 @@ %if trans.get_user() is not None: <div style="margin: 0px 0px 5px 10px"> - <a href="#" onclick="$('#tags-and-annotation').toggle('fast')">Edit Tags and Annotation/Notes</a> - <div id="tags-and-annotation" style="display: none"> - ## Tagging elt. - <div class="form-row"> - <label>Tags:</label> - <div style="float: right"><a id="workflow-tag" title="Tag" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='workflow', action='annotate_async' )}"></a></div> - <style> - .tag-area { - border: none; - } - </style> - ${render_individual_tagging_element(user=trans.get_user(), tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20", render_add_tag_button=False)} - <div style="clear: both"></div> - </div> - - ## Annotation elt. - <div id="history-annotation-area" class="form-row"> - <label>Annotation / Notes:</label> - <div style="float: right"><a id="history-annotate" title="Annotate" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='history', action='annotate_async' )}"></a></div> - %if annotation: - <div id="history-annotation">${annotation | h}</div> - %else: - <div id="history-annotation"></div> - %endif - <div style="clear: both"></div> + ## Tagging elt. + <div id="history-tag-area" class="form-row" style="display: none"> + <label>Tags:</label> + <style> + .tag-area { + border: none; + } + </style> + ${render_individual_tagging_element(user=trans.get_user(), tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20")} + </div> + + ## Annotation elt. + <div id="history-annotation-area" class="form-row" style="display: none"> + <label>Annotation / Notes:</label> + <div class="tooltip"> + %if annotation: + <span id="history-annotation">${annotation | h}</span> + %else: + <span id="history-annotation">None</span> + %endif + <span class="tip">Click to edit annotation</span> </div> </div> + </div> %endif diff -r 7163a2128267 -r 9e2ba4cf4494 templates/tagging_common.mako --- a/templates/tagging_common.mako Fri Feb 05 11:53:06 2010 -0500 +++ b/templates/tagging_common.mako Fri Feb 05 14:18:37 2010 -0500 @@ -72,17 +72,20 @@ %endfor ## Add tag input field. If element is in form, tag input is a textarea; otherwise element is a input type=text. - %if editable: - %if in_form: - <textarea class="tag-input" rows='1' cols='${input_size}'></textarea> - %else: - <input class="tag-input" type='text' size='${input_size}'/> + <div class="tooltip"> + %if editable: + %if in_form: + <textarea class="tag-input" rows='1' cols='${input_size}'></textarea> + %else: + <input class="tag-input" type='text' size='${input_size}'/> + %endif + ## Add "add tag" button. + %if render_add_tag_button: + <img src='${h.url_for('/static/images/add_icon.png')}' rollover='${h.url_for('/static/images/add_icon_dark.png')}' class="add-tag-button"/> + %endif %endif - ## Add "add tag" button. - %if render_add_tag_button: - <img src='${h.url_for('/static/images/add_icon.png')}' rollover='${h.url_for('/static/images/add_icon_dark.png')}' class="add-tag-button"/> - %endif - %endif + <span class="tip">Click to add tags</span> + </div> </div> </div> </%def>

1 0

[hg] galaxy 3338: Have sam2interval provide a (partial) header s...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/7163a2128267 changeset: 3338:7163a2128267 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Feb 05 11:53:06 2010 -0500 description: Have sam2interval provide a (partial) header so that strand is automatically set in metadata. diffstat: test-data/sam2interval_noprintAll.dat | 1 + test-data/sam2interval_printAll.dat | 1 + tools/samtools/sam2interval.py | 2 ++ 3 files changed, 4 insertions(+), 0 deletions(-) diffs (28 lines): diff -r 8b3c1f064bef -r 7163a2128267 test-data/sam2interval_noprintAll.dat --- a/test-data/sam2interval_noprintAll.dat Fri Feb 05 11:49:51 2010 -0500 +++ b/test-data/sam2interval_noprintAll.dat Fri Feb 05 11:53:06 2010 -0500 @@ -1,3 +1,4 @@ +#chrom start end strand ref 6 22 + ref 8 19 + ref 8 14 + diff -r 8b3c1f064bef -r 7163a2128267 test-data/sam2interval_printAll.dat --- a/test-data/sam2interval_printAll.dat Fri Feb 05 11:49:51 2010 -0500 +++ b/test-data/sam2interval_printAll.dat Fri Feb 05 11:53:06 2010 -0500 @@ -1,3 +1,4 @@ +#chrom start end strand ref 6 22 + r001 163 ref 7 30 8M2I4M1D3M = 37 39 TTAGATAAAGGATACTA * ref 8 19 + r002 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA * ref 8 14 + r003 0 ref 9 30 5H6M * 0 0 AGCTAA * NM:i:1 diff -r 8b3c1f064bef -r 7163a2128267 tools/samtools/sam2interval.py --- a/tools/samtools/sam2interval.py Fri Feb 05 11:49:51 2010 -0500 +++ b/tools/samtools/sam2interval.py Fri Feb 05 11:53:06 2010 -0500 @@ -76,6 +76,8 @@ cigar = re.compile( '\d+M|\d+N|\d+D|\d+P' ) + print '#chrom\tstart\tend\tstrand' # provide a (partial) header so that strand is automatically set in metadata + for line in infile: line = line.rstrip( '\r\n' ) if line and not line.startswith( '#' ) and not line.startswith( '@' ) :

1 0

[hg] galaxy 3337: Fix Twill Test Framework: diffs were no longer...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/8b3c1f064bef changeset: 3337:8b3c1f064bef user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Feb 05 11:49:51 2010 -0500 description: Fix Twill Test Framework: diffs were no longer being reported (all functional tests not writing to stderr were passing regardless of failure). diffstat: test/base/twilltestcase.py | 1 + 1 files changed, 1 insertions(+), 0 deletions(-) diffs (11 lines): diff -r 22c1284782fb -r 8b3c1f064bef test/base/twilltestcase.py --- a/test/base/twilltestcase.py Fri Feb 05 11:20:13 2010 -0500 +++ b/test/base/twilltestcase.py Fri Feb 05 11:49:51 2010 -0500 @@ -82,6 +82,7 @@ for char in line: if ord( char ) > 128: raise AssertionError( "Binary data detected, not displaying diff" ) + raise AssertionError( "".join( diff_slice ) ) def get_filename( self, filename ): full = os.path.join( self.file_dir, filename)

1 0