| blob | 4079219458a3d987fdb29e50d1baf9496a59efe3 |
1 FILES THAT HAVE BEEN VALIDATED FOR XHTML
2 (ROOT sgn/cgi-bin)
3 (Evan Herbst, Jan 2007)
5 file date comments
6 ----------------------------------------------------------------------------------------
7 .:
8 index.pl 1/5
9 oldevents.pl 1/7
10 oldhighlights.pl 1/7
11 oldpublications.pl 1/7
12 testgd.pl not html
14 ./about:
15 Summer_Internship_2005.pl 1/7
16 about_solanaceae.pl 1/6
17 align_term.pl 1/7
18 clone_policy.pl 1/7
19 clustal_file.pl 1/7
20 fam_align_analysis.pl 1/7
21 fam_tree_analysis.pl 1/7
22 family_analysis.pl 1/7
23 index.pl 1/8
24 italy.pl 1/7
25 release_20040301.pl 1/7
26 solanum_nomenclature.pl 1/6
27 status.pl can't locate SGN.pm in @INC -- has been superseded? doesn't seem recent
28 temp.pl graphs server-room temperature? has been superseded?
29 tomato_project_overview.pl 1/8
30 tomato_sequencing.pl 1/8
31 tomato_sequencing_scope.pl 1/7
32 us_tomato_sequencing.pl 1/7
34 ./about/ecosol:
35 index.pl 1/7
37 ./about/release_notes:
38 tomato_unigene_build1.pl 1/7
40 ./about/tomato_project:
41 index.pl 1/7
43 ./about/tomato_project/nsf_9872617:
44 footer.pl not top-level
45 index.pl 1/7
46 members.pl 1/7
47 progress.pl 1/7
48 project.pl 1/7
49 publications.pl 1/7
50 websites.pl 1/7
52 ./about/tomato_sequencing:
53 index.pl 1/7
55 ./bulk:
56 display.pl 1/7 with and without summary=1
57 download.pl 1/7
58 index.pl 1/7
59 input.pl 1/7
61 ./community:
62 index.pl 1/6
64 ./community/feature:
65 200403.pl 1/6
66 200404.pl 1/6
67 200405.pl 1/6
68 200406.pl 1/6
69 200407.pl 1/6
70 200408.pl 1/6
71 200409.pl 1/6
72 200410.pl 1/6
73 200503.pl 1/6
74 200504.pl 1/6
75 200507.pl 1/6
76 200510.pl 1/6
77 200601.pl 1/6
78 200612.pl 1/6
79 index.pl 1/6
80 kjb_lab.pl 1/6
81 paran_lab.pl 1/6
83 ./community/genomics_forum:
84 index.pl 1/6
85 schedule_summer_2005.pl 1/6
87 ./community/links:
88 genefinding.pl 1/6
89 index.pl 1/6
90 journals.pl 1/6
91 related_sites.pl 1/6
92 seed_companies.pl 1/6
94 ./community/meetings:
95 index.pl 1/6
97 ./community/snp_consortium:
98 Labate_tomato_tech.pl 1/6
99 index.pl 1/6
101 ./content:
102 coffee.pl 1/6
103 fish.pl 1/6
104 index.pl 1/6
105 library_info.pl 1/6
106 map_submissions.pl 1/6
107 sgn_data.pl duplicate element ID having to do with Solanum habrochaites, coming from a database; also, the 'database schema' link is broken -- 1/6
108 unigene_builds.pl 1/6
110 ./content/libraries:
111 breakerfruit.pl 1/7
112 callus.pl 1/7
113 deficientroot.pl 1/7
114 developingfruit.pl 1/7
115 flowerbudctoa.pl 1/7
116 flowerbudctob.pl 1/7
117 flowerbudctoc.pl 1/7
118 germinatingseed.pl 1/7
119 hirsutumtrichome.pl 1/7
120 index.pl 1/7
121 maturegreenfruit.pl 1/7
122 mixedelicitor.pl 1/7
123 openflowerctod.pl 1/7
124 ovary.pl 1/7
125 pennelliitrichome.pl 1/7
126 pseudomonasresponse.pl 1/7
127 pseudomonasresponse_s.pl 1/7
128 quiescentseed.pl 1/7
129 rootatfruitset.pl 1/7
130 rootlibraries.pl 1/7
131 rootsatvegetative.pl 1/7
132 shoot.pl 1/7
133 tomatoredripe.pl 1/7
135 ./content/unigene_builds:
136 Lycopersicon_Combined.pl 1/6
137 index.pl 1/6
139 ./cview:
140 index.pl 1/6
141 map.pl 1/8 try eg ?map_id=13; also, there could still be bad html in the abstracts; also the image-map ID has a '#' in it
142 view_chromosome.pl 1/6
143 view_maps.pl 1/6
145 ./data-submit:
146 check-chromas.pl 1/6
147 check-idfile-format.pl 1/6
148 confirm-chromas.pl 1/6
149 confirm-identifiers.pl 1/6
150 facility-form.pl 1/6
151 index.pl 1/6
152 library-form.pl 1/6
153 load-identifiers.pl 1/6
154 submit-main.pl 1/6
155 top-level.pl 1/6
156 update-facility.pl 1/6
157 update-library.pl 1/6
158 upload_chromas.pl 1/6
160 ./forum:
161 add_post.pl 1/6
162 add_topic.pl 1/6
163 forum_post_delete.pl 1/6
164 index.pl 1/6
165 posts.pl 1/6
166 return_comments.pl not for viewing; a subroutine for ajax
167 topics.pl 1/5
169 ./gbrowse:
170 help.pl 1/5
171 index.pl 1/6
173 ./help:
174 cview.pl 1/5
175 downloading.pl 1/6
176 faq.pl 1/6
177 index.pl 1/5
178 marker_search_help.pl 1/5
179 planned_outages.pl 1/6
180 quick_search.pl 1/5
181 toolbar.pl 1/5
183 ./help/ordering:
184 index.pl 1/6
186 ./image:
187 add_image.pl 1/6
188 index.pl 1/8 be sure to give it action=something ('new' works)
190 ./insitu:
191 help.pl 1/6
192 index.pl 1/6
193 manage.pl 1/6
194 search.pl 1/6
196 ./insitu/detail:
197 add_image.pl 1/6
198 experiment.pl 1/8 be sure to give it action=something ('new' works)
199 image.pl 1/8 be sure to give it action=something ('new' works)
200 organism.pl 1/6
201 primer.pl superseded by probe.pl
202 probe.pl 1/6
203 tag.pl 1/8 be sure to give it action=something ('new' works)
205 ./insitu/upload:
206 index.pl 1/6
208 ./maps:
209 index.pl 1/6
211 ./maps/lpimp_ibl:
212 chromosome1.pl 1/6
213 chromosome10.pl 1/6
214 chromosome11.pl 1/6
215 chromosome12.pl 1/6
216 chromosome2.pl 1/6
217 chromosome3.pl 1/6
218 chromosome4.pl 1/6
219 chromosome5.pl 1/6
220 chromosome6.pl 1/6
221 chromosome7.pl 1/6
222 chromosome8.pl 1/6
223 chromosome9.pl 1/6
224 index.pl 1/6
226 ./maps/pennellii_il:
227 chr1.pl 1/6
228 chr10.pl 1/6
229 chr11.pl 1/6
230 chr12.pl 1/6
231 chr2.pl 1/6
232 chr3.pl 1/6
233 chr4.pl 1/6
234 chr5.pl 1/6
235 chr6.pl 1/6
236 chr7.pl 1/6
237 chr8.pl 1/6
238 chr9.pl 1/6
239 index.pl 1/6
241 ./maps/pepper_korea:
242 index.pl 1/6
243 lg1.pl 1/6
244 lg10.pl 1/6
245 lg11.pl 1/6
246 lg12.pl 1/6
247 lg13.pl 1/6
248 lg14.pl 1/6
249 lg15.pl 1/6
250 lg16.pl 1/6
251 lg2.pl 1/6
252 lg3.pl 1/6
253 lg4.pl 1/6
254 lg5.pl 1/6
255 lg6.pl 1/6
256 lg7.pl 1/6
257 lg9.pl 1/6
259 ./maps/physical:
260 clone_annot_download.pl how to use?
261 clone_info.pl 1/6 under 'more criteria', tried 'search in genome browser'; got that /gbrowse/gbrowse/tomato died; couldn't find something in @INC
262 clone_read_info.pl 1/6
263 clone_restriction_gel_image.pl how to use?
264 clone_search.pl 1/8 get to from direct_search
265 clone_sequence.pl how to use?
266 index.pl 1/6
267 list_bacs_by_plate.pl 1/6
268 list_overgo_plate_probes.pl 1/6
269 overgo_process_explained.pl 1/6
270 overgo_stats.pl 1/6
271 vector_info.pl 1/6
272 view_fish.pl how to use?
274 ./maps/tomato_arabidopsis:
275 chr10_split.pl 1/6
276 chr10a.pl 1/6
277 chr10b.pl 1/6
278 chr10c.pl 1/6
279 chr10d.pl 1/6
280 chr10e.pl 1/6
281 chr11_split.pl 1/6
282 chr11a.pl 1/6
283 chr11b.pl 1/6
284 chr11c.pl 1/6
285 chr11d.pl 1/6
286 chr11e.pl 1/6
287 chr12_split.pl 1/6
288 chr12a.pl 1/6
289 chr12b.pl 1/6
290 chr12c.pl 1/6
291 chr12d.pl 1/6
292 chr12e.pl 1/6
293 chr1_split.pl 1/6
294 chr1a.pl 1/6
295 chr1b.pl 1/6
296 chr1c.pl 1/6
297 chr1d.pl 1/6
298 chr1e.pl 1/6
299 chr2_split.pl 1/6
300 chr2a.pl 1/6
301 chr2b.pl 1/6
302 chr2c.pl 1/6
303 chr2d.pl 1/6
304 chr2e.pl 1/6
305 chr3_split.pl 1/6
306 chr3a.pl 1/6
307 chr3b.pl 1/6
308 chr3c.pl 1/6
309 chr3d.pl 1/6
310 chr3e.pl 1/6
311 chr4_split.pl 1/6
312 chr4a.pl 1/6
313 chr4b.pl 1/6
314 chr4c.pl 1/6
315 chr4d.pl 1/6
316 chr4e.pl 1/6
317 chr5_split.pl 1/6
318 chr5a.pl 1/6
319 chr5b.pl 1/6
320 chr5c.pl 1/6
321 chr5d.pl 1/6
322 chr5e.pl 1/6
323 chr6_split.pl 1/6
324 chr6a.pl 1/6
325 chr6b.pl 1/6
326 chr6c.pl 1/6
327 chr6d.pl 1/6
328 chr6e.pl 1/6
329 chr7_split.pl 1/6
330 chr7a.pl 1/6
331 chr7b.pl 1/6
332 chr7c.pl 1/6
333 chr7d.pl 1/6
334 chr7e.pl 1/6
335 chr8_split.pl 1/6
336 chr8a.pl 1/6
337 chr8b.pl 1/6
338 chr8c.pl 1/6
339 chr8d.pl 1/6
340 chr8e.pl 1/6
341 chr9_split.pl 1/6
342 chr9a.pl 1/6
343 chr9b.pl 1/6
344 chr9c.pl 1/6
345 chr9d.pl 1/6
346 chr9e.pl 1/6
347 index.pl 1/6
349 ./markers:
350 cos_markers.pl 1/5
351 cosii_markers.pl 1/6
352 index.pl 1/6
353 microsats.pl 1/6
355 ./methods:
356 index.pl 1/6
358 ./methods/unigene:
359 index.pl 1/6
360 unigene-builds.pl 1/6
361 unigene-methods.pl 1/6
362 unigene-precluster.pl 1/6
363 unigene-process-2.pl 1/6
364 unigene-validation.pl 1/6
366 ./misc:
367 index.pl 1/6
369 ./misc/codon_usage:
370 codon_histogram.pl 1/6
371 codon_usage.pl 1/6
372 index.pl 1/6
374 ./moby:
375 dispatcher.pl not intended to generate html
377 ./mutants:
378 index.pl 1/6
379 mutants_main.pl 1/6
381 ./outreach:
382 index.pl 1/7
384 ./phenome:
385 allele.pl how to use? can't just view
386 allele_synonym.pl how to use? can't just view
387 claim_locus_ownership.pl 1/6
388 individual.pl how to use? can't just view
389 locus_display.pl 1/7
390 locus_synonym.pl 1/7
392 ./phenotype:
393 display_image_and_data.pl 1/7
394 display_plants_from_genotype.pl 1/7
395 display_plants_from_property.pl 1/7
396 display_prop_list.pl 1/8
397 display_property_data_from_plant.pl 1/7
398 display_samples_from_plant.pl 1/7
399 index.pl 1/7
400 population.pl 1/7
402 ./search:
403 all_unig_for_annot.pl 1/8
404 annotation_search_result.pl 1/8
405 clone-order.pl 1/14 try going to "EST details -- SGN-E362772" first to get the cart icon
406 direct_search.pl 1/8
407 est.pl 1/5 with and without show_hierarchy on
408 family.pl 1/8 try ?family_id=782
409 family_align.pl 1/8 family_id=782 is small enough to work
410 family_build.pl 1/8
411 glossarysearch.pl 1/5
412 index.pl 1/7
413 library_search.pl 1/8 to get to: do a quicksearch for 'lib' and check out cDNA libraries
414 locus_display.pl used?
415 locus_search.pl 1/7
416 phenosearch.pl used? does gene + phenotype searches
417 phenotype_search.pl 1/7
418 quick_search.pl 1/8
419 route-order.pl used? has to do with shopping cart
420 tigrtc.pl 1/7 example parameters: tigr_tc=115721&tcindex_id=1
421 trace_download.pl no html printed; actually downloads a GZ
422 ug-ad2.pl 1/7
423 unigene-all-blast-matches.pl 1/6
424 unigene-estscan-detail.pl 1/6
425 unigene.pl 1/5
427 ./search/markers:
428 cos_list.pl 1/5
429 index.pl 1/6
430 markerinfo.pl 1/6
431 markersearch.pl 1/6
432 rflp_list.pl 1/6
433 ssr_list.pl 1/6
434 view_rflp.pl marker image not found when tested w/ marker_id=293
436 ./secretary:
437 geneview.pl
438 index.pl no validate link
439 mylist.pl
440 query.pl no validate link; also 'You really shouldn't call this function directly, hence the extra magic needed (2nd parameter)! at /usr/local/lib/site_perl/CXGN/UserList/Hotlist.pm line 65'
442 ./secretary/scraps:
443 hotlist.pl XML Parsing Error: no element found / Location: http://henbane.sgn.cornell.edu/secretary/scraps/hotlist.pl / Line 15, Column 9
444 scrap.pl can't locate Page::Scrap.pm in @INC
445 test.pl can't locate Page::Scrap.pm in @INC
447 ./secretary/tools:
448 http_error_handler.pl You really shouldn't call this function directly, hence the extra magic needed (2nd parameter)! at /usr/local/lib/site_perl/CXGN/UserList/Hotlist.pm line 65
450 ./secretom:
451 index.pl 1/7
453 ./sequencing:
454 agp.pl 1/6
455 bac_registry_discrepancies.pl 'sorry, this page is temporarily unavailable'
456 tpf.pl 1/6
458 ./sgn_photos:
459 index.pl 1/6
461 ./solanaceae-project:
462 call_for_BACS.pl 1/6
463 index.pl 1/6
464 seed_bac_selection.pl 1/6
465 summary.pl 1/6
467 ./solanaceae-project/docs:
468 index.pl 1/6
470 ./solanaceae-project/meeting_2005:
471 index.pl 1/6
473 ./solanaceae-project/sol-bioinformatics:
474 ghent2006_report.pl 1/8
475 index.pl 1/6
477 ./solpeople:
478 account-confirm.pl 1/5
479 attribute_bacs.pl 1/5
480 change-account.pl 1/5
481 contact-info.pl 1/5
482 contact-update.pl 1/5
483 cosii_submission.pl 1/5
484 image_404_test.pl 1/6
485 index.pl 1/6
486 login.pl 1/5
487 new-account.pl 1/5
488 people_detail.pl 1/7 there will still be noncompliant pieces of html that were previously put in the database
489 people_search.pl 1/7
490 research-info.pl 1/5
491 research-update.pl 1/5
492 send-password.pl 1/5
493 submit_marker.pl 1/5
494 top-level.pl 1/8
495 update-account.pl 1/5
496 update-bacs.pl 1/6
498 ./solpeople/admin:
499 attribute.pl 1/6
500 crash_test.pl 1/6
501 create_organization.pl 1/6
502 get_person.pl 1/6
503 quick_create_account.pl 1/6
504 stats.pl 1/6
506 ./supplement:
507 index.pl 1/6
509 ./supplement/plantcell-14-1441:
510 bac_annotation.pl 1/6
511 index.pl 1/6
513 ./supplement/plantcell-14-1441/GenPept:
514 index.pl 1/6
516 ./supplement/plantcell-14-1441/artmenis:
517 index.pl 1/6
519 ./supplement/plantcell-14-1441/atpath:
520 index.pl 1/6
522 ./supplement/plantcell-14-1441/le_con_2:
523 index.pl 1/6
525 ./supplement/plantcell-14-1441/sgn_estdb:
526 index.pl 1/6
528 ./tag:
529 index.pl 1/8 need to give it an action=; 'new' works
531 ./tools:
532 contact.pl 1/5
533 http_error_handler.pl 'does not exist on this server'
534 index.pl 1/7
535 sixframe_translate.pl 1/5
536 trace_view.pl chromatogram viewer, needs an EST argument; the 'view' link for chromatograms on search/est.pl is disabled -- ?
537 wait.pl no validation link
539 ./tools/align_viewer:
540 index.pl 1/6
541 show_align.pl 1/7
543 ./tools/blast: they all require the 'blastall' executable, blast it all; you'll need to set $blast_path='/usr/bin'
544 blast_result.pl 1/8 doesn't write html except on error; also couldn't find tomato-EST database
545 index.pl 1/8
546 upload.pl 1/6
547 upload_cron.pl
548 upload_delete.pl
549 upload_result.pl
550 view_result.pl Bio::GMOD::Blast::Graph::showGraph() doesn't do proper xhtml!
551 wait_result.pl superseded by tools/wait.pl?
553 ./tools/caps_designer:
554 caps_input.pl 1/7
555 find_caps.pl 1/7
557 ./tools/convert:
558 convert.pl 1/7
559 index.pl 1/7
560 input.pl 1/7
562 ./tools/dna_digestion:
563 digestion.pl 1/7
565 ./tools/fastmapping:
566 help.pl 1/7
567 index.pl 1/7
569 ./tools/intron_detection:
570 display_introns.pl 1/8
571 find_introns.pl 1/6
572 index.pl 1/6
573 intron_finder_command_line.pl internal (backend)
575 ./tools/primer3:
576 help.pl 1/7
577 index.pl 1/7
578 results.pl Cannot find /data/shared/primer3/src/primer3_core executable
579 results_help.pl 1/7
581 ./tools/seedbac:
582 chr_sbfinder.pl 1/7
583 index.pl 1/7
584 sbfinder.pl 1/7
586 ./tools/sigpep_finder:
587 input.pl 1/7
588 sigpep_find.pl 1/8
590 ./tools/solcyc:
591 index.pl 1/7
593 ./tools/ssr:
594 index.pl 1/7
595 show_ssr.pl 1/7
597 ./tools/tree_browser:
598 index.pl 1/7