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598 lines (519 loc) · 25.9 KB
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FILES THAT HAVE BEEN VALIDATED FOR XHTML
(ROOT sgn/cgi-bin)
(Evan Herbst, Jan 2007)
file date comments
----------------------------------------------------------------------------------------
.:
index.pl 1/5
oldevents.pl 1/7
oldhighlights.pl 1/7
oldpublications.pl 1/7
testgd.pl not html
./about:
Summer_Internship_2005.pl 1/7
about_solanaceae.pl 1/6
align_term.pl 1/7
clone_policy.pl 1/7
clustal_file.pl 1/7
fam_align_analysis.pl 1/7
fam_tree_analysis.pl 1/7
family_analysis.pl 1/7
index.pl 1/8
italy.pl 1/7
release_20040301.pl 1/7
solanum_nomenclature.pl 1/6
status.pl can't locate SGN.pm in @INC -- has been superseded? doesn't seem recent
temp.pl graphs server-room temperature? has been superseded?
tomato_project_overview.pl 1/8
tomato_sequencing.pl 1/8
tomato_sequencing_scope.pl 1/7
us_tomato_sequencing.pl 1/7
./about/ecosol:
index.pl 1/7
./about/release_notes:
tomato_unigene_build1.pl 1/7
./about/tomato_project:
index.pl 1/7
./about/tomato_project/nsf_9872617:
footer.pl not top-level
index.pl 1/7
members.pl 1/7
progress.pl 1/7
project.pl 1/7
publications.pl 1/7
websites.pl 1/7
./about/tomato_sequencing:
index.pl 1/7
./bulk:
display.pl 1/7 with and without summary=1
download.pl 1/7
index.pl 1/7
input.pl 1/7
./community:
index.pl 1/6
./community/feature:
200403.pl 1/6
200404.pl 1/6
200405.pl 1/6
200406.pl 1/6
200407.pl 1/6
200408.pl 1/6
200409.pl 1/6
200410.pl 1/6
200503.pl 1/6
200504.pl 1/6
200507.pl 1/6
200510.pl 1/6
200601.pl 1/6
200612.pl 1/6
index.pl 1/6
kjb_lab.pl 1/6
paran_lab.pl 1/6
./community/genomics_forum:
index.pl 1/6
schedule_summer_2005.pl 1/6
./community/links:
genefinding.pl 1/6
index.pl 1/6
journals.pl 1/6
related_sites.pl 1/6
seed_companies.pl 1/6
./community/meetings:
index.pl 1/6
./community/snp_consortium:
Labate_tomato_tech.pl 1/6
index.pl 1/6
./content:
coffee.pl 1/6
fish.pl 1/6
index.pl 1/6
library_info.pl 1/6
map_submissions.pl 1/6
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
unigene_builds.pl 1/6
./content/libraries:
breakerfruit.pl 1/7
callus.pl 1/7
deficientroot.pl 1/7
developingfruit.pl 1/7
flowerbudctoa.pl 1/7
flowerbudctob.pl 1/7
flowerbudctoc.pl 1/7
germinatingseed.pl 1/7
hirsutumtrichome.pl 1/7
index.pl 1/7
maturegreenfruit.pl 1/7
mixedelicitor.pl 1/7
openflowerctod.pl 1/7
ovary.pl 1/7
pennelliitrichome.pl 1/7
pseudomonasresponse.pl 1/7
pseudomonasresponse_s.pl 1/7
quiescentseed.pl 1/7
rootatfruitset.pl 1/7
rootlibraries.pl 1/7
rootsatvegetative.pl 1/7
shoot.pl 1/7
tomatoredripe.pl 1/7
./content/unigene_builds:
Lycopersicon_Combined.pl 1/6
index.pl 1/6
./cview:
index.pl 1/6
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
view_chromosome.pl 1/6
view_maps.pl 1/6
./data-submit:
check-chromas.pl 1/6
check-idfile-format.pl 1/6
confirm-chromas.pl 1/6
confirm-identifiers.pl 1/6
facility-form.pl 1/6
index.pl 1/6
library-form.pl 1/6
load-identifiers.pl 1/6
submit-main.pl 1/6
top-level.pl 1/6
update-facility.pl 1/6
update-library.pl 1/6
upload_chromas.pl 1/6
./forum:
add_post.pl 1/6
add_topic.pl 1/6
forum_post_delete.pl 1/6
index.pl 1/6
posts.pl 1/6
return_comments.pl not for viewing; a subroutine for ajax
topics.pl 1/5
./gbrowse:
help.pl 1/5
index.pl 1/6
./help:
cview.pl 1/5
downloading.pl 1/6
faq.pl 1/6
index.pl 1/5
marker_search_help.pl 1/5
planned_outages.pl 1/6
quick_search.pl 1/5
toolbar.pl 1/5
./help/ordering:
index.pl 1/6
./image:
add_image.pl 1/6
index.pl 1/8 be sure to give it action=something ('new' works)
./insitu:
help.pl 1/6
index.pl 1/6
manage.pl 1/6
search.pl 1/6
./insitu/detail:
add_image.pl 1/6
experiment.pl 1/8 be sure to give it action=something ('new' works)
image.pl 1/8 be sure to give it action=something ('new' works)
organism.pl 1/6
primer.pl superseded by probe.pl
probe.pl 1/6
tag.pl 1/8 be sure to give it action=something ('new' works)
./insitu/upload:
index.pl 1/6
./maps:
index.pl 1/6
./maps/lpimp_ibl:
chromosome1.pl 1/6
chromosome10.pl 1/6
chromosome11.pl 1/6
chromosome12.pl 1/6
chromosome2.pl 1/6
chromosome3.pl 1/6
chromosome4.pl 1/6
chromosome5.pl 1/6
chromosome6.pl 1/6
chromosome7.pl 1/6
chromosome8.pl 1/6
chromosome9.pl 1/6
index.pl 1/6
./maps/pennellii_il:
chr1.pl 1/6
chr10.pl 1/6
chr11.pl 1/6
chr12.pl 1/6
chr2.pl 1/6
chr3.pl 1/6
chr4.pl 1/6
chr5.pl 1/6
chr6.pl 1/6
chr7.pl 1/6
chr8.pl 1/6
chr9.pl 1/6
index.pl 1/6
./maps/pepper_korea:
index.pl 1/6
lg1.pl 1/6
lg10.pl 1/6
lg11.pl 1/6
lg12.pl 1/6
lg13.pl 1/6
lg14.pl 1/6
lg15.pl 1/6
lg16.pl 1/6
lg2.pl 1/6
lg3.pl 1/6
lg4.pl 1/6
lg5.pl 1/6
lg6.pl 1/6
lg7.pl 1/6
lg9.pl 1/6
./maps/physical:
clone_annot_download.pl how to use?
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
clone_read_info.pl 1/6
clone_restriction_gel_image.pl how to use?
clone_search.pl 1/8 get to from direct_search
clone_sequence.pl how to use?
index.pl 1/6
list_bacs_by_plate.pl 1/6
list_overgo_plate_probes.pl 1/6
overgo_process_explained.pl 1/6
overgo_stats.pl 1/6
vector_info.pl 1/6
view_fish.pl how to use?
./maps/tomato_arabidopsis:
chr10_split.pl 1/6
chr10a.pl 1/6
chr10b.pl 1/6
chr10c.pl 1/6
chr10d.pl 1/6
chr10e.pl 1/6
chr11_split.pl 1/6
chr11a.pl 1/6
chr11b.pl 1/6
chr11c.pl 1/6
chr11d.pl 1/6
chr11e.pl 1/6
chr12_split.pl 1/6
chr12a.pl 1/6
chr12b.pl 1/6
chr12c.pl 1/6
chr12d.pl 1/6
chr12e.pl 1/6
chr1_split.pl 1/6
chr1a.pl 1/6
chr1b.pl 1/6
chr1c.pl 1/6
chr1d.pl 1/6
chr1e.pl 1/6
chr2_split.pl 1/6
chr2a.pl 1/6
chr2b.pl 1/6
chr2c.pl 1/6
chr2d.pl 1/6
chr2e.pl 1/6
chr3_split.pl 1/6
chr3a.pl 1/6
chr3b.pl 1/6
chr3c.pl 1/6
chr3d.pl 1/6
chr3e.pl 1/6
chr4_split.pl 1/6
chr4a.pl 1/6
chr4b.pl 1/6
chr4c.pl 1/6
chr4d.pl 1/6
chr4e.pl 1/6
chr5_split.pl 1/6
chr5a.pl 1/6
chr5b.pl 1/6
chr5c.pl 1/6
chr5d.pl 1/6
chr5e.pl 1/6
chr6_split.pl 1/6
chr6a.pl 1/6
chr6b.pl 1/6
chr6c.pl 1/6
chr6d.pl 1/6
chr6e.pl 1/6
chr7_split.pl 1/6
chr7a.pl 1/6
chr7b.pl 1/6
chr7c.pl 1/6
chr7d.pl 1/6
chr7e.pl 1/6
chr8_split.pl 1/6
chr8a.pl 1/6
chr8b.pl 1/6
chr8c.pl 1/6
chr8d.pl 1/6
chr8e.pl 1/6
chr9_split.pl 1/6
chr9a.pl 1/6
chr9b.pl 1/6
chr9c.pl 1/6
chr9d.pl 1/6
chr9e.pl 1/6
index.pl 1/6
./markers:
cos_markers.pl 1/5
cosii_markers.pl 1/6
index.pl 1/6
microsats.pl 1/6
./methods:
index.pl 1/6
./methods/unigene:
index.pl 1/6
unigene-builds.pl 1/6
unigene-methods.pl 1/6
unigene-precluster.pl 1/6
unigene-process-2.pl 1/6
unigene-validation.pl 1/6
./misc:
index.pl 1/6
./misc/codon_usage:
codon_histogram.pl 1/6
codon_usage.pl 1/6
index.pl 1/6
./moby:
dispatcher.pl not intended to generate html
./mutants:
index.pl 1/6
mutants_main.pl 1/6
./outreach:
index.pl 1/7
./phenome:
allele.pl how to use? can't just view
allele_synonym.pl how to use? can't just view
claim_locus_ownership.pl 1/6
individual.pl how to use? can't just view
locus_display.pl 1/7
locus_synonym.pl 1/7
./phenotype:
display_image_and_data.pl 1/7
display_plants_from_genotype.pl 1/7
display_plants_from_property.pl 1/7
display_prop_list.pl 1/8
display_property_data_from_plant.pl 1/7
display_samples_from_plant.pl 1/7
index.pl 1/7
population.pl 1/7
./search:
all_unig_for_annot.pl 1/8
annotation_search_result.pl 1/8
clone-order.pl 1/14 try going to "EST details -- SGN-E362772" first to get the cart icon
direct_search.pl 1/8
est.pl 1/5 with and without show_hierarchy on
family.pl 1/8 try ?family_id=782
family_align.pl 1/8 family_id=782 is small enough to work
family_build.pl 1/8
glossarysearch.pl 1/5
index.pl 1/7
library_search.pl 1/8 to get to: do a quicksearch for 'lib' and check out cDNA libraries
locus_display.pl used?
locus_search.pl 1/7
phenosearch.pl used? does gene + phenotype searches
phenotype_search.pl 1/7
quick_search.pl 1/8
route-order.pl used? has to do with shopping cart
tigrtc.pl 1/7 example parameters: tigr_tc=115721&tcindex_id=1
trace_download.pl no html printed; actually downloads a GZ
ug-ad2.pl 1/7
unigene-all-blast-matches.pl 1/6
unigene-estscan-detail.pl 1/6
unigene.pl 1/5
./search/markers:
cos_list.pl 1/5
index.pl 1/6
markerinfo.pl 1/6
markersearch.pl 1/6
rflp_list.pl 1/6
ssr_list.pl 1/6
view_rflp.pl marker image not found when tested w/ marker_id=293
./secretary:
geneview.pl
index.pl no validate link
mylist.pl
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'
./secretary/scraps:
hotlist.pl XML Parsing Error: no element found / Location: http://henbane.sgn.cornell.edu/secretary/scraps/hotlist.pl / Line 15, Column 9
scrap.pl can't locate Page::Scrap.pm in @INC
test.pl can't locate Page::Scrap.pm in @INC
./secretary/tools:
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
./secretom:
index.pl 1/7
./sequencing:
agp.pl 1/6
bac_registry_discrepancies.pl 'sorry, this page is temporarily unavailable'
tpf.pl 1/6
./sgn_photos:
index.pl 1/6
./solanaceae-project:
call_for_BACS.pl 1/6
index.pl 1/6
seed_bac_selection.pl 1/6
summary.pl 1/6
./solanaceae-project/docs:
index.pl 1/6
./solanaceae-project/meeting_2005:
index.pl 1/6
./solanaceae-project/sol-bioinformatics:
ghent2006_report.pl 1/8
index.pl 1/6
./solpeople:
account-confirm.pl 1/5
attribute_bacs.pl 1/5
change-account.pl 1/5
contact-info.pl 1/5
contact-update.pl 1/5
cosii_submission.pl 1/5
image_404_test.pl 1/6
index.pl 1/6
login.pl 1/5
new-account.pl 1/5
people_detail.pl 1/7 there will still be noncompliant pieces of html that were previously put in the database
people_search.pl 1/7
research-info.pl 1/5
research-update.pl 1/5
send-password.pl 1/5
submit_marker.pl 1/5
top-level.pl 1/8
update-account.pl 1/5
update-bacs.pl 1/6
./solpeople/admin:
attribute.pl 1/6
crash_test.pl 1/6
create_organization.pl 1/6
get_person.pl 1/6
quick_create_account.pl 1/6
stats.pl 1/6
./supplement:
index.pl 1/6
./supplement/plantcell-14-1441:
bac_annotation.pl 1/6
index.pl 1/6
./supplement/plantcell-14-1441/GenPept:
index.pl 1/6
./supplement/plantcell-14-1441/artmenis:
index.pl 1/6
./supplement/plantcell-14-1441/atpath:
index.pl 1/6
./supplement/plantcell-14-1441/le_con_2:
index.pl 1/6
./supplement/plantcell-14-1441/sgn_estdb:
index.pl 1/6
./tag:
index.pl 1/8 need to give it an action=; 'new' works
./tools:
contact.pl 1/5
http_error_handler.pl 'does not exist on this server'
index.pl 1/7
sixframe_translate.pl 1/5
trace_view.pl chromatogram viewer, needs an EST argument; the 'view' link for chromatograms on search/est.pl is disabled -- ?
wait.pl no validation link
./tools/align_viewer:
index.pl 1/6
show_align.pl 1/7
./tools/blast: they all require the 'blastall' executable, blast it all; you'll need to set $blast_path='/usr/bin'
blast_result.pl 1/8 doesn't write html except on error; also couldn't find tomato-EST database
index.pl 1/8
upload.pl 1/6
upload_cron.pl
upload_delete.pl
upload_result.pl
view_result.pl Bio::GMOD::Blast::Graph::showGraph() doesn't do proper xhtml!
wait_result.pl superseded by tools/wait.pl?
./tools/caps_designer:
caps_input.pl 1/7
find_caps.pl 1/7
./tools/convert:
convert.pl 1/7
index.pl 1/7
input.pl 1/7
./tools/dna_digestion:
digestion.pl 1/7
./tools/fastmapping:
help.pl 1/7
index.pl 1/7
./tools/intron_detection:
display_introns.pl 1/8
find_introns.pl 1/6
index.pl 1/6
intron_finder_command_line.pl internal (backend)
./tools/primer3:
help.pl 1/7
index.pl 1/7
results.pl Cannot find /data/shared/primer3/src/primer3_core executable
results_help.pl 1/7
./tools/seedbac:
chr_sbfinder.pl 1/7
index.pl 1/7
sbfinder.pl 1/7
./tools/sigpep_finder:
input.pl 1/7
sigpep_find.pl 1/8
./tools/solcyc:
index.pl 1/7
./tools/ssr:
index.pl 1/7
show_ssr.pl 1/7
./tools/tree_browser:
index.pl 1/7