Migration

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LEGEND:

tester / gbrowse compliance / which production node it has been tested on

eg:

todd / gb1 & gb2 / freeze1

Tested by todd, gb1 and gb2 compliant, tested on freeze1

./cell:
-rwxrwxr-x  1 todd wormbase  20053 Jul  6 14:06 cell.cgi
-rwxrwxr-x  1 todd wormbase   3916 Jul  6 14:06 make_pedigree.cgi
-rwxrwxr-x  1 todd wormbase    253 Jul  6 14:06 mindofworm
-rwxrwxr-x  1 todd wormbase 303783 Jul  6 14:06 neato
drwxrwsr-x  4 todd wormbase   4096 Jul  6 14:06 neuron
-rwxrwxr-x  1 todd wormbase   4042 Jul  6 14:06 neuron.cgi
-rw-rw-r--  1 todd wormbase   1318 Jul  6 14:06 Pedigree.pm

./cell/neuron:
total 336
-rwxrwxr-x  1 todd wormbase   1876 Jul  6 14:06 dot2png.cgi
drwxrwsr-x  3 todd wormbase   4096 Jul  6 14:06 img
-rwxrwxr-x  1 todd wormbase 303783 Jul  6 14:06 neato
-rwxrwxr-x  1 todd wormbase   3726 Jul  6 14:06 neuron.cgi
-rwxrwxr-x  1 todd wormbase   3419 Jul  6 14:06 neuron_png.pl
-rwxrwxr-x  1 todd wormbase   2108 Jul  6 14:06 plain2png.pl

./curate:
total 28
-rwxrwxr-x  1 todd wormbase 6812 Jul  6 14:07 base
-rwxrwxr-x  1 todd wormbase 3865 Jul  6 14:07 online_forms
-rwxrwxr-x  1 todd wormbase 8474 Jul  6 14:07 submit

./gene:
total 932
-rwxrwxr-x  1 todd wormbase  50302 Jul  6 14:07 allele                   DEPRECATED
-rwxrwxr-x  1 todd wormbase   4767 Jul  6 14:07 antibody                 todd / gb1 & gb2 / freeze1
-rwxrwxr-x  1 todd wormbase  22832 Jul  6 14:07 expression            todd / not tested yet in production
-rwxrwxr-x  1 todd wormbase   6467 Jul  6 14:07 expr_profile         todd / not tested yet in production
-rwxrwxr-x  1 todd wormbase 140250 Jul 13 13:14 gene                       todd / not tested yet in production
-rwxrwxr-x  1 todd wormbase   4397 Jul  6 14:07 geneapplet               DEPRECATED
-rwxrwxr-x  1 todd wormbase   7058 Jul  6 14:07 gene_class               todd / gb1 & gb2 / freeze1
-rwxrwxr-x  1 todd wormbase   1682 Jul  6 14:07 gene_in_profile
-rwxrwxr-x  1 todd wormbase   4466 Jul  6 14:07 genetable
-rwxrwxr-x  1 todd wormbase  14333 Jul  6 14:07 gmap
-rwxrwxr-x  1 todd wormbase   8019 Jul  6 14:07 homology_group
-rwxrwxr-x  1 todd wormbase  23764 Jul  6 14:07 interaction
-rwxrwxr-x  1 todd wormbase   2305 Jul  6 14:07 interaction_details
-rwxrwxr-x  1 todd wormbase  11293 Jul  6 14:07 locus                    BROKEN
-rwxrwxr-x  1 todd wormbase   4477 Jul  6 14:07 mapping_data
-rwxrwxr-x  1 todd wormbase   3353 Jul  6 14:07 motif                      todd / gb1 & gb2 / freeze1
-rw-rw-r--  1 todd wormbase  23335 Jul  6 14:07 mountains_coords.txt
-rwxrwxr-x  1 todd wormbase   3088 Jul  6 14:07 operon                    todd / gb1 & gb2 / freeze1
-rwxrwxr-x  1 todd wormbase  29456 Jul  6 14:07 rearrange             todd / not tested yet in production
-rwxrwxr-x  1 todd wormbase   5440 Jul  6 14:07 regulation                todd / gb1 & gb2 / freeze1
drwxrwsr-x  3 todd wormbase   4096 Jul  6 14:07 sk_map
-rwxrwxr-x  1 todd wormbase  12043 Jul  6 14:07 strain                    todd / gb1 & gb2 / freeze1
-rwxrwxr-x  1 todd wormbase   5348 Jul  6 14:07 structure_data
-rwxrwxr-x  1 todd wormbase   5308 Jul  6 14:07 transgene               todd / not tested yet in production
-rwxrwxr-x  1 todd wormbase   6108 Jul  6 14:07 transgene_tbls
-rwxrwxr-x  1 todd wormbase  92220 Jul  6 14:07 variation

./generic:
total 16
-rwxrwxr-x  1 todd wormbase 1237 Jul  6 14:06 acetable
-rw-rw-r--  1 todd wormbase 1380 Jul  6 14:06 report
-rwxrwxr-x  1 todd wormbase 3945 Jul  6 14:06 tree

./lib:
total 528
drwxrwsr-x  3 todd wormbase   4096 Jul  6 14:06 CGI
drwxrwsr-x  4 todd wormbase   4096 Jul  6 14:07 CSS
-rwxrwxr-x  1 todd wormbase   6580 Jul  6 14:06 CSS.pm
-rw-rw-r--  1 todd wormbase   1337 Jul  6 14:06 develSubs.pm
-rw-rw-r--  1 todd wormbase   1314 Jul  6 14:06 ElegansOligos.pm
-rw-rw-r--  1 todd wormbase 130862 Jul  9 12:33 ElegansSubs.pm
-rw-rw-r--  1 todd wormbase  38711 Jul  6 14:06 GBsyn.pm
-rw-rw-r--  1 todd wormbase   5780 Jul  6 14:06 MerlynAO.pm
-rw-rw-r--  1 todd wormbase   3742 Jul  6 14:06 MerlynGO.pm
-rwxrwxr-x  1 todd wormbase    612 Jul  1 13:02 OntologySubs.pl
-rwxrwxr-x  1 todd wormbase    172 Jul  6 14:06 OrthologySubs.pm
-rw-rw-r--  1 todd wormbase   7651 Jul  6 14:06 pICalculator.pm
drwxrwsr-x  5 todd wormbase   4096 Jul  9 12:33 RSS
-rw-rw-r--  1 todd wormbase   8658 Jul  6 14:06 Seqview.pm
drwxrwsr-x  5 todd wormbase   4096 Jul  6 14:06 SKMAP
-rw-rw-r--  1 todd wormbase   5069 Jul  6 14:07 Splicer.pm
-rw-rw-r--  1 todd wormbase   6891 Jul  6 14:06 StandardURLDumpers.pm
-rw-rw-r--  1 todd wormbase   1283 Jul  6 14:06 Util.pm
drwxrwsr-x  4 todd wormbase   4096 Jul  9 12:33 WormBase
-rw-rw-r--  1 todd wormbase    395 Jul  6 14:06 WormBase.pm

./lib/RSS:
total 60
drwxrwsr-x  4 todd wormbase  4096 Jul  6 14:07 DB
-rw-rw-r--  1 todd wormbase 14687 Jul  9 12:33 ObjectHistory.pm
-rwxrwxr-x  1 todd wormbase  1475 Jul  6 14:07 populate_database.pl
-rw-rw-r--  1 todd wormbase  3885 Jul  6 14:07 README
drwxrwsr-x  3 todd wormbase  4096 Jul  6 14:07 sql
-rwxrwxr-x  1 todd wormbase   185 Jul  6 14:07 test.pl
-rwxrwxr-x  1 todd wormbase  1192 Jul  6 14:07 update_static_feeds.pl

./lib/RSS/DB:
total 12
drwxrwsr-x  3 todd wormbase 4096 Jul  6 14:07 History
-rw-rw-r--  1 todd wormbase  125 Jul  6 14:07 History.pm

./lib/RSS/DB/History:
total 12
-rw-rw-r--  1 todd wormbase  403 Jul  6 14:07 History.pm
-rw-rw-r--  1 todd wormbase  476 Jul  6 14:07 Objects.pm

./lib/RSS/sql:
total 8
-rw-rw-r--  1 todd wormbase 1024 Jul  6 14:07 create_schema.sql

./lib/SKMAP:
total 24
-rw-rw-r--  1 todd wormbase 2657 Jul  6 14:06 Config.pm
-rw-rw-r--  1 todd wormbase 1270 Jul  6 14:06 Coordinates.pm
drwxrwsr-x  3 todd wormbase 4096 Jul  6 14:06 Data
drwxrwsr-x  3 todd wormbase 4096 Jul  6 14:06 Image
-rwxrwxr-x  1 todd wormbase 1472 Jul  6 14:06 Search.pm

./lib/SKMAP/Image:
-rw-rw-r--  1 todd wormbase 2537 Jul  6 14:06 Figures.pm

./lib/WormBase:
-rw-rw-r--  1 todd wormbase 10048 Jul  6 14:06 AutocompleteLoad.pm
-rw-rw-r--  1 todd wormbase 13389 Jul  9 12:33 Autocomplete.pm
-rw-rw-r--  1 todd wormbase 16606 Jul  6 14:06 FetchData.pm
-rw-rw-r--  1 todd wormbase  6073 Jul  6 14:06 Formatting.pm
-rw-rw-r--  1 todd wormbase  5329 Jul  6 14:06 GMapView.pm
-rw-rw-r--  1 todd wormbase 12659 Jul  9 12:33 Table.pm
-rw-rw-r--  1 todd wormbase  9358 Jul  6 14:06 Toggle.pm
drwxrwsr-x  3 todd wormbase  4096 Jul  6 14:06 Util
-rw-rw-r--  1 todd wormbase  1293 Jul  6 14:06 Util.pm

./lib/WormBase/Util:
total 8
-rw-rw-r--  1 todd wormbase 1304 Jul  6 14:06 Rearrange.pm

./mapview:
total 16
-rwxrwxr-x  1 todd wormbase 2668 Jul  6 14:06 dasdraw2                    DEPRECATED
-rwxrwxr-x  1 todd wormbase 2467 Jul  6 14:06 geneticmap                DEPRECATED
-rwxrwxr-x  1 todd wormbase 3360 Jul  6 14:06 sequenceapplet         DEPRECATED 

./microarray:
total 68
-rwxrwxr-x  1 todd wormbase  2671 Jul  6 14:06 cluster
-rwxrwxr-x  1 todd wormbase 13308 Jul  6 14:06 download
-rwxrwxr-x  1 todd wormbase  3304 Jul  6 14:06 expression_cluster
-rwxrwxr-x  1 todd wormbase  6600 Jul  6 14:06 microarray_aff
-rwxrwxr-x  1 todd wormbase  1246 Jul  6 14:06 microarray_smd
-rwxrwxr-x  1 todd wormbase 13412 Jul  6 14:06 results
-rwxrwxr-x  1 todd wormbase 10833 Jul  6 14:06 search

./misc:
-rwxrwxr-x  1 todd wormbase 14247 Jul  6 14:06 2005_survey
-rwxrwxr-x  1 todd wormbase   840 Jul  6 14:06 acedb
-rwxrwxr-x  1 todd wormbase  5528 Jul  6 14:06 author
-rwxrwxr-x  1 todd wormbase   991 Jul  6 14:06 author_example
-rwxrwxr-x  1 todd wormbase  8758 Jul  6 14:06 biblio
-rwxrwxr-x  1 todd wormbase  5837 Jul  6 14:06 c2c
-rwxrwxr-x  1 todd wormbase 11056 Jul  6 14:06 database_stats
-rwxrwxr-x  1 todd wormbase  5530 Jul  6 14:06 digest
-rwxrwxr-x  1 todd wormbase   699 Jul  6 14:06 download_features
-rwxrwxr-x  1 todd wormbase   728 Jul  6 14:06 download_sequence
-rwxrwxr-x  1 todd wormbase 13963 Jul  6 14:06 epic
-rwxrwxr-x  1 todd wormbase  5294 Jul  6 14:06 etree
-rwxrwxr-x  1 todd wormbase  6215 Jul  6 14:06 feedback
-rwxrwxr-x  1 todd wormbase  6353 Jul  6 14:06 format_datamining_example
-rwxrwxr-x  1 todd wormbase  3004 Jul  6 14:06 gbrowse_popup
-rwxrwxr-x  1 todd wormbase  3280 Jul  6 14:06 geo_map_by_paper
-rwxrwxr-x  1 todd wormbase  9692 Jul  6 14:06 glossary
-rwxrwxr-x  1 todd wormbase  1242 Jul  6 14:06 help
-rwxrwxr-x  1 todd wormbase  3779 Jul  6 14:06 inline_feed
-rwxrwxr-x  1 todd wormbase  6796 Jul  6 14:06 laboratory
-rwxrwxr-x  1 todd wormbase  4731 Jul  6 14:06 life_stage
-rwxrwxr-x  1 todd wormbase  1809 Jul  6 14:06 marc
-rwxrwxr-x  1 todd wormbase  3402 Jul  6 14:06 model
-rwxrwxr-x  1 todd wormbase   665 Jul  6 14:06 not_found
-rwxrwxr-x  1 todd wormbase 11723 Jul  6 14:06 paper
-rwxrwxr-x  1 todd wormbase 20521 Jul  6 14:06 person
-rwxrwxr-x  1 todd wormbase 10560 Jul  6 14:06 person_name
-rwxrwxr-x  1 todd wormbase 18882 Jul  6 14:06 phenotype
-rwxrwxr-x  1 todd wormbase   701 Jul  6 14:06 random_pic
-rwxrwxr-x  1 todd wormbase   188 Jul  6 14:06 redirect
-rwxrwxr-x  1 todd wormbase  3394 Jul  6 14:06 release_stats
-rwxrwxr-x  1 todd wormbase  2180 Jul  6 14:06 session
-rwxrwxr-x  1 todd wormbase 38513 Jul  6 14:06 site_map                  todd / gb1 & gb2 / freeze1
-rwxrwxr-x  1 todd wormbase  5056 Jul  6 14:06 standard_urls
-rwxrwxr-x  1 todd wormbase  7434 Jul  6 14:06 submit_feedback
-rwxrwxr-x  1 todd wormbase   857 Jul  6 14:06 text
-rwxrwxr-x  1 todd wormbase  3860 Jul  6 14:06 wb_people
-rwxrwxr-x  1 todd wormbase   938 Jul  6 14:06 xml
-rwxrwxr-x  1 todd wormbase   916 Jul  6 14:06 xml_md5

./ontology:
-rwxrwxr-x  1 todd wormbase   35612 Jul  6 14:06 anatomy
-rwxrwxr-x  1 todd wormbase    7734 Jul  6 14:06 anatomy_browser
-rwxrwxr-x  1 todd wormbase   25040 Jul  6 14:06 browse
-rwxrwxr-x  1 todd wormbase    4703 Jul  6 14:06 browser
drwxrwsr-x  3 todd wormbase    4096 Jul  6 14:06 browser_lib
-rwxrwxr-x  1 todd wormbase   23926 Jul  6 14:06 browse_tree
-rwxrwxr-x  1 todd wormbase   24283 Jul  6 14:06 gene
-rwxrwxr-x  1 todd wormbase    9034 Jul  6 14:06 go_dag
-rwxrwxr-x  1 todd wormbase    7608 Jul  6 14:06 go_detail
-rwxrwxr-x  1 todd wormbase    8812 Jul  6 14:06 goterm
-rw-rw-r--  1 todd wormbase 1330936 Jul  6 14:06 id2name.txt
-rw-rw-r--  1 todd wormbase  964896 Jul  6 14:06 id2parents.txt
-rw-rw-r--  1 todd wormbase  536044 Jul  6 14:06 parent2ids.txt
-rwxrwxr-x  1 todd wormbase   17870 Jul  6 14:06 search
-rw-rw-r--  1 todd wormbase 8741690 Jul  6 14:06 search_data.txt
-rwxrwxr-x  1 todd wormbase   11945 Jul  6 14:06 tree_lister

./ontology/browser_lib:
-rwxrwxr-x  1 todd wormbase  2704 Jul  6 14:06 browser.initd
-rwxrwxr-x  1 todd wormbase  1029 Jul  6 14:06 launch_ontology_sockets.sh
-rw-rw-r--  1 todd wormbase 22464 Jul  6 14:06 OBrowse.pm
-rw-rw-r--  1 todd wormbase   765 Jul  6 14:06 README

./orthology:
total 36
-rwxrwxr-x  1 todd wormbase 11398 Jul  6 14:06 disease
-rwxrwxr-x  1 todd wormbase 10591 Jul  6 14:06 gene
-rwxrwxr-x  1 todd wormbase  5841 Jul  6 14:06 search

./private:
total 24
-rwxrwxr-x  1 todd wormbase 6514 Jul  6 14:06 manage_newsfeeds
-rwxrwxr-x  1 todd wormbase 3288 Jul  6 14:06 test_urls
-rwxrwxr-x  1 todd wormbase 5939 Jul  6 14:06 update_newsfeed

./searches:
total 600
drwxrwsr-x  3 todd wormbase  4096 Jul  6 14:06 advanced
-rwxrwxr-x  1 todd wormbase  7784 Jul  6 14:06 aql_query
-rwxrwxr-x  1 todd wormbase 17902 Jul  6 14:06 basic
-rwxrwxr-x  1 todd wormbase 55519 Jul  6 14:06 batch_genes
-rwxrwxr-x  1 todd wormbase 20537 Jul  6 14:06 blast0212
-rwxrwxr-x  1 todd wormbase 47081 Jul  6 14:06 blast_blat
-rwxrwxr-x  1 todd wormbase  9731 Jul  6 14:06 blast_ori
-rwxrwxr-x  1 todd wormbase   154 Jul  6 14:06 blat
-rwxrwxr-x  1 todd wormbase  2484 Jul  6 14:06 browser
-rwxrwxr-x  1 todd wormbase  4222 Jul  6 14:06 class_query
-rwxrwxr-x  1 todd wormbase 11843 Jul  6 14:06 dasview
-rwxrwxr-x  1 todd wormbase  4391 Jul  6 14:06 download_index
-rwxrwxr-x  1 todd wormbase 13931 Jul  6 14:06 epcr
-rwxrwxr-x  1 todd wormbase 95462 Jul  6 14:06 expr_search
-rwxrwxr-x  1 todd wormbase  5457 Jul  6 14:06 fast_facts
-rwxrwxr-x  1 todd wormbase  5437 Jul  6 14:06 gotable
-rwxrwxr-x  1 todd wormbase  8860 Jul  6 14:06 graf.cgi
-rwxrwxr-x  1 todd wormbase 13523 Jul  6 14:06 hunter.cgi
-rwxrwxr-x  1 todd wormbase 35626 Jul  6 14:06 info_dump
-rwxrwxr-x  1 todd wormbase  8016 Jul  6 14:06 interval
-rwxrwxr-x  1 todd wormbase 18785 Jul  6 14:06 markers
-rwxrwxr-x  1 todd wormbase 10634 Jul  6 14:06 multi
-rwxrwxr-x  1 todd wormbase  4865 Jul  6 14:06 multi.search
-rwxrwxr-x  1 todd wormbase  3830 Jul  6 14:06 neuron302.cgi
-rwxrwxr-x  1 todd wormbase 28272 Jul  6 14:06 neuron_display
-rwxrwxr-x  1 todd wormbase  5183 Jul  6 14:06 neuron_graf.cgi
-rwxrwxr-x  1 todd wormbase  8858 Jul  6 14:06 pedigree
-rwxrwxr-x  1 todd wormbase  6165 Jul  6 14:06 query
-rwxrwxr-x  1 todd wormbase 15846 Jul  6 14:06 rnai_search
-rwxrwxr-x  1 todd wormbase  4415 Jul  6 14:06 search_index
-rwxrwxr-x  1 todd wormbase  1697 Jul  6 14:06 standard_urls
-rwxrwxr-x  1 todd wormbase 36155 Jul  6 14:06 strains
-rwxrwxr-x  1 todd wormbase  2358 Jul  6 14:06 text
-rwxrwxr-x  1 todd wormbase  1926 Jul  6 14:06 text302
-rwxrwxr-x  1 todd wormbase  6349 Jul  6 14:06 wb_query

./searches/advanced:
total 60
-rwxrwxr-x  1 todd wormbase 43224 Jul  6 14:06 dumper
-rwxrwxr-x  1 todd wormbase  4289 Jul  6 14:06 dumper.cfg
-rw-rw-r--  1 todd wormbase  2268 Jul  6 14:06 dumper.methods.txt

./seq:
-rwxrwxr-x  1 todd wormbase   1009 Jul  6 14:06 align                            DEPRECATED
-rwxrwxr-x  1 todd wormbase  11448 Jul  6 14:06 aligner                       BROKEN
-rwxrwxr-x  1 todd wormbase  11644 Jul  6 14:06 clone
-rwxr-xr-x  1 root wormbase  34287 Jul 13 12:33 das
-rwxrwxr-x  1 todd wormbase   2202 Jul  6 14:06 dasdraw
-rwxrwxr-x  1 todd wormbase   2390 Jul  6 14:06 dna
-rwxrwxr-x  1 todd wormbase   4985 Jul  6 14:06 do_align
-rwxrwxr-x  1 todd wormbase  24840 Jul  6 14:06 ebsyn
-rwxrwxr-x  1 todd wormbase  15999 Jul  6 14:06 frend
drwxr-sr-x  2 todd wormbase   4096 Jul 10 10:00 gb2
-rwxr-xr-x  1 root wormbase   9258 Jul 13 12:33 gbgff
-rwxr-xr-x  1 todd wormbase 125302 Jul 13 12:41 gbrowse
-rwxr-xr-x  1 todd wormbase  15843 Jul 13 12:33 gbrowse_details
-rwxr-xr-x  1 todd wormbase   4654 Jul 13 12:33 gbrowse_est
-rwxr-xr-x  1 todd wormbase  35795 Jul 13 12:33 gbrowse_img
-rwxr-xr-x  1 todd wormbase  50095 Jul 13 12:33 gbrowse_moby
-rwxr-xr-x  1 todd wormbase  50059 Jul 13 12:33 gbrowse_syn
-rwxrwxr-x  1 todd wormbase   4292 Jul  6 14:06 interaction
-rwxrwxr-x  1 todd wormbase   3571 Jul  6 14:06 interaction_viewer
-rwxr-xr-x  1 root wormbase    993 Jul 13 12:33 moby_server
-rwxrwxr-x  1 todd wormbase   7636 Jul  6 14:06 pcr                           todd / not tested yet in production
-rwxrwxr-x  1 todd wormbase   7634 Jul  6 14:06 position_matrix
-rwxrwxr-x  1 todd wormbase   4047 Jul  6 14:06 promoter
-rwxrwxr-x  1 todd wormbase  34886 Jul  6 14:06 protein                  todd / gb1 & gb2 / freeze1
-rwxrwxr-x  1 todd wormbase  17613 Jul  6 14:06 rnai                         BROKEN
-rwxrwxr-x  1 todd wormbase   8614 Jul  6 14:06 sage
-rwxrwxr-x  1 todd wormbase  45150 Jul  6 14:06 sequence
-rwxrwxr-x  1 todd wormbase  13506 Jul  6 14:06 show_mult_align
-rwxrwxr-x  1 todd wormbase  24250 Jul  6 14:06 transcript
-rwxrwxr-x  1 todd wormbase  24282 Jul  6 14:06 tr_script
-rwxr-xr-x  1 root wormbase   4166 Jul 13 12:33 tutorial_test.pl
-rwxrwxr-x  1 todd wormbase   3256 Jul  6 14:06 wtp
-rwxrwxr-x  1 todd wormbase   2405 Jul  6 14:06 y2h

./seq/gb2:
total 76
-r--r--r--  1 todd wormbase  1119 Jul 10 09:34 gbgff
-r-xr-xr-x  1 todd wormbase   671 Jul 10 09:34 gbrowse
-r-xr-xr-x  1 todd wormbase 18077 Jul 10 09:34 gbrowse_details
-r-xr-xr-x  1 todd wormbase 21468 Jul 10 09:34 gbrowse_gmap
-r-xr-xr-x  1 todd wormbase 20962 Jul 10 09:34 gbrowse_img

./SR_expression:
total 80
-rwxrwxr-x  1 todd wormbase 10605 Jul  6 14:06 SRcell.pl                               DEPRECATED
-rwxrwxr-x  1 todd wormbase 21958 Jul  6 14:06 SR_expression.pl                DEPRECATED
-rwxrwxr-x  1 todd wormbase 11220 Jul  6 14:06 SRsearch.pl                          DEPRECATED
-rwxrwxr-x  1 todd wormbase 26697 Jul  6 14:06 SRsubmit.pl                         DEPRECATED