-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathHISTORY
1605 lines (1379 loc) · 39.1 KB
/
HISTORY
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
TAG: mirror_wget-6-0-25-1
DATE: 02/04/2025
e4g-127/Process Alliance File to Load SNP_ConsensusSnp_Marker
# modified: alliancegenome.org.variants
TAG: mirror_wget-6-0-24-5
DATE: 12/03/2024
as part of the wts2-1109/e4g-13/postgres upgrade/IT training
removed "remote_user=anonymous
removed "[email protected]"
# deleted: ftp.informatics.jax.org.imsr
TAG: mirror_wget-6-0-24-4
DATE: 12/02/2024
wts2-1585/e4g-88/Jax Pheno Strain Info Curl Issue
# new file: phenome.jax.org
# modified: packagelist.weekly
TAG: mirror_wget-6-0-24-3
DATE: 11/19/2024
wts2-1580/e4g-77/mirror_wget/bhmgiimsr01.jax.org.imsr_allStrains -> bhmgiimsr02lp.jax.org issue
# deleted: bhmgiimsr01.jax.org.imsr_allStrains
# new file: bhmgiimsr02lp.jax.org.imsr_allStrains
# modified: packagelist.weekly
TAG: mirror_wget-6-0-24-2
DATE: 08/29/2024
wts2-1528/fl2-951/Add NCBI regulatory regions/biological_region to MGIreg.gff3 file
# new file: ftp.ncbi.nih.gov.regulator
TAG: mirror_wget-6-0-24-1
DATE: 08/26/2024
wts2-1540/fl2-955/added --no-check-certificate
# modified: data.glygen.org
TAG: mirror_wget-6-0-23-3
DATE: 04/09/2024
remove unused go files
# modified: packagelist.daily
TAG: mirror_wget-6-0-23-2
TAG: mirror_wget-6-0-23-1
DATE: 03/29/2024
wts2-1155/GOC taking over GOA mouse, GOA human, etc.
wts2-575/fl2-743/Add GlyGen links to MGI gene detail pages (TR13475)
# new file: data.glygen.org
# new file: snapshot.geneontology.org.goload
#
# modified: ftp.ebi.ac.uk.goload
# modified: ftp.ebi.ac.uk.interpro
# modified: packagelist.daily
# modified: packagelist.weekly
# modified: purl.obolibrary.org.hp.obo
#
# renamed: ftp.geneontology.org.external2go -> snapshot.geneontology.org.uniprotload
#
# deleted: bhmgiimsrtest-01lt.jax.org.imsr_allStrains
# deleted: cgd.jax.org
# deleted: ftp.geneontology.org.goload
# deleted: research.bioinformatics.udel.edu
# deleted: snapshot.geneontology.org.goload.noctua
#
TAG: mirror_wget-6-0-22-19
DATE: 11/14/2023
STAFF: dbm
CHANGES:
Remove cgd.jax.org: retired genmapload
TAG: mirror_wget-6-0-22-18
DATE: 10/20/2023
STAFF: sc
CHANGES: updated www.gentar.org.es_cell
The targetedalleleload was turned off/archived on 10/19/23
We continue to download the file for qc reports
TAG: mirror_wget-6-0-22-17
DATE: 06/27/2023
STAFF: dbm
CHANGES:
www.findmice.org.imsrwi: ignore robots.txt file that causes 404 error
TAG: mirror_wget-6-0-22-16
DATE: 05/12/2023
STAFF: lec
CHANGES:
wts2-1095/fl2-149/Mouse models of human disease report (1)
wts2-1120/fl2-204/Mouse models of human disease report (2)
bhmgiimsrtest-01lt.jax.org.imsr_allStrains
TAG: mirror_wget-6-0-22-15
TAG: mirror_wget-6-0-22-14
DATE: 05/03/2023
STAFF: sc
CHANGES: fl2-315 - download alliance human coord file. New package
alliancegenome.org.human_coordload
rm ftp.ncbi.nih.gov.mapview (old human coord package)
TAG: mirror_wget-6-0-22-13
DATE: 04/11/2023
STAFF: dbm
CHANGES:
1) purl.obolibrary.org.ma.obo: retired package
2) purl.obolibrary.org.mod.obo: retired package
3) www.genetraps.org.igtc: retired package
4) www.gensat.org.EntrezGeneIds: retired package
5) www.sequenceontology.org.current_release.obo: retired package
fl2-278 clean-up
TAG: mirror_wget-6-0-22-12
DATE: 03/24/2023
STAFF: lec
CHANGES:
wts2-1143/fl2-258/snapshot.geneontology.org.goload.noctua
TAG: mirror_wget-6-0-22-11
DATE: 02/21/2023
STAFF: lec
CHANGES:
wts2-1125/fl2-220/Modify the Noctua load to only include the noctua_mgi file.
TAG: mirror_wget-6-0-22-10
TAG: mirror_wget-6-0-22-9
STAFF: sc
CHANGES: wts2-1037
ftp.ensembl.org.mouse_regulatory - updated the hardcoded filename to a wildcard - date suffix
changes with each release. Also, this was never added to packagelist.weekly
TAG: mirror_wget-6-0-22-8
DATE: 11/29/2022
STAFF: sc
CHANGES: www.gentar.org.crispr - changed url to mgi_initial_crispr
This is for the new 9 col file provided by Robert
TAG: mirror_wget-6-0-22-7
DATE: 11/14/2022
STAFF: sc
CHANGES: http://wts.informatics.jax.org/searches/tr.detail.cgi?TR_Nr=11893
Return Human Gene-Associated Diseases from HMDC Pheno Queries
Added raw.githubusercontent.com.mp_hp and listed it in packagelist.weekly
TAG: mirror_wget-6-0-22-6
DATE: 10/13/2022
STAFF: sc
CHANGES: wts2-412 Skip load processing if input files do not exist (TR12754)
ftp.geneontology.org.goload - set do_deletes=false
download_package - report when deleting local files
TAG: mirror_wget-6-0-22-5
DATE: 09/30/2022
STAFF: sc
CHANGES: wts2-558
* remove www.mousephenotyping.reports mirror
* added:
* www.gentar.org.mgi_crispr
* www.gentar.org.mgi_modification
* www.gentar.org.mgi_es_cell
* www.gentar.org.mgi_phenotyping
TAG: mirror_wget-6-0-22-4
DATE: 09/20/2022
STAFF: dbm
CHANGES:
wts2-982/Update Xenbase link
TAG: mirror_wget-6-0-22-3
DATE: 08/31/2022
STAFF: dbm
CHANGES:
wts2-969/Update EBI FTP link for InterPro files
TAG: mirror_wget-6-0-22-2
TAG: mirror_wget-6-0-22-1
TAG: mirror_wget-6-0-21-3
DATE: 07/21/2022, 07/25/2022, 08/01/2022
STAFF: lec
CHANGES:
wts2-646/ftp.ncbi.nih.gov/gene/DATA/mim2gene_medgen : keep
TAG: mirror_wget-6-0-21-2
DATE: 07/07/2022
STAFF: dbm
CHANGES:
1) www.uniprot.org.pirsfload: new URL to get the input file
TAG: mirror_wget-6-0-21-1
DATE: 07/05/2022
STAFF: lec
CHANGES:
wts2-921/TSS_Region (SO:0001240) is obsolete
TAG: mirror_wget-6-0-19-1
DATE: 04/12/2022
STAFF: lec
CHANGES:
wts2-808/New OMIM load API key/modify OMIM load/data.omim.org.omim
TAG: mirror_wget-6-0-18-2
TAG: mirror_wget-6-0-18-1
DATE: 03/08/2022
STAFF: lec
CHANGES:
wts2-813/Load ENSEMBL and VISTA Regulatory Elements/ftp.ensembl.org.mouse_regulatory
ftp.ncbi.nih.gov.entrez_gene/re-added mim2gene_medgen:
TAG: mirror_wget-6-0-17-6
DATE: 12/30/2021
STAFF: sc
CHANGES:
1) remove mygene.info.wikipedia
2) remove mygene.info.wikipedia from pakagelist.weekly
TAG: mirror_wget-6-0-17-5
DATE: 10/18/2021
STAFF: dbm
CHANGES:
1) ftp.nextprot.org.nextprot: removed - ftp site is no longer available
2) download.nextprot.org: new package
3) packagelist.weekly: replaced nextprot package file name
TAG: mirror_wget-6-0-17-4
DATE: 10/15/2021
STAFF: dbm
CHANGES:
1) data.omim.org.omim: revert certificate change because Mike updated the certificate on our servers to allow the connection
TAG: mirror_wget-6-0-17-3
DATE: 10/14/2021
STAFF: dbm
CHANGES:
1) data.omim.org.omim: added "--no-check-certificate" option to wget call
because the mirror was failing certification
TAG: mirror_wget-6-0-17-2
DATE: 06/16/2021
STAFF: sc
CHANGES: removed ftp.proteininformationresource.org.pirsfload and call in
packagelist.weekly
TAG: mirror_wget-6-0-17-1
DATE: 06/10/2021
STAFF: sc
CHANGES: WTS2-620 - new package file for pirsfload www.uniprot.org.pirsfload
need to remove ftp.proteininformationresource.org.pirsfload
once load is tested
TAG: mirror_wget-6-0-16-19
TAG: mirror_wget-6-0-16-18
DATE: 05/04/2021
STAFF: dbm
CHANGES:
1) removed: ftp.pir.georgetown.edu.pirsfload
2) added: ftp.proteininformationresource.org.pirsfload
3) modified: packagelist.weekly with new package name
TAG: mirror_wget-6-0-16-17
DATE: 04/27/2021
STAFF: lec
CHANGES:
wts2-606/Human gene COV report has mouse genes
alliancegenome.org.humandisease
TAG: mirror_wget-6-0-16-16
DATE: 04/26/2021
STAFF: dbm
CHANGES:
1) removed ftp.ncbi.nih.gov.unigene
2) removed ftp.ncbi.nih.gov.unists
TAG: mirror_wget-6-0-16-15
DATE: 04/16/2021
STAFF: sc
CHANGES: TR11349
1) deleted ftp.ensembl.org.mouse_gff3.v92
2) updated ftp.ensembl.org.mouse_gff3
TAG: mirror_wget-6-0-16-14
DATE: 04/12/2021
STAFF: sc
CHANGES: TR13484 retire mirroring of genbank & refseq release files
# deleted: ftp.ncbi.nih.gov.gbRel
# deleted: ftp.ncbi.nih.gov.refseqVertebrate
# deleted: packagelist.refseq.release
# modified: packagelist.genbank.release, removed ftp.ncbi.nih.gov.gbRel
TAG: mirror_wget-6-0-16-13
DATE: 04/06/2021
TAFF: sc
CHANGES: TR13349 - Build39 project
alliancegenome.org.humandisease - new for public covid human disease rpt
alliancegenome.org.orthology - updated with static url
TAG: mirror_wget-6-0-16-12
DATE: 04/05/2021
STAFF: dbm
CHANGES: TR13481
1) alliancegenome.org.gene_descriptions: New package for GO text load
2) packagelist.daily: Added new package
TAG: mirror_wget-6-0-16-11
DATE: 03/19/2021
STAFF: sc
CHANGES: tr13349 - remove ftp.ncbi.nih.gov.homologene
it is not being called by any of the packagelist scripts
see tag mirror_wget-6-0-12-8
TAG: mirror_wget-6-0-16-10
DATE: 03/04/2021
STAFF: lec
CHANGES:
TR13471/Changes to Proper places to get GO mapping files
ftp.geneontology.org.external2go
TAG: mirror_wget-6-0-16-9
DATE: 02/24/2021
STAFF: dbm
CHANGES:
1) ftp.hgu.mrc.ac.uk.emage: removed - obsolete
2) packagelist.daily: remove ftp.hgu.mrc.ac.uk.emage
TAG: mirror_wget-6-0-16-8
DATE: 02/23/2021
STAFF: dbm
CHANGES: TR13468
1) compbio.charite.de.phenotype_annotation: removed - obsolete
2) purl.obolibrary.org.phenotype.hpoa: new
3) packagelist.weekly: updated with new package name
TAG: mirror_wget-6-0-16-7
DATE: 01/27/2021
STAFF: sc
CHANGES: Added package to download Alliance Homology
Added package to weekly package list
TAG: mirror_wget-6-0-16-6
DATE: 09/28/2020
STAFF: sc
CHANGES: packagelist.weekly - moved sprot and trembl
packages to end of list. See comment at top of the
file
TAG: mirror_wget-6-0-16-5
DATE: 09/28/2020
STAFF: sc
CHANGES:
TR13235 www.ebi.ac.uk.arrayexpress.json
TAG: mirror_wget-6-0-16-4
DATE: 09/22/2020
STAFF: lec
CHANGES:
TR13390/raw.githubusercontent.com.diseaseontology : change "master" to "main"
TAG: mirror_wget-6-0-16-3
DATE: 09/01/2020
STAFF: lec
CHANGES: TR13272/GO meeting/CalTech/tasks to-do
remove: purl.obolibrary.org.ro
TAG: mirror_wget-6-0-16-2
DATE: 08/31/2020
STAFF: sc
CHANGES: B39 assembly mirror
TAG: mirror_wget-6-0-16-1
DATE: 08/25/2020
STAFF: lec
CHANGES: TR13272/GO meeting/CalTech/tasks to-do
add: purl.obolibrary.org.ro
TAG: mirror_wget-6-0-15-3
DATE: 05/04/2020
STAFF: lec
CHANGES: TR13299
remove: purl.obolibrary.org.pr.obo
add: purl.obolibrary.org.pr
TAG: mirror_wget-6-0-15-1
DATE: 03/02/2020
STAFF: sc
CHANGES: TR13275
1) compbio.charite.de.phenotype_annotation - changed file path at source
TAG: mirror_wget-6-0-14-9
DATE: 12/17/2019
STAFF: dbm
CHANGES:
1) update compbio.charite.de.phenotype_annotation with new file path
TAG: mirror_wget-6-0-14-8
DATE: 11/13/2019
STAFF: dbm
CHANGES:
1) Remove pir.georgetown.edu.proisoform package (obsolete)
2) Remove pir.georgetown.edu.proisoform from packagelist.daily
TAG: mirror_wget-6-0-14-7
TAG: mirror_wget-6-0-14-6
TAG: mirror_wget-6-0-14-5
DATE: 09/23/2019
STAFF: sc
CHANGES: typo in ftp.ncbi.nih.gov.refseqVertebrate
causing download of extraneous files
download_files - For refseq, first rm/make directory (to start fresh)
then download
TAG: mirror_wget-6-0-14-4
DATE: 08/19/2019
STAFF: lec
CHANGES: TR13132
data.omim.org.omim : change to "https"
TAG: mirror_wget-6-0-14-3
DATE: 06/04/2019
STAFF: lec
CHANGES: TR13052
remove: research.bioinformatics.udel.edu
replaced with: proconsortium.org
changed: purl.obolibrary.org.pr.obo
TAG: mirror_wget-6-0-14-2
DATE: 04/22/2019
STAFF: sc
CHANGES:
TR13065 - update to mirror refseq vertebrate instead of entire
release
TAG: mirror_wget-6-0-14-1
DATE: 04/11/2019
STAFF: lec
CHANGES: TR13081
* remove dmdd.org.uk.htmpload
* remove from packagelist.weekly
TAG: mirror_wget-6-0-13-13
DATE: 04/03/2019
STAFF: sc
CHANGES: TR13065 - moving from refseq complete release
to vertebrate only. Changes:
* remove ftp.ncbi.nih.gov.refseqRel
* add ftp.ncbi.nih.gov.refseqVertebrate
* update packagelist.refseq.release
TAG: mirror_wget-6-0-13-12
TAG: mirror_wget-6-0-13-11
DATE: 03/26/2019
STAFF: sc
CHANGES: TR13059 - new URL/filename
TAG: mirror_wget-6-0-13-10
DATE: 03/13/2019
STAFF: sc
CHANGES: TR13054 - new omim/hpo annotload file
updated: compbio.charite.de.phenotype_annotation
TAG: mirror_wget-6-0-13-9
TAG: mirror_wget-6-0-13-8
DATE: 01/30/2019
STAFF: lec
CHANGES:
TR13011/noctua
TR13029/CFP/goc
obsolete: build.berkeleybop.org.gpad.goload
obsolete: build.berkeleybop.org.goload
added CFP to this new package
new : snapshot.geneontology.org.goload.noctua
TAG: mirror_wget-6-0-13-7
TAG: mirror_wget-6-0-13-6
TAG: mirror_wget-6-0-13-5
DATE: 01/28/2019
STAFF: lec
CHANGES:
TR13011
obsolete: build.berkeleybop.org.gpad.goload
new : snapshot.geneontology.org.goload.noctua
put the obsoleted package back in due to GO/input issues.
TAG: mirror_wget-6-0-13-4
DATE: 1/3/2019
STAFF: dbm
CHANGES:
1) packagelist.daily: removed www.gensat.org.EntrezGeneIds because the gensat
site is not operational (per Connie)
TAG: mirror_wget-6-0-13-3
DATE: 12/11/2018
STAFF: dbm
CHANGES:
added "/custom" to URL in www.genenames.org.hgnc to get hgnc.tsv file
TAG: mirror_wget-6-0-13-2
DATE: 12/05/2018
STAFF: jsb
CHANGES:
added raw.githubusercontent.com.sequenceontology (SO vocab) for DADT release;
added it to packagelist.weekly
TAG: mirror_wget-6-0-13-1
DATE: 11/30/2018
STAFF: sc
CHANGES: www.ebi.ac.uk.impc.json - add back in LOCAL_DIR=$REMOTE_SITE
so file is downloaded to the proper place for the impc htmpload to find
it. TR12994
TAG: mirror_wget-6-0-12-10
DATE: 09/13/2018
STAFF: lec
CHANGES:
TR12955/purl.obolibrary.org.go-basic.obo changes
TAG: mirror_wget-6-0-12-9
DATE: 09/04/2018
STAFF: lec
CHANGES:
remove ftp.hgu.mrc.ac.uk.emage from packagelist.daily
TAG: mirror_wget-6-0-12-8
DATE: 09/04/2018
STAFF: lec
CHANGES:
remove ftp.ncbi.nih.gov.homologene from packagelist.weekly
TAG: mirror_wget-6-0-12-7
DATE: 09/04/2018
STAFF: lec
CHANGES:
remove ftp.ncbi.nih.gov.mapview from packagelist.weekly
TAG: mirror_wget-6-0-12-6
TAG: mirror_wget-6-0-12-5
DATE: 08/29/2018
STAFF: sc
CHANGES: TR12044 - New HGNC biomart call
www.genenames.org.hgnc - updated biomart url
TAG: mirror_wget-6-0-12-4
DATE: 08/15/2018
STAFF: lec
CHANGES: TR12918/change in goload/gorefgen (PAINT)
add snapshot.geneontology.org.goload
remove paint from ftp.geneontology.org.goload
TAG: mirror_wget-6-0-12-3
DATE: 07/12/2018
STAFF: sc
CHANGES: TR12115
add new crispr file to www.mousephenotype.org.reports
TAG: mirror_wget-6-0-12-2
DATE: 05/10/2018
STAFF: sc
CHANGES: TR12734 - saved ftp.ensembl.org.mouse_gff3 as ftp.ensembl.org.mouse_gff3.v91
updated ftp.ensembl.org.mouse_gff3 to v92
TAG: mirror_wget-6-0-12-1
DATE: 04/26/2018
STAFF: lec
CHANGES: TR12834/new GO qualifiers & pr.gpad file
build.berkeleybop.org.gpad.goload : new url, add pr.gpad
TAG: mirror_wget-6-0-11-11
DATE: 04/05/2018
STAFF: sc
CHANGES: TR12734 Added ftp.ensembl.org.mouse_gff3 and packagelist.gff3.release
TAG: mirror_wget-6-0-11-10
DATE: 03/28/2018
STAFF: lec
CHANGES:
add '--no-check-certificate' to purl.obolibrary.org.pr.obo
TAG: mirror_wget-6-0-11-9
DATE: 03/19/2018
STAFF: lec
CHANGES: TR12827/PRO_mgi.txt
mv ftp.pir.georgetown.edu.proload to https://research.bioinformatics.udel.edu
TAG: mirror_wget-6-0-11-8
DATE: 03/15/2018
STAFF: sc
CHANGES: TR12817
www.mousephenotype.org.reports - add --no-check-certificate
TAG: mirror_wget-6-0-11-7
DATE: 03/05/2018
STAFF: lec
CHANGES:
moved into packagelist.daily
purl.obolibrary.org.pr.obo
pir.georgetown.edu.proisoform
TAG: mirror_wget-6-0-11-6
DATE: 03/01/2018
STAFF:
CHANGES: TR12802
rm ftp.sanger.ac.uk.vega_cdna ftp.sanger.ac.uk.vega_gtf ftp.sanger.ac.uk.vega_ncrna ftp.sanger.ac.uk.vega_prot
TAG: mirror_wget-6-0-11-5
TAG: mirror_wget-6-0-11-4
DATE: 02/05/2018, 03/01/2018
STAFF: lec
CHANGES:
1) TR12783
purl.obolibrary.org.pr.obo : new
ftp.pir.georgetown.edu.proisoform : obsolete
TAG: mirror_wget-6-0-11-3
DATE: 12/11/2017
STAFF: dbm
CHANGES:
1) dmdd.org.uk.htmpload: Updated remote path to file
TAG: mirror_wget-6-0-11-2
DATE: 11/13/2017
STAFF: sc
CHANGES: TR12662/GMC Project
1) remove ontologies.berkeleybop.org.uberon - we will use the already downloaded obo
file instead.
TAG: mirror_wget-6-0-11-1
DATE: 11/09/2017
STAFF: sc
CHANGES: TR12662/GMC Project
1) added new package: ontologies.berkeleybop.org.uberon to packagelist.daily
TAG: mirror_wget-6-0-10-2
DATE: 07/10/2017
STAFF: dbm
CHANGES:
1) run_mirror.sh: New script to download package lists
2) run_mirror_logged.sh: New wrapper for downloading/logging in radar
3) packagelist.daily: New daily package list
4) packagelist.weekly: New weekly package list
5) packagelist.weekly.logged: New weekly logged package list
6) packagelist.genbank.release: New Genbank release package list
7) packagelist.refseq.release: New Refseq release package list
8) ftp.ncbi.nih.gov.refseqRel: Removed release*.removed-records.gz
9) dailycron.sh, weeklycron.sh, weeklycron-logged.sh,
genbankRel.sh, refseqRel.sh, check_mirror_logs.sh: Retired
TAG: mirror_wget-6-0-10-1
DATE: 06/08/2017
STAFF: sc
CHANGES: TR12083 seqdeleter fix
1) add ftp.ncbi.nih.gov.refseq_deletes to dailycron.sh
TAG: mirror_wget-6-0-9-2
DATE: 04/06/2017
STAFF: lec
CHANGES: TR12504/IMPC/lacZ
new file: www.ebi.ac.uk.impc_lacz_alz.json
new file: www.ebi.ac.uk.impc_lacz_elz.json
TAG: mirror_wget-6-0-9-1
DATE: 04/04/2017
STAFF: sc
CHANGES: Merge tr12488 to trunk
TAG: mirror_wget-tr12488-2
DATE: 03/23/2017
STAFF: lnh
CHANGES:scrum bob contigs epic
1) removed ftp.ncbi.nih.gov.gbGenomicRel and gbGenomicRel.sh -
restored gb release contig files in ftp.ncbi.nih.gov.gbRel
2) removed ftp.ncbi.nih.gov.refseqGenomicRel and refseqGenomicRel.sh -
Added RefSeq genomic files in ftp.ncbi.nih.gov.refseqGenomicRel
DATE: 03/22/2017
STAFF: sc
CHANGES:scrum bob contigs epic
1) removed gb release contig files from ftp.ncbi.nih.gov.gbRel created
ftp.ncbi.nih.gov.gbGenomicRel
2) new:
ftp.ncbi.nih.gov.gbGenomicRel - genbank genomic release package file
ftp.ncbi.nih.gov.refseqGenomicRel - refseq genomic release package file
genbankGenomicRel.sh - run adhoc genbank genomic mirror
refseqGenomicRel.sh - run adhoc refseq genomic mirror
TAG: mirror_wget-tr12488-1
DATE: 03/14/2017
STAFF: sc
CHANGES:scrum bob contigs epic
1) add contig non-cums to ftp.ncbi.nih.gov.gbNC
2) add contig release files to ftp.ncbi.nih.gov.gbRel
TAG: no tag needed
DATE: 02/28/2017
STAFF: lec
CHANGES:
1) TR12504/www.ebi.ac.uk.impc_lacz.json
TAG: mirror_wget-6-0-7-4
DATE: 02/07/2017
STAFF: lec
CHANGES:
1) added ftp.pir.georgetown.edu.proisoform to weeklycron.sh
TAG: mirror_wget-6-0-7-3
DATE: 01/26/2017
STAFF: lec
CHANGES:
1) www.ebi.ac.uk.impc_lacz.json fix
TAG: mirror_wget-6-0-7-2
DATE: 01/20/2017
STAFF: lec
CHANGES:
TR12447/DMDD phenotype data load
1) dmdd.org.uk.htmpload
2) weeklycron.sh
TAG: mirror_wget-6-0-7-1
DATE: 1/4/2017
STAFF: dbm
CHANGES:
1) emnet.informatics.jax.org.imsr_allStrains: removed package
2) bhmgiimsr01.jax.org.imsr_allStrains: added package
3) weeklycron.sh: replaced emnet package with bhmgiimsr01 package
TAG: mirror_wget-6-0-6-??
DATE: 01/03/2017
STAFF: lec
CHANGES:
1) TR12427/Disease Ontology (DO)
raw.githubusercontent.com.diseaseontology
TAG: mirror_wget-6-0-6-11
DATE: 12/19/2016
STAFF: lec
CHANGES:
1) TR12486/raw.githubusercontent.com.evidenceontology
purl.obolibrary.org.eco.obo/removed/obsolete
TAG: mirror_wget-6-0-6-10
DATE: 12/08/2016
STAFF: lec
CHANGES:
1) TR12474/build.berkeleybop.org.goload
remote directory changed
TAG: mirror_wget-6-0-6-9
DATE: 12/01/2016
STAFF: lec
CHANGES:
1) TR12468/build.berkeleybop.org.gpad.goload
remote directory changed
TAG: mirror_wget-6-0-6-8
DATE: 11/28/2016
STAFF: lec
CHANGES:
1) weeklycron.sh : added pir.georgetown.edu.proisoform
TAG: mirror_wget-6-0-6-7
DATE: 11/10/2016
STAFF: lec
CHANGES:
1) ftp.ncbi.nih.gov.homologene/pub.HomologGene/current/homologene.data
has not been updated since 5/6/2014
removing from dailycron.sh
TAG: mirror_wget-6-0-6-6
DATE: 10/25/2016
STAFF: lec
CHANGES:
1) purl.obolibrary.org.cl-basic.obo
moved from dailycron.sh to weeklycron.sh
TAG: mirror_wget-6-0-6-4
DATE: 10/05/2016
STAFF: lec
CHANGES: TR12427/DO (Disease Ontology)
1) raw.githubusercontent.com.diseaseontology
2) weeklycron.sh : added DO
TAG: mirror_wget-6-0-6-3
DATE: 09/27/2016
STAFF: sc
CHANGES: TR12370 - GXD HT project
* www.ebi.ac.uk.arrayexpress.json - updated to fetch four years of data
TAG: mirror_wget-6-0-6-2
TAG: mirror_wget-6-0-6-1
DATE: 09/08/2016
STAFF: lec
CHANGES: TR12349/TR12345/gone-dor + more/gpad,
TR12378/adding isoforms
remove human from ftp.geneontology.org.goload
build.berkeleybop.org.goload
build.berkeleybop.org.gpad.goload
ftp.ebi.ac.uk.goload
ftp.geneontology.org.goload
TAG: mirror_wget-6-0-5-7
DATE: 08/03/2016
STAFF: lec
CHANGES: TR12345/gpad, TR12378/adding isoforms
new: ftp.ebi.ac.uk.goload : add goa_human.gaf.gz, goa_human_isoform.gaf.gz
TAG: mirror_wget-6-0-5-6
TAG: mirror_wget-6-0-5-5
DATE: 08/01/2016
STAFF: lec
CHANGES: TR12345/gpad, TR12378/adding isoforms
ftp.ebi.ac.uk.goload : add goa_mouse_isoform.gaf.gz
build.berkeleybop.org.gpad.goload : added for goload/goamousenoctua
TAG: mirror_wget-6-0-5-4
DATE: 07/13/2016
STAFF: lec
CHANGES:
1) ftp.ebi.ac.uk.goload
there is not HISTORY for 6-0-5-1, 2, 3?
TAG: mirror_wget-6-0-4-15
TAG: mirror_wget-6-0-4-14
DATE: 07/01/2016
STAFF: lnh
CHANGES:
1) ftp.ncbi.nih.gov.gbRel: Converted it to new format
2) ftp.ncbi.nih.gov.refseqRel: Converted it to new format
3) Added wrapper scripts genbankRel.sh and refseqRel.sh
to run Genbank release and Refseq release packages
TAG: mirror_wget-tr12317-1
DATE: 05/11/2016
STAFF: sc
CHANGES: updated URL to exclude MGP and EUPH' www.ebi.ac.uk.impc.json
TAG: mirror_wget-tr12317-BP
DATE: 05/11/2016
STAFF: sc
CHANGES: Branch Point Tag TR12317 IMPC ri data
TAG: mirror_wget-6-0-4-13
TAG: mirror_wget-6-0-4-12
TAG: mirror_wget-6-0-4-11
DATE: 06/28/2016
STAFF: lnh
CHANGES:
1) www.genenames.org.hgnc: Added a new variable 'is_xml_query'
2) download_package: Added a check for 'is_xml_query' variable
3) weeklycron.sh: Scheduled the www.genenames.org.hgnc package
TAG: mirror_wget-6-0-4-10
DATE: 06/28/2016
STAFF: lec
CHANGES:
for new proisoformload:
1) ftp.pir.georgetown.edu.proisoform
2) pir.georgetown.edu.proisoform
for proload/documentation
rename:
ftp.pir.georgetown.edu.pro_ids
to
ftp.pir.georgetown.edu.proload
and moved to weeklycron.sh
for pirsfload:
rename:
ftp.pir.georgetown.edu.iproclass
to:
ftp.pir.georgetown.edu.pirsfload
and moved to weeklycron.sh
TAG: mirror_wget-6-0-4-9
DATE: 06/16/2016
STAFF: dbm
CHANGES:
1) ftp.ebi.ac.uk.interpro: remote directory changed from "Current" to "current"
TAG: mirror_wget-6-0-4-8
TAG: mirror_wget-6-0-4-7
TAG: mirror_wget-6-0-4-6
DATE: 06/14/2016, 06/16/2016
STAFF: lec
CHANGES: TR12340/GOA file name changes
1) ftp.geneontology.org.gene-associations -> ftp.geneontology.org.goload
2) ftp.geneontology.org.gene-associations.paint -> ftp.geneontology.org.goload
3) dailycron2.sh merged into dailycron.sh
TAG: mirror_wget-6-0-4-5
TAG: mirror_wget-6-0-4-4
TAG: mirror_wget-6-0-4-3
TAG: mirror_wget-6-0-4-2
DATE: 06/01/2016
STAFF: lec
CHANGES:
removed from dailycron.sh (obsolete):
www.sequenceontology.org.current_release.obo
www.genetrap.igtc
purl.obolibrary.org.emap.obo purl.obolibrary.org.ma.obo purl.obolibrary.org.mod.obo
removed from dailycron.sh/weeklycron.sh : on demand only:
ftp.ncbi.nih.gov.unigene
removed:
purl.obolibrary.org.emap.obo
TAG: mirror_wget-6-0-4-1
DATE: 05/31/2016
STAFF: lec
CHANGES: TR12340/GOA file name changes
1) ftp.geneontology.org.gene-associations
2) ftp.ebi.ac.uk.goa
3) removing ANNOTATIONS variable
4) adding github repository name (load name) to "comment" variable
TAG: mirror_wget-6-0-3-7
DATE: 04/19/2016
STAFF: lnh
CHANGES: TR 12327
1) dailycron.sh: Added ftp.sanger.ac.uk.vega_ncrna package
TAG: mirror_wget-6-0-3-6
DATE: 04/18/2016
STAFF: lnh
CHANGES: TR 12327
1) mirror_lock: Removed step that sources th Configuration
2) ftp.sanger.ac.uk.vega_ncrna: Added VEGA ncrna package
TAG: mirror_wget-6-0-3-5
DATE: 04/15/2016
STAFF: lnh
CHANGES:
1) check_mirror_logs.sh: Added support the email recipient modification - EMAIL_TO
1) Configuration.default: Added the email recipient variable - EMAIL_TO
TAG: mirror_wget-6-0-3-4
DATE: 04/15/2016
STAFF: lnh
CHANGES:
1) Configuration.default: Added setting path and sourcing master config
2) All the wrapper script: dailycron* weeklycron* -
removed sourcing of live mgiconfig master.config script
TAG: mirror_wget-6-0-3-3
DATE: 04/14/2016
STAFF: lnh
CHANGES: TR12266 - Retire mirror_ftp
1) Added an Install script to create the Configuration file
2) Configuration.default:
Moved the DATADOWNLOADS and MIRRORLOG setting in the Configuration file
3) download_package script: Removed the host server restriction
TAG: mirror_wget-6-0-3-2
DATE: 04/13/2016
STAFF: lnh
CHANGES: TR12266 - Retire mirror_ftp
1) Migrated all mirror_ftp packages to mirror_wget
2) Converted mirror_wget daily and weekly packages to the new format
3) Wrote mirror_check_log script and scheduled it to be called by
daily and weekly mirrors wrapper scripts
4) Converted all the wraper scripts to sh shell
5) Removed obsolete packages as needed
TAG: mirror_wget-6-0-3-1
DATE: 03/31/2016
STAFF: lec
CHANGES: TR12273/IMPC load (htmpload)
1) www.mousephenotype.org : add new imits report (mp2_load_phenotyping_colonies_report.tsv)
2) remove : ikmc.vm.bytemark.co.uk
TAG: mirror_wget-6-0-2-10
DATE: 3/08/2016
STAFF: sc
CHANGES: TR12273/IMPC load (htmpload)
1) www.mousephenotype.org : add new imits report (mp2_load_phenotyping_colonies_report.tsv)
2) remove : ikmc.vm.bytemark.co.uk
TAG: mirror_wget-6-0-2-10
DATE: 3/08/2016
STAFF: sc
CHANGES: TR12267
2) added: purl.obolibrary7.org using wget to ht -O option so local filepath
does not reflect the redirect path from the site. replaces i
purl.obolibrary8.org (as I skipped 8 inadvertently)
2) updated weeklycron.csh to reflect above
TAG: mirror_wget-6-0-2-8
DATE: 3/07/2016
STAFF: sc
CHANGES: TR12267 - this is a BAD tag
TAG: mirror_wget-6-0-2-8
DATE: 3/04/2016
STAFF: sc
CHANGES: TR12267
1) added: compbio.charite.de and purl.obolibrary8.org
2) added above to weeklycron.csh
TAG: mirror_wget-6-0-2-7
DATE: 2/25/2016
STAFF: lnh
CHANGES: TR12225