Commits for hiram

6428d3411111567658e7496a9d131dcbe85034f6 Tue Jul 19 11:36:26 2022 -0700

platypus to platypus per user request refs #29753
- src/hg/makeDb/doc/asmHubs/lastzRuns.txt - lines changed 79, context: html, text, full: html, text

d1c7d424a88170e9153809be96213b4a30259187 Tue Jul 19 13:48:36 2022 -0700

split of sections of trackDb to individual track includes refs #29762trackDb.ra
- src/hg/makeDb/trackDb/human/hs1/assembly.trackDb.ra - lines changed 16, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hs1/cpgIslands.trackDb.ra - lines changed 25, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hs1/gc5Base.trackDb.ra - lines changed 17, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hs1/simpleRepeat.trackDb.ra - lines changed 9, context: html, text, full: html, text

3e88efb3cf44c9e58c3297c0aeb2a2c36bd27dfe Tue Jul 19 13:58:02 2022 -0700

75fb410e4222543ccdc30335f02247649e0d7186 Wed Jul 20 12:51:15 2022 -0700

output nothing when nothing to output no redmine
- src/utils/bedSingleCover.pl - lines changed 2, context: html, text, full: html, text

6cb40b8c7c2d15cf867031a5039a1ed1f198d04f Wed Jul 20 17:18:42 2022 -0700

adding all human viruses from refseq about 150 refs #29484
- src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv - lines changed 152, context: html, text, full: html, text

3c8ffb11a3e0a8830f64c3e19ca7f7ff8b167f33 Wed Jul 20 17:19:51 2022 -0700

handle cases where there is no result from RepeatMasker or TRF simple repeats for virus browser building refs #29484
- src/hg/utils/automation/asmHubRepeatMasker.sh - lines changed 24, context: html, text, full: html, text
- src/hg/utils/automation/asmHubTrackDb.sh - lines changed 3, context: html, text, full: html, text
- src/hg/utils/automation/doAssemblyHub.pl - lines changed 32, context: html, text, full: html, text

8f226d9ae51d5aa0907e717fb310cab91a54cf87 Wed Jul 20 17:21:05 2022 -0700

better choice of common names and manage lower valid track count for viruses refs #29484
- src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh - lines changed 7, context: html, text, full: html, text

38596ae2e82cc2e3d6e7b037aaa5bfc609e03177 Wed Jul 20 17:24:33 2022 -0700

adding 150 human virus genome builds refs #29484
- src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 150, context: html, text, full: html, text

837e1e89d23da949d16c0f9e6cd00eed3788642c Wed Jul 20 19:10:24 2022 -0700

no need to have SARS-CoV-2 on this list refs #29484
- src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv - lines changed 1, context: html, text, full: html, text

035f7ea1c057b4923fc64f7bea14b3bae513ea2e Thu Jul 21 09:24:08 2022 -0700

catch up listing with zoo241 genomes refs #29545
- src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 2, context: html, text, full: html, text

fe31f12c7713e5cfa4612a64f70752388646c424 Thu Jul 21 09:25:50 2022 -0700

catch up listing with zoo241 genomes refs #29545
- src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 10, context: html, text, full: html, text

d017527e4dddb716147a243efe2bb38d1acff329 Thu Jul 21 09:27:24 2022 -0700

catch up listing with zoo241 genomes refs #29545
- src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 13, context: html, text, full: html, text

a15d57f02b4b49c9e3dbceaad6234e340ec96bbd Thu Jul 21 17:04:25 2022 -0700

improve the legacy index page with a GenArk clade indication refs #29545
- src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 222, context: html, text, full: html, text

2862b2a8ea3a56805265df693bf94a4ed7d07cca Thu Jul 21 18:04:51 2022 -0700

adding the viral group to the index page footer table and special sets of columns for virus index pages refs #29545
- src/hg/makeDb/doc/asmHubs/commonHtml.pm - lines changed 4, context: html, text, full: html, text
- src/hg/makeDb/doc/asmHubs/mkHubIndex.pl - lines changed 29, context: html, text, full: html, text
- src/hg/makeDb/doc/asmHubs/trackData.pl - lines changed 18, context: html, text, full: html, text

5b5a242f38f695c23bc52e5388b941b8335307df Thu Jul 21 20:18:42 2022 -0700

properly eliminate rmsk from trackDb when there are no items in the track refs #29545
- src/hg/utils/automation/asmHubTrackDb.sh - lines changed 20, context: html, text, full: html, text

7a68602b325c40864c6937bc5803c4afd606bc9d Thu Jul 21 20:19:43 2022 -0700

customize the track table for viral genomes refs #29545
- src/hg/makeDb/doc/asmHubs/trackData.pl - lines changed 2, context: html, text, full: html, text

e027227ddfc859d20fdf629f9ea606b5a578861e Fri Jul 22 22:31:34 2022 -0700

adding another set of viruses related to human diseases refs #29484
- src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 101, context: html, text, full: html, text

50060dece064d88d993690dfbb67a802c7d3578e Fri Jul 22 22:51:33 2022 -0700

adding another set of viruses related to human diseases refs #29484
- src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv - lines changed 236, context: html, text, full: html, text

41a463cd8f3d221e36fd583e4d58dd12993f0975 Fri Jul 22 23:40:10 2022 -0700

this one GCA_004026985.1_MyoMyo_v1_BIUU is in legacy refs #29545
- src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 1, context: html, text, full: html, text

3ceca135069039ba2ce2290cc909128f3777dcc4 Fri Jul 22 23:40:38 2022 -0700

this one GCF_000951615.1_common_carp_genome is in legacy refs #29545
- src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 1, context: html, text, full: html, text

5654588935d1aa4ea6cbc928d2b5706d275a6249 Fri Jul 22 23:41:56 2022 -0700

this one GCA_000738955.1_M_pentadactyla-1.1.1 is in mammals not legacy yet refs #29545
- src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 1, context: html, text, full: html, text