File Changes for hiram

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v437_preview2 to v437_base (2022-09-12 to 2022-09-19) v437

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src/hg/gar/gar.cgi.pl
- lines changed 5, context: html, text, full: html, text
  a0b5687117ecc4f594719d5bd97fcf6ee3f51921 Fri Sep 16 12:02:02 2022 -0700
  more strict acceptance of the five required arguments refs #30003
src/hg/makeDb/doc/chm13v2.0userData/trackDb/t2tRepeatMasker.trackDb.txt
- lines changed 4, context: html, text, full: html, text
  66dc4a7ff27cb4b452b51e554c7591c824f8438d Mon Sep 19 10:18:09 2022 -0700
  set max window to draw at 5Mb to avoid timeout on large views refs #29995
src/hg/makeDb/doc/danRer11/lastzRuns.txt
- lines changed 83, context: html, text, full: html, text
  92bbe798bc4650f7f91cf6cd0fa4b5294ca7553b Tue Sep 13 10:41:59 2022 -0700
  per user request danRer11 vs dm6 lastz/chain/net refs #29981
src/hg/makeDb/doc/dm6/lastzRuns.txt
- lines changed 87, context: html, text, full: html, text
  92bbe798bc4650f7f91cf6cd0fa4b5294ca7553b Tue Sep 13 10:41:59 2022 -0700
  per user request danRer11 vs dm6 lastz/chain/net refs #29981
src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
- lines changed 1, context: html, text, full: html, text
  db68c943281694d716659cfc7ea7ccd2a8f5a14f Thu Sep 15 18:11:38 2022 -0700
  adding GCA_019973935.1_Tncv_1.0 golden silk orb-weaver (2021) per user request refs #30015
src/hg/makeDb/trackDb/TOGAannotation.html
- lines changed 53, context: html, text, full: html, text
  d2ac08231c388dcae68ce7031d5a7dddb91beb97 Mon Sep 12 10:55:19 2022 -0700
  expanded documentation from Michael refs #29982
src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 1, context: html, text, full: html, text
  30d97725dc1081e029f6577d12ccef896e7d10b9 Fri Sep 16 10:01:05 2022 -0700
  need bigGenePred on colorByStrand no redmine
src/hg/makeDb/trackDb/virus/mpxv2022/assembly.html
- lines changed 33, context: html, text, full: html, text
  5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
  initial set of docs for mpxv2022 refs #30012
src/hg/makeDb/trackDb/virus/mpxv2022/chainNet.html
- lines changed 148, context: html, text, full: html, text
  5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
  initial set of docs for mpxv2022 refs #30012
src/hg/makeDb/trackDb/virus/mpxv2022/cpgIslands.html
- lines changed 78, context: html, text, full: html, text
  5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
  initial set of docs for mpxv2022 refs #30012
src/hg/makeDb/trackDb/virus/mpxv2022/description.html
- lines changed 123, context: html, text, full: html, text
  5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
  initial set of docs for mpxv2022 refs #30012
src/hg/makeDb/trackDb/virus/mpxv2022/gc5Base.html
- lines changed 21, context: html, text, full: html, text
  5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
  initial set of docs for mpxv2022 refs #30012
src/hg/makeDb/trackDb/virus/mpxv2022/ncbiGene.html
- lines changed 16, context: html, text, full: html, text
  5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
  initial set of docs for mpxv2022 refs #30012
src/hg/makeDb/trackDb/virus/mpxv2022/pcrAmplicon.html
- lines changed 57, context: html, text, full: html, text
  5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
  initial set of docs for mpxv2022 refs #30012
src/hg/makeDb/trackDb/virus/mpxv2022/pcrAmplicon.ra
- lines changed 8, context: html, text, full: html, text
  5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
  initial set of docs for mpxv2022 refs #30012
src/hg/makeDb/trackDb/virus/mpxv2022/repeatMasker.html
- lines changed 261, context: html, text, full: html, text
  5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
  initial set of docs for mpxv2022 refs #30012
src/hg/makeDb/trackDb/virus/mpxv2022/simpleRepeat.html
- lines changed 48, context: html, text, full: html, text
  5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
  initial set of docs for mpxv2022 refs #30012
src/hg/makeDb/trackDb/virus/mpxv2022/tanDups.html
- lines changed 101, context: html, text, full: html, text
  5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
  initial set of docs for mpxv2022 refs #30012
src/hg/makeDb/trackDb/virus/mpxv2022/trackDb.ra
- lines changed 204, context: html, text, full: html, text
  5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
  initial set of docs for mpxv2022 refs #30012
src/hg/makeDb/trackDb/virus/mpxv2022/windowMasker.html
- lines changed 38, context: html, text, full: html, text
  5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
  initial set of docs for mpxv2022 refs #30012
- lines changed 3, context: html, text, full: html, text
  84e11afc2e82703669b4da2481ea2072bb9f2f8b Fri Sep 16 09:33:46 2022 -0700
  can not have $ signs in trackDb html refs #30012
src/hg/utils/automation/asmHubChainNet.pl
- lines changed 4, context: html, text, full: html, text
  92509db0231e9b1ae83aa0c85182883dd8eabc9b Wed Sep 14 13:59:35 2022 -0700
  fixup chainNet trackDb and now sending files to dynablat and arranging hub files to place it in use refs #29811
src/hg/utils/automation/asmHubChainNetComposite.pl
- lines changed 4, context: html, text, full: html, text
  92509db0231e9b1ae83aa0c85182883dd8eabc9b Wed Sep 14 13:59:35 2022 -0700
  fixup chainNet trackDb and now sending files to dynablat and arranging hub files to place it in use refs #29811
src/hg/utils/automation/asmHubChainNetTrackDb.pl
- lines changed 11, context: html, text, full: html, text
  92509db0231e9b1ae83aa0c85182883dd8eabc9b Wed Sep 14 13:59:35 2022 -0700
  fixup chainNet trackDb and now sending files to dynablat and arranging hub files to place it in use refs #29811
src/hg/utils/automation/asmHubChainNetTrackDb.sh
- lines changed 19, context: html, text, full: html, text
  92509db0231e9b1ae83aa0c85182883dd8eabc9b Wed Sep 14 13:59:35 2022 -0700
  fixup chainNet trackDb and now sending files to dynablat and arranging hub files to place it in use refs #29811
src/hg/utils/automation/asmHubChromAlias.pl
- lines changed 19, context: html, text, full: html, text
  f9ce722d011fb87c9f61a4d892b9140ef7fa9047 Mon Sep 12 20:38:56 2022 -0700
  now working through step chromAlias and fixup that procedure to work correctly on ucsc names refs #29811
- lines changed 13, context: html, text, full: html, text
  5308f161d60d310ffe5a80e7755e835ff7ea7a9f Tue Sep 13 12:47:32 2022 -0700
  OK to allow duplicate names no redmine
- lines changed 4, context: html, text, full: html, text
  0f9627d32b1a95d56c1078595924d387375e487d Tue Sep 13 14:37:39 2022 -0700
  the chromAlias needs to know about the NCBI asmId refs #29811
src/hg/utils/automation/asmHubGatewayPage.pl
- lines changed 4, context: html, text, full: html, text
  ad8d6746d5d68ff4e893262d2ff28d9b2a71ac26 Mon Sep 12 11:45:58 2022 -0700
  no longer any need for asmHubName argument to gateway page no redmine
- lines changed 7, context: html, text, full: html, text
  2248d4012416d220927d54ea0c47295560792625 Mon Sep 12 22:06:58 2022 -0700
  now working through gatewayPage although it needs to have URLs for downloads adjusted refs #29811
src/hg/utils/automation/asmHubNcbiGene.pl
- lines changed 10, context: html, text, full: html, text
  92509db0231e9b1ae83aa0c85182883dd8eabc9b Wed Sep 14 13:59:35 2022 -0700
  fixup chainNet trackDb and now sending files to dynablat and arranging hub files to place it in use refs #29811
src/hg/utils/automation/asmHubTrackDb.sh
- lines changed 23, context: html, text, full: html, text
  9595301c34b8e4818baa37a72eff7e5cbfcfcb4e Tue Sep 13 13:20:15 2022 -0700
  now working thru trackDb although the generated html needs to be fixed up refs #29811
- lines changed 21, context: html, text, full: html, text
  92509db0231e9b1ae83aa0c85182883dd8eabc9b Wed Sep 14 13:59:35 2022 -0700
  fixup chainNet trackDb and now sending files to dynablat and arranging hub files to place it in use refs #29811
- lines changed 2, context: html, text, full: html, text
  729ef3108c56a032423a2a3d47f454d671d1a89c Thu Sep 15 18:31:43 2022 -0700
  remove debug statement not needed no redmine
src/hg/utils/automation/asmHubWindowMasker.pl
- lines changed 3, context: html, text, full: html, text
  4d29ce62c5c76ed62d132f9e2ed05cfa61f7fc1a Fri Sep 16 10:04:48 2022 -0700
  can not use bare dollar sign in html text causes confusion for trackDb make refs #30012
src/hg/utils/automation/doAssemblyHub.pl
- lines changed 12, context: html, text, full: html, text
  ad8d6746d5d68ff4e893262d2ff28d9b2a71ac26 Mon Sep 12 11:45:58 2022 -0700
  no longer any need for asmHubName argument to gateway page no redmine
- lines changed 38, context: html, text, full: html, text
  03886581a00e4d626316a657c170287b1f266e35 Mon Sep 12 15:55:14 2022 -0700
  beginning a oneAndDone browser build script and therefore adding a new argument to the assembly build for a concise UCSC style dbName refs #29811
- lines changed 14, context: html, text, full: html, text
  f9ce722d011fb87c9f61a4d892b9140ef7fa9047 Mon Sep 12 20:38:56 2022 -0700
  now working through step chromAlias and fixup that procedure to work correctly on ucsc names refs #29811
- lines changed 9, context: html, text, full: html, text
  2248d4012416d220927d54ea0c47295560792625 Mon Sep 12 22:06:58 2022 -0700
  now working through gatewayPage although it needs to have URLs for downloads adjusted refs #29811
- lines changed 4, context: html, text, full: html, text
  8fcf6d7d3fd31a5f0ff9d1793ab00eec67c7b04d Mon Sep 12 22:12:21 2022 -0700
  now working thru gc5Base refs #29811
- lines changed 51, context: html, text, full: html, text
  7f813719b7ad2dde53149de49c2ec989b9630ea7 Tue Sep 13 12:09:58 2022 -0700
  now working through augustus step refs #29811
- lines changed 3, context: html, text, full: html, text
  9595301c34b8e4818baa37a72eff7e5cbfcfcb4e Tue Sep 13 13:20:15 2022 -0700
  now working thru trackDb although the generated html needs to be fixed up refs #29811
- lines changed 1, context: html, text, full: html, text
  0f9627d32b1a95d56c1078595924d387375e487d Tue Sep 13 14:37:39 2022 -0700
  the chromAlias needs to know about the NCBI asmId refs #29811
- lines changed 9, context: html, text, full: html, text
  92509db0231e9b1ae83aa0c85182883dd8eabc9b Wed Sep 14 13:59:35 2022 -0700
  fixup chainNet trackDb and now sending files to dynablat and arranging hub files to place it in use refs #29811
src/hg/utils/automation/oneAndDoneBrowser.sh
- lines changed 175, context: html, text, full: html, text
  03886581a00e4d626316a657c170287b1f266e35 Mon Sep 12 15:55:14 2022 -0700
  beginning a oneAndDone browser build script and therefore adding a new argument to the assembly build for a concise UCSC style dbName refs #29811
- lines changed 18, context: html, text, full: html, text
  f9ce722d011fb87c9f61a4d892b9140ef7fa9047 Mon Sep 12 20:38:56 2022 -0700
  now working through step chromAlias and fixup that procedure to work correctly on ucsc names refs #29811
- lines changed 11, context: html, text, full: html, text
  7f813719b7ad2dde53149de49c2ec989b9630ea7 Tue Sep 13 12:09:58 2022 -0700
  now working through augustus step refs #29811
- lines changed 40, context: html, text, full: html, text
  92509db0231e9b1ae83aa0c85182883dd8eabc9b Wed Sep 14 13:59:35 2022 -0700
  fixup chainNet trackDb and now sending files to dynablat and arranging hub files to place it in use refs #29811

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