Commits for hiram

v476_preview2 to v476_base (2025-01-06 to 2025-01-13) v476

4e20c4ec97228975702e46227080f1a7ea14a1e7 Tue Jan 7 13:08:52 2025 -0800

• adding phyloP for 241-way data refs #35032add
  • src/hg/makeDb/trackDb/cat/felCat8/trackDb.241way.ra - lines changed 15, context: html, text, full: html, text

ff6a56bb89e1bdb95a639ba1e89c8a917c0e7cc8 Tue Jan 7 13:09:17 2025 -0800

• adding phyloP for 241-way data refs #35032
  • src/hg/makeDb/trackDb/cat/felCat8/trackDb.ra - lines changed 2, context: html, text, full: html, text

fac69064e72ae464ea9f34d137cd0a7bc38a0ee2 Tue Jan 7 13:15:53 2025 -0800

• adding phyloP for 241-way data refs #35032
  • src/hg/makeDb/doc/felCat8/cactus241way.txt - lines changed 154, context: html, text, full: html, text

eab384506ebd6032e9bdb874ff1007449f1e7cf4 Thu Jan 9 16:02:50 2025 -0800

• adding a couple per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv - lines changed 2, context: html, text, full: html, text

5d3f8e7077604794f7eef4181971e7ab1f901216 Fri Jan 10 15:20:01 2025 -0800

• broken build extra space sonLib .a no redmine
  • src/inc/common.mk - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

18db2d3611d35ea9df50bd5773fda2925299a2a4 Sat Jan 11 14:44:58 2025 -0800

• adding hgwdev-new temporarily for testing on the new hgwdev machine refs #34990
  • src/hg/utils/automation/HgAutomate.pm - lines changed 5, context: html, text, full: html, text

d3eeae30481c6834f1b1505f6220f2ac07d40fa1 Sun Jan 12 11:56:00 2025 -0800

• adding per user request and testing new hgwdev for building assemblies refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 1, context: html, text, full: html, text

12cbc1fdde9c30c87616b8bb86dbbad764a55129 Mon Jan 13 09:19:55 2025 -0800

• clean up the duplicated -lm and use static zlib and bz2lib when available refs #35048
  • src/ameme/makefile - lines changed 1, context: html, text, full: html, text
  • src/inc/common.mk - lines changed 19, context: html, text, full: html, text

714017d05fd5c43c04909b45b79023859619e520 Mon Jan 13 09:55:40 2025 -0800

• eliminate the duplication of the -lm library refs #35048
  • src/hg/altSplice/affySplice/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/altSplice/agxToXml/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/altSplice/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/axtCountBeds/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/altSplice/exonWalk/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/altSplice/filterEdges/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/altSplice/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/spliceWalk/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwCreateUser/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/orthoMap/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/raSqlQuery/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/tdbQuery/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/bedClip/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/bedGraphToBigWig/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/bedPileUps/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/bedToBigBed/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/bigBedInfo/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/bigBedNamedItems/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/bigBedSummary/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/bigBedToBed/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/bigWigAverageOverBed/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/bigWigInfo/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/bigWigMerge/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/bigWigSummary/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/bigWigToBedGraph/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/bigWigToWig/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/twoBitDup/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/wigCorrelate/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/wigToBigWig/makefile - lines changed 1, context: html, text, full: html, text

153a91e0067b0c2ccc9988dfb2a82507a8c8589f Mon Jan 13 10:27:33 2025 -0800

• eliminate the duplication of the -lm library refs #35048
  • src/hg/affyTransciptome/makefile - lines changed 1, context: html, text, full: html, text