Commits for markd

v477_preview2 to v477_base (2025-01-27 to 2025-02-03) v477

07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800

• work on docker utils build
  • src/hg/liftOver/makefile - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/hgGcPercent/makefile - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/hgGoldGapGl/makefile - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadBed/makefile - lines changed 82, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadMaf/makefile - lines changed 80, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadWiggle/makefile - lines changed 102, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/makefile - lines changed 40, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/pslCDnaFilter.c - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/bedExtendRanges/makefile - lines changed 19, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/makefile - lines changed 21, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/makefile - lines changed 19, context: html, text, full: html, text
  • src/hg/utils/hubCheck/makefile - lines changed 51, context: html, text, full: html, text
  • src/hg/utils/makeTableList/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/overlapSelect/makefile - lines changed 32, context: html, text, full: html, text
  • src/hg/utils/overlapSelect/overlapSelect.c - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/pslLiftSubrangeBlat/makefile - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/pslToBigPsl/makefile - lines changed 51, context: html, text, full: html, text
  • src/hg/utils/pslToBigPsl/tests/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/tdbQuery/makefile - lines changed 16, context: html, text, full: html, text
  • src/inc/cgiLoader.mk - lines changed 42, context: html, text, full: html, text
  • src/inc/common.mk - lines changed 40, context: html, text, full: html, text
  • src/inc/userApp.mk - lines changed 27, context: html, text, full: html, text
  • src/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/makefile - lines changed 6, context: html, text, full: html, text

4d1132fe8af3037e9bc3f4ff419151cebcc10fc1 Sun Jan 19 11:28:49 2025 -0800

• userApps working as before on hgwdev
  • src/ameme/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgGoldGapGl/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadWiggle/makefile - lines changed 20, context: html, text, full: html, text
  • src/hg/utils/chainToBigChain/makefile - lines changed 51, context: html, text, full: html, text
  • src/hg/utils/overlapSelect/makefile - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/inc/cgiLoader.mk - lines changed 21, context: html, text, full: html, text
  • src/inc/common.mk - lines changed 14, context: html, text, full: html, text
  • src/inc/userApp.mk - lines changed 3, context: html, text, full: html, text
  • src/utils/bedToBigBed/makefile - lines changed 64, context: html, text, full: html, text

1c002ea441ef48d4580156e0e80f23a8b7dc3eec Sun Jan 19 13:05:19 2025 -0800

• CGI loaders working
  • .gitignore - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/hgGoldGapGl/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadBed/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadMaf/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/hubCheck/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslToBigPsl/makefile - lines changed 1, context: html, text, full: html, text
  • src/inc/cgiLoader.mk - lines changed 14, context: html, text, full: html, text
  • src/inc/cgiVars.mk - lines changed 26, context: html, text, full: html, text
  • src/inc/cgi_build_rules.mk - lines changed 23, context: html, text, full: html, text

3542507725a5bdeceaf09f2e8376bbe5808a6a08 Sun Jan 19 13:45:13 2025 -0800

• use user cgi-bin for default make
  • src/inc/cgiLoader.mk - lines changed 1, context: html, text, full: html, text
  • src/inc/cgiVars.mk - lines changed 4, context: html, text, full: html, text

8f59e41056ede9739e9b9ea81d52443c18ad90dd Tue Jan 21 22:14:04 2025 -0800

• with specific user
  • src/inc/cgiVars.mk - lines changed 4, context: html, text, full: html, text
  • src/inc/common.mk - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/weeklybld/userApps.dockerfile - lines changed 55, context: html, text, full: html, text
  • src/utils/qa/weeklybld/userAppsCompileInDocker - lines changed 48, context: html, text, full: html, text
  • src/utils/qa/weeklybld/userAppsCreateDockerImage - lines changed 21, context: html, text, full: html, text

f1e2c1529d1222a0793a30bc4997a65e6f6694c9 Wed Jan 22 07:40:55 2025 -0800

• run docker as current user
  • src/utils/qa/weeklybld/makeUserApps.csh - lines changed 8, context: html, text, full: html, text
  • src/utils/qa/weeklybld/userApps.dockerfile - lines changed 20, context: html, text, full: html, text
  • src/utils/qa/weeklybld/userAppsCompileInDocker - lines changed 29, context: html, text, full: html, text
  • src/utils/qa/weeklybld/userAppsCreateDockerImage - lines changed 8, context: html, text, full: html, text

c2da02cbbc11577b49eddb96740144ec4f24e872 Tue Jan 28 18:59:29 2025 -0800

• add script to check that SEMI_STATIC userApp are linked with only the allowed shared libraries
  • src/inc/userApp.mk - lines changed 6, context: html, text, full: html, text
  • src/utils/qa/weeklybld/userAppsCheckLinking - lines changed 36, context: html, text, full: html, text
  • src/utils/qa/weeklybld/userAppsCompileInDocker - lines changed 11, context: html, text, full: html, text

7478677e5ba8806f2ffde474524dccd6fc37ed72 Thu Jan 30 20:10:01 2025 -0800

• added my old tabFmt command due to popular demand
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/tabFmt/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/tabFmt/tabFmt.c - lines changed 274, context: html, text, full: html, text
  • src/utils/tabFmt/tests/expected/defaultTest.txt - lines changed 8, context: html, text, full: html, text
  • src/utils/tabFmt/tests/expected/numRightPassNoTabTest.txt - lines changed 15, context: html, text, full: html, text
  • src/utils/tabFmt/tests/expected/numRightTest.txt - lines changed 8, context: html, text, full: html, text
  • src/utils/tabFmt/tests/expected/passNoTabTest.txt - lines changed 13, context: html, text, full: html, text
  • src/utils/tabFmt/tests/expected/rightTest.txt - lines changed 8, context: html, text, full: html, text
  • src/utils/tabFmt/tests/expected/specialTest.txt - lines changed 3, context: html, text, full: html, text
  • src/utils/tabFmt/tests/input/basic.tab - lines changed 8, context: html, text, full: html, text
  • src/utils/tabFmt/tests/input/numRightPassNoTab.tab - lines changed 15, context: html, text, full: html, text
  • src/utils/tabFmt/tests/input/special.tab - lines changed 3, context: html, text, full: html, text
  • src/utils/tabFmt/tests/input/statsLabels.tab - lines changed 13, context: html, text, full: html, text
  • src/utils/tabFmt/tests/makefile - lines changed 39, context: html, text, full: html, text

ed2c9e2f464996fffa38546987be244ada38c07a Fri Jan 31 19:42:06 2025 -0800

• echo the docker run command when building userApps
  • src/utils/qa/weeklybld/userAppsCompileInDocker - lines changed 3, context: html, text, full: html, text