All File Changes

v423_preview to v423_preview2 (2021-10-25 to 2021-11-01) v423

• .gitignore
  • lines changed 48, context: html, text, full: html, text
    7ac25ae99f0b09760b750e88afb5b8711380cfd5 Mon Oct 25 14:24:46 2021 -0700
    improve gitingore to make it easier to check for forgotten commits'
  • lines changed 3, context: html, text, full: html, text
    1288a4961387d06d4a5458ae493f7ad25f88e932 Fri Oct 29 14:59:22 2021 -0700
    add more to .gitignore
• src/hg/cgilib/gtexBoxplot.c
  • lines changed 1, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 3, context: html, text, full: html, text
    c3f13e90a8837357a7f4bdf8d07ddfc3ea7ab9b5 Sat Oct 30 01:01:38 2021 -0700
    CIRM: finished fixing cdwWebBrowse to be compatible with Jims variable name change.
• src/hg/hgGene/rnaStructure.c
  • lines changed 3, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 35, context: html, text, full: html, text
    61a71c293d9ad89a53d4d8f7729915015a7ab9dd Thu Oct 28 09:33:19 2021 -0700
    Adding links, updating format, and changing wording for hubConnect page. Refs #28324
  • lines changed 3, context: html, text, full: html, text
    e71297f98349413d94cb9663901d874dd587ad9f Fri Oct 29 09:57:22 2021 -0700
    Adding back link to hosting to main page since it's a common MLQ refs #28324
  • lines changed 1, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 1, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 2, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/hg/hgSession/backup.c
  • lines changed 1, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/hg/hgSession/hgSession.c
  • lines changed 2, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/hg/hgc/barChartClick.c
  • lines changed 1, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/hg/hgc/hgdpClick.c
  • lines changed 3, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/hg/hgc/rnaFoldClick.c
  • lines changed 2, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/hg/htdocs/goldenPath/help/query.html
  • lines changed 17, context: html, text, full: html, text
    436dedc0123ecccf59296615c87beccb3ecdb8bd Tue Oct 26 17:55:03 2021 -0700
    Updating query examples with new ones and removing an old broken one refs #28072
• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 1, context: html, text, full: html, text
    68aa5b78633877fa3b395918d10a9493826c214c Fri Oct 29 10:30:18 2021 -0700
    Changing wording of Third Party Mirrors to Euro/Asia Mirrors in menu -noticed when helping users in live WebEx conference refs #28402
  • lines changed 1, context: html, text, full: html, text
    66bb7aa580ffafaa007b73d98caf714ede06683d Fri Oct 29 11:58:40 2021 -0700
    turning on google analytics for static pages (i.e. hgdownload) no redmine
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    68aa5b78633877fa3b395918d10a9493826c214c Fri Oct 29 10:30:18 2021 -0700
    Changing wording of Third Party Mirrors to Euro/Asia Mirrors in menu -noticed when helping users in live WebEx conference refs #28402
• src/hg/htdocs/training/index.html
  • lines changed 30, context: html, text, full: html, text
    276d219f7bb003efd10c060cf38f773b74cd4041 Sun Oct 31 15:57:33 2021 -0700
    updating to remove completed workshops
  • lines changed 44, context: html, text, full: html, text
    6e4a9a6b4386c954aea09f0dc3b6adb4c9338d5c Sun Oct 31 16:08:57 2021 -0700
    rearranged videos to put Basics first
• src/hg/inc/partitionSort.h
  • lines changed 1, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/hg/js/analytics.js
  • lines changed 2, context: html, text, full: html, text
    4fe89c911c3147acf9d10c512bbfbb61b2c2e4d3 Wed Oct 27 15:36:25 2021 -0700
    adding a key for hgdownload refs #26352
• src/hg/lib/customAdjacency.c
  • lines changed 1, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/hg/lib/customFactory.c
  • lines changed 8, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 11, context: html, text, full: html, text
    c145bf5570f99207de8810661ce1f88691780e02 Mon Oct 25 13:03:30 2021 -0700
    catching up with 11 bird VGP assemblies no redmine
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 14, context: html, text, full: html, text
    c145bf5570f99207de8810661ce1f88691780e02 Mon Oct 25 13:03:30 2021 -0700
    catching up with 11 bird VGP assemblies no redmine
• src/hg/makeDb/doc/hg38/gtexCov.txt
  • lines changed 9, context: html, text, full: html, text
    20e0ec9de93e6ac1012120e23edc98bd3dc81079 Thu Oct 28 01:48:20 2021 -0700
    adding makedoc for gtexcov track, refs #27964
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    33c101c3b16cef3a6f5510b97574260f9ed172cd Wed Oct 27 10:55:43 2021 -0700
    some birds have become legacy refs #28411
• src/hg/makeDb/doc/oviAri3.txt
  • lines changed 101, context: html, text, full: html, text
    1519f260b2bc9fca15f37cd26496b7cd5e5b2383 Fri Oct 29 17:59:39 2021 -0700
    oviAri3 vs. sheep GCF_002742125.1 lastz/chain/net run for user, refs #28409
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 10, context: html, text, full: html, text
    c5fcd4806b4831b7fc96ab7965547a6943e75d76 Mon Oct 25 13:44:23 2021 -0700
    catching up some bird assemblies no redmine
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 25, context: html, text, full: html, text
    c5fcd4806b4831b7fc96ab7965547a6943e75d76 Mon Oct 25 13:44:23 2021 -0700
    catching up some bird assemblies no redmine
• src/hg/makeDb/hgLoadMafFrames/hgLoadMafFrames.c
  • lines changed 1, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/hg/makeDb/hgLoadPsl/hgLoadPsl.c
  • lines changed 4, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/hg/makeDb/trackDb/human/dbSnp153Composite.html
  • lines changed 11, context: html, text, full: html, text
    9a31f94233618b5b6c16814d550efddc226d5340 Thu Oct 28 16:29:22 2021 -0700
    minor wording changes
• src/hg/makeDb/trackDb/human/hg19/dbSnpArchiveHg19.ra
  • lines changed 1, context: html, text, full: html, text
    d39f4ea234530e50d795fc17f2aab02e497c935d Wed Oct 27 16:01:51 2021 -0700
    Squashing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    d39f4ea234530e50d795fc17f2aab02e497c935d Wed Oct 27 16:01:51 2021 -0700
    Squashing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV38lift37.ra
  • lines changed 1, context: html, text, full: html, text
    d39f4ea234530e50d795fc17f2aab02e497c935d Wed Oct 27 16:01:51 2021 -0700
    Squashing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg38/dbSnpArchiveHg38.ra
  • lines changed 1, context: html, text, full: html, text
    d39f4ea234530e50d795fc17f2aab02e497c935d Wed Oct 27 16:01:51 2021 -0700
    Squashing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 2, context: html, text, full: html, text
    d39f4ea234530e50d795fc17f2aab02e497c935d Wed Oct 27 16:01:51 2021 -0700
    Squashing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    d39f4ea234530e50d795fc17f2aab02e497c935d Wed Oct 27 16:01:51 2021 -0700
    Squashing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV38.ra
  • lines changed 1, context: html, text, full: html, text
    d39f4ea234530e50d795fc17f2aab02e497c935d Wed Oct 27 16:01:51 2021 -0700
    Squashing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/human/revel.ra
  • lines changed 1, context: html, text, full: html, text
    d39f4ea234530e50d795fc17f2aab02e497c935d Wed Oct 27 16:01:51 2021 -0700
    Squashing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/mouse/mm10/dbSnpArchiveMm10.ra
  • lines changed 1, context: html, text, full: html, text
    d39f4ea234530e50d795fc17f2aab02e497c935d Wed Oct 27 16:01:51 2021 -0700
    Squashing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    d39f4ea234530e50d795fc17f2aab02e497c935d Wed Oct 27 16:01:51 2021 -0700
    Squashing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM27.ra
  • lines changed 1, context: html, text, full: html, text
    d39f4ea234530e50d795fc17f2aab02e497c935d Wed Oct 27 16:01:51 2021 -0700
    Squashing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    d39f4ea234530e50d795fc17f2aab02e497c935d Wed Oct 27 16:01:51 2021 -0700
    Squashing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.html
  • lines changed 4, context: html, text, full: html, text
    319b4cb808712fd5ef90e41eb89415908174b7ee Wed Oct 27 13:07:56 2021 -0700
    added a comment about pseudouracil
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMutsV2.html
  • lines changed 1, context: html, text, full: html, text
    38f9fc31b536f3b5a2c8bbe5c5b7d3d6b37855eb Wed Oct 27 11:12:54 2021 -0700
    Changing phrasing for CR refs #28396
• src/hg/utils/automation/pairLastz.sh
  • lines changed 26, context: html, text, full: html, text
    210af3aaa6d9d894afa8ee28875526cc3428e41e Wed Oct 27 10:30:16 2021 -0700
    now sending email upon completion refs #28409
• src/hg/utils/hubClone/hubClone.c
  • lines changed 1, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/inc/pipeline.h
  • lines changed 3, context: html, text, full: html, text
    902dd7f624e16a660ad582533f264b720ffcdb41 Thu Oct 28 12:07:31 2021 -0700
    don't create a process group on pipelineOpen, stay in the parent process group
  • lines changed 3, context: html, text, full: html, text
    86bb9f0fdcc838887b2d4a84154eea0e0f7b8631 Fri Oct 29 14:57:24 2021 -0700
    Revert "don't create a process group on pipelineOpen, stay in the parent process group" Another appoch is going to be tried to kill runaway process that requires the process group. This reverts commit 902dd7f624e16a660ad582533f264b720ffcdb41.
  • lines changed 17, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/lib/dnaMotif.c
  • lines changed 2, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/lib/linefile.c
  • lines changed 3, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/lib/mailViaPipe.c
  • lines changed 1, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/lib/md5.c
  • lines changed 2, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/lib/pipeline.c
  • lines changed 113, context: html, text, full: html, text
    902dd7f624e16a660ad582533f264b720ffcdb41 Thu Oct 28 12:07:31 2021 -0700
    don't create a process group on pipelineOpen, stay in the parent process group
  • lines changed 113, context: html, text, full: html, text
    86bb9f0fdcc838887b2d4a84154eea0e0f7b8631 Fri Oct 29 14:57:24 2021 -0700
    Revert "don't create a process group on pipelineOpen, stay in the parent process group" Another appoch is going to be tried to kill runaway process that requires the process group. This reverts commit 902dd7f624e16a660ad582533f264b720ffcdb41.
  • lines changed 45, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/lib/psGfx.c
  • lines changed 1, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/lib/tests/expected/pipelineExecError.parent.err
  • lines changed 1, context: html, text, full: html, text
    902dd7f624e16a660ad582533f264b720ffcdb41 Thu Oct 28 12:07:31 2021 -0700
    don't create a process group on pipelineOpen, stay in the parent process group
  • lines changed 1, context: html, text, full: html, text
    86bb9f0fdcc838887b2d4a84154eea0e0f7b8631 Fri Oct 29 14:57:24 2021 -0700
    Revert "don't create a process group on pipelineOpen, stay in the parent process group" Another appoch is going to be tried to kill runaway process that requires the process group. This reverts commit 902dd7f624e16a660ad582533f264b720ffcdb41.
• src/lib/tests/expected/pipelineTimeout.parent.err
  • lines changed 2, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/lib/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/lib/tests/pipelineTester.c
  • lines changed 8, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/lib/textOut.c
  • lines changed 1, context: html, text, full: html, text
    6f949e90b1ba3de976455fbcf9da21897761d134 Fri Oct 29 16:11:58 2021 -0700
    add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    e309ecc2117e8b1eefe17075279d8c6eac26372d Mon Nov 1 10:01:07 2021 -0700
    v423 preview2

• lines changed: 778
• files changed: 71