Commits for hiram

v359_preview2 to v359_base (2017-12-11 to 2017-12-18) v359

8acb7920b83dc4ab19a7ea3f4d6fe6e00b40c40a Mon Dec 11 19:03:11 2017 -0800

• working fairly well outside UCSC environment refs #18874
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 112, context: html, text, full: html, text

93cb2e7253ed63c45e098f4d94ba873c18a29363 Tue Dec 12 13:43:36 2017 -0800

• adding v91 definitions refs #20696
  • src/hg/utils/automation/EnsGeneAutomate.pm - lines changed 353, context: html, text, full: html, text

7fadab3508b2b27ef03c1e60259e8c6a564483eb Tue Dec 12 13:51:57 2017 -0800

• correcting v91 definitions refs #20696
  • src/hg/utils/automation/EnsGeneAutomate.pm - lines changed 1, context: html, text, full: html, text

83981f86e707d9432c16723208f4c92fa3d5d753 Wed Dec 13 11:36:13 2017 -0800

• send hgCustom error messages to apache error log and commify the number of lines refs #20695
  • src/hg/hgCustom/hgCustom.c - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadBed/hgLoadBed.c - lines changed 3, context: html, text, full: html, text

5b084725369bcf0eab67fe011aa031de2e12d71d Thu Dec 14 09:53:41 2017 -0800

• check for 2bit file at the beginning refs #20696
  • src/hg/utils/automation/doIdKeys.pl - lines changed 4, context: html, text, full: html, text

56511591e22f84aa3d52b7170c08f6f0bd44c6dc Thu Dec 14 10:53:48 2017 -0800

• use actual URLs in the error message for data line limit refs #20541
  • src/hg/makeDb/hgLoadBed/hgLoadBed.c - lines changed 1, context: html, text, full: html, text

04bb3e4f6b8dc30d3c2b659d03a15e6d3980255b Fri Dec 15 09:36:20 2017 -0800

• the error message URLs to help doc should be relative references refs #20541
  • src/hg/makeDb/hgLoadBed/hgLoadBed.c - lines changed 1, context: html, text, full: html, text

d66c4e262de72e7ec06e5c24dce10dd69a600505 Fri Dec 15 14:37:35 2017 -0800

• fixing up chromAlias tables for new Ensembl v91 release refs #20696
  • src/hg/makeDb/doc/aotNan1/initialBuild.txt - lines changed 43, context: html, text, full: html, text
  • src/hg/makeDb/doc/cebCap1/initialBuild.txt - lines changed 42, context: html, text, full: html, text
  • src/hg/makeDb/doc/cerAty1/initialBuild.txt - lines changed 47, context: html, text, full: html, text
  • src/hg/makeDb/doc/colAng1/initialBuild.txt - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/doc/felCat8/initialBuild.txt - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/doc/gorGor4/initialBuild.txt - lines changed 99, context: html, text, full: html, text
  • src/hg/makeDb/doc/macFas5/initialBuild.txt - lines changed 121, context: html, text, full: html, text
  • src/hg/makeDb/doc/macNem1/initialBuild.txt - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/doc/manLeu1/initialBuild.txt - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/doc/micMur3/initialBuild.txt - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/doc/nomLeu3.txt - lines changed 74, context: html, text, full: html, text
  • src/hg/makeDb/doc/panPan2/initialBuild.txt - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/doc/panTro5/initialBuild.txt - lines changed 39, context: html, text, full: html, text
  • src/hg/makeDb/doc/proCoq1/initialBuild.txt - lines changed 42, context: html, text, full: html, text
  • src/hg/makeDb/doc/rhiBie1/initialBuild.txt - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/doc/rhiRox1/initialBuild.txt - lines changed 73, context: html, text, full: html, text
  • src/hg/makeDb/doc/saiBol1.txt - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/doc/tarSyr2/initialBuild.txt - lines changed 43, context: html, text, full: html, text

c501813df9f6a642b5523c817da4930ebb052b78 Fri Dec 15 14:49:22 2017 -0800

• ensGene v91 update procedure refs #20696
  • src/hg/makeDb/doc/makeEnsembl.txt - lines changed 104, context: html, text, full: html, text

3fdba4b89cc6b806d11c0040f4aadc77bf338f45 Sat Dec 16 08:32:06 2017 -0800

• done with build QA ready refs #20265
  • src/hg/makeDb/doc/eulFla1/initialBuild.txt - lines changed 4, context: html, text, full: html, text

5920f716b5c80b2430580c6241e618494303d417 Sat Dec 16 08:33:07 2017 -0800

• build in progress refs #19883
  • src/hg/makeDb/doc/neoSch1/initialBuild.txt - lines changed 57, context: html, text, full: html, text

8a4b1dbd2b586657fce97abec548578f8bbd4313 Sat Dec 16 08:34:35 2017 -0800

• QA ready refs #19937
  • src/hg/makeDb/doc/staAur1/initialBuild.txt - lines changed 268, context: html, text, full: html, text

c691f61b66a5040f3eb41babb1f8ef5f37a12300 Sat Dec 16 08:35:12 2017 -0800

• lastz chainNet tupChi1 to cavPor3 no redmine
  • src/hg/makeDb/doc/cavPor3.txt - lines changed 64, context: html, text, full: html, text

4bf397ff14cd06a9714f6fd89c530a6eecab7f86 Sat Dec 16 08:36:14 2017 -0800

• catching up a couple of result outputs refs #19665
  • src/hg/makeDb/doc/hg38/hg38Patch11.txt - lines changed 21, context: html, text, full: html, text

95a4e63664fb67eff044cf38bcbb9abfcebf2a2a Sat Dec 16 08:37:25 2017 -0800

• ensGene build v89 completed refs #19526
  • src/hg/makeDb/doc/danRer10/drBlastTab.txt - lines changed 28, context: html, text, full: html, text

760729304e81fdf6c338f81203a1735f2dffb5bb Sat Dec 16 08:40:30 2017 -0800

• fixup manual featureBits calculation and fixing recip best procedures refs #18874
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/automation/doRecipBest.pl - lines changed 40, context: html, text, full: html, text

cd77fe9cfc5d64ab7ba0bb0a759f9ebdb77037c5 Sat Dec 16 08:44:24 2017 -0800

• do not need the -lm since libm.a is now available in the hgwdev environment no redmine
  • src/hg/hgTracks/makefile - lines changed 1, context: html, text, full: html, text

8f6e01ecbc95a96dc24b64f027fbfcbf327e0537 Sat Dec 16 08:46:05 2017 -0800

• adding gold table search rule refs @20237
  • src/hg/makeDb/trackDb/primate/cebCap1/trackDb.ra - lines changed 5, context: html, text, full: html, text

7605a5c48a00769c900cd8d9485e368de1c837d3 Sat Dec 16 08:47:00 2017 -0800

• catching up with some new assemblies no redmine
  • src/hg/utils/phyloTrees/commonNames.sh - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/vertebrates.txt - lines changed 7, context: html, text, full: html, text

7aa626855041b85534cfa3855a924583e553d3c7 Sat Dec 16 08:48:21 2017 -0800

• improve output format refs #18969
  • src/utils/crisprKmers/crisprKmers.c - lines changed 2, context: html, text, full: html, text

69c0748fd0bb62b57cb9e7588ee086263f7fe955 Sat Dec 16 08:49:30 2017 -0800

• add gold table search rule and ncbiGene track refs #19937
  • src/hg/makeDb/trackDb/bacteria/staAur1/trackDb.ra - lines changed 17, context: html, text, full: html, text

a478c5eddb546a8a6c683f529b74e3567deedb2c Sat Dec 16 08:51:03 2017 -0800

• better recognition of common name refs #18706
  • src/hg/utils/automation/prepConfig.pl - lines changed 6, context: html, text, full: html, text

d63897007e6ea85ec4fd1d0d5f827ce08295a3fa Sat Dec 16 08:52:38 2017 -0800

• tweaking for hg38 stsMap build refs #15524
  • src/hg/pslFilterPrimers/pslFilterPrimers.c - lines changed 4, context: html, text, full: html, text

601b8695a7fb926e8019bff9d73d74ccddc4fc4a Sat Dec 16 20:49:10 2017 -0800

• cavPor3 6-way alignment no redmine
  • src/hg/htdocs/images/phylo/cavPor3_6way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

a6114beb5f9f5f73737c47c4db6efdf5c2437b38 Sat Dec 16 23:45:20 2017 -0800

• adding 6-way alignment no redmine
  • src/hg/makeDb/trackDb/guineaPig/cavPor3/cons6way.html - lines changed 424, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.5way.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.6way.ra - lines changed 102, context: html, text, full: html, text

b72a30eddc43cd4470521e6b40556004a1b8ec50 Sat Dec 16 23:47:47 2017 -0800

• adding 6-way alignment no redmine
  • src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.ra - lines changed 1, context: html, text, full: html, text

bd30e8ea58cec93fae6d5c2e1f100ecac40143d6 Sun Dec 17 09:07:50 2017 -0800

• hg38 5 way alignment no redmine;
  • src/hg/htdocs/images/phylo/hg38_5way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

0fbc37d8eca80218c7af2a7a03c6964d4837e9d6 Sun Dec 17 20:59:41 2017 -0800

• running up 6-way alignment no redmine
  • src/hg/makeDb/doc/cavPor3.txt - lines changed 1509, context: html, text, full: html, text

ff47ba19daadc0b6608d6069750d559b6c880af2 Mon Dec 18 09:52:54 2017 -0800

• v359 final build refs #20654
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text

a918c18ac10288dfd3c9e8742358ccd8dc890f18 Mon Dec 18 09:53:40 2017 -0800

• New version number v359
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text
  • src/inc/srcVersion.h - lines changed 1, context: html, text, full: html, text