Commits for hiram

v332_base to v333_preview (2016-05-02 to 2016-05-09) v333

c8a3f2f43eb4f12007408a767bce133ab98bcfde Mon May 2 14:07:34 2016 -0700

• gBiB v332 now using new gateway phylo tree image refs #17202
  
  • src/browserbox/usr/local/apache/cgi-bin/hg.conf - lines changed 3, context: html, text, full: html, text

d390a45c2e67726a563a7db85c3139793c7cc05c Tue May 3 12:19:31 2016 -0700

• lastz run to galGal1 refs #17180
  
  • src/hg/makeDb/doc/mm10.txt - lines changed 66, context: html, text, full: html, text

9d85b4c0cb35e2be8b1b41277d7d5a7e1d79aaa3 Tue May 3 12:48:49 2016 -0700

• 5-way phylo tree for Malayan flying lemur refs #17180
  
  • src/hg/htdocs/images/phylo/galVar1_5way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

aa8251bd333deaa55fff02b1df38775160e0ab58 Tue May 3 14:01:27 2016 -0700

• 5-way multiz done refs #17180
  
  • src/hg/makeDb/doc/galVar1/lastzRuns.txt - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/doc/galVar1/multiz5way.txt - lines changed 1564, context: html, text, full: html, text

5399f1fc35a8da92c078bf4753235fab3b02c268 Tue May 3 14:57:18 2016 -0700

• lastz run on galVar1 refs #17180
  
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 69, context: html, text, full: html, text

1f78713caba1393510be4f29850bc395074f0492 Tue May 3 15:18:59 2016 -0700

• adding multiz 5-way alignment track refs #17180
  
  • src/hg/makeDb/trackDb/galVar/galVar1/trackDb.5way.ra - lines changed 102, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/galVar/galVar1/trackDb.ra - lines changed 7, context: html, text, full: html, text

3d953a2264e19f75f2ff2f26efb04ef9ddf31830 Tue May 3 15:42:04 2016 -0700

• no frames yet refs #17180
  
  • src/hg/makeDb/trackDb/galVar/galVar1/trackDb.5way.ra - lines changed 2, context: html, text, full: html, text

0828e268f41122eb4a3d48b22a823b9151c37fdb Tue May 3 15:51:27 2016 -0700

• adding 5-way multiz refs #17180
  
  • src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.5way.ra - lines changed 102, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.ra - lines changed 2, context: html, text, full: html, text

4d05ee12364aabb2ea43c2751538ef834001d77b Tue May 3 16:20:18 2016 -0700

• correct grep command to find running boxes refs #17202
  
  • src/utils/qa/weeklybld/boxRelease.csh - lines changed 2, context: html, text, full: html, text

c925f0b56667c9987c4c16f3833f78b15d248d6e Thu May 5 10:02:29 2016 -0700

• gap annotation done refs #17180
  
  • src/hg/makeDb/doc/galVar1/multiz5way.txt - lines changed 24, context: html, text, full: html, text

18e1d22e10b537ad3813c365bd4cae8c59f59d87 Thu May 5 12:31:53 2016 -0700

• handle the case of no curated genes and sparse/missing description text refs #13673
  
  • src/hg/utils/automation/accRsu.pl - lines changed 21, context: html, text, full: html, text
  • src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 27, context: html, text, full: html, text

798885291382ef8378541aca4da24d307b05f02b Thu May 5 15:12:26 2016 -0700

• turning on frames feature refs #17180
  
  • src/hg/makeDb/trackDb/galVar/galVar1/trackDb.5way.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.5way.ra - lines changed 2, context: html, text, full: html, text

033b8ed0e57429271ce63c0e781d75df5a958a0a Thu May 5 15:19:44 2016 -0700

• 5-way phylo tree for cavPor3 refs #17180
  
  • src/hg/htdocs/images/phylo/cavPor3.5way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

b47d3a1cba5a433a2b145e1021ccb3f52deb2ae1 Thu May 5 15:25:55 2016 -0700

• 5-way phylo tree for cavPor3 refs #17180
  
  • src/hg/htdocs/images/phylo/cavPor3_5way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

329d0f2f0ebe4a6a826c4db6bfdd60392e416442 Thu May 5 15:29:13 2016 -0700

• frames done refs #17180
  
  • src/hg/makeDb/doc/galVar1/multiz5way.txt - lines changed 113, context: html, text, full: html, text

fb489d6bfc25b542c4cca14e61e38c3eb1353298 Thu May 5 15:29:45 2016 -0700

• multiz5way frames done refs #17180
  
  • src/hg/makeDb/doc/cavPor3.txt - lines changed 1501, context: html, text, full: html, text

7276e8318a5765c41ca1183ac4941f39f910ea51 Thu May 5 15:30:53 2016 -0700

• incorrect name for 5way.png
  
  • src/hg/htdocs/images/phylo/cavPor3.5way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

fbdd2992e994a348c9b2d14922f872d85edc66f7 Mon May 9 09:58:19 2016 -0700

• adding chainCleaner code from Michael Hiller refs #17286
  
  • src/hg/mouseStuff/chainCleaner/NetFilterNonNested.perl - lines changed 462, context: html, text, full: html, text
  • src/hg/mouseStuff/chainCleaner/chainCleaner.c - lines changed 1900, context: html, text, full: html, text
  • src/hg/mouseStuff/chainCleaner/makefile - lines changed 3, context: html, text, full: html, text

b05b7e03048f62c7a326227876ca7153843f08fe Mon May 9 10:08:59 2016 -0700

• v333 preview1 refs #17287
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text