Commits for kent

v335_base to v336_preview (2016-07-04 to 2016-07-11) v336

ca4f189d5ff96544ae97d110590c8a168e8c5ae4 Wed Jun 29 12:57:18 2016 -0700

• Improving usage message.
  
  • src/hg/cirm/cdw/cdwChangeAccess/cdwChangeAccess.c - lines changed 4, context: html, text, full: html, text

711aa7e038188c526492e407cf0afb63c44ffbab Wed Jun 29 12:57:48 2016 -0700

• Improving usage statement.
  
  • src/hg/cirm/cdw/cdwGroupFile/cdwGroupFile.c - lines changed 4, context: html, text, full: html, text

f0174240d1c0716a6bbe71bc3be4bdd6517cb57b Wed Jun 29 12:58:55 2016 -0700

• Making it set initial permissions of files based on access metadata tag. Removing life_stage from required fields list.
  
  • src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c - lines changed 39, context: html, text, full: html, text

851f04b27b65e968b4476cf13b87528916237e3e Thu Jul 7 10:02:14 2016 -0700

• Making system look for paired end just within same submission directory.
  
  • src/hg/cirm/cdw/cdwMakePairedEndQa/cdwMakePairedEndQa.c - lines changed 1, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwQaEvaluate/cdwQaEvaluate.c - lines changed 1, context: html, text, full: html, text
  • src/hg/cirm/cdw/inc/cdwLib.h - lines changed 1, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwLib.c - lines changed 3, context: html, text, full: html, text

d7edb65495f80479330fb733533505cc2a55895f Thu Jul 7 10:02:54 2016 -0700

• Stripping NOSQLINJ out of error message to prevent an error when sticking error message into database.
  
  • src/hg/cirm/cdw/cdwRunDaemon/cdwRunDaemon.c - lines changed 1, context: html, text, full: html, text

968e50be18fd23411e431708c37a4c2c5f385981 Thu Jul 7 19:23:21 2016 -0700

• Making cdwReserveTempFile make file with our normal permissions.
  
  • src/hg/cirm/cdw/lib/cdwLib.c - lines changed 2, context: html, text, full: html, text

f6807cb2b73ec99113aad8cf086dc5d429d0db40 Thu Jul 7 19:24:55 2016 -0700

• Removing makeReadableTemp and replacing it with calls to cdwReserveTempFile, which now makes readable files as well.
  
  • src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c - lines changed 13, context: html, text, full: html, text