Keeping sandbox tracks separated on hgwdev: Difference between revisions

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(Created page with "If you want your own trackDb hierarchy whic is not in git and shows up only in your sandbox and will never appear on hgwdev there a few steps: * add another "sandbox-only" track...")
 
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   EXTRA=-sqlDir=~kent/src/hg/lib
   EXTRA=-sqlDir=~kent/src/hg/lib
   REALTRACKDBDIR=~kent/src/hg/makeDb/trackDb
   REALTRACKDBDIR=~kent/src/hg/makeDb/trackDb
   update:
   update:
           $(REALTRACKDBDIR)/loadTracks ${EXTRA} trackDb_${USER} hgFindSpec_${USER} ${DBS}
           $(REALTRACKDBDIR)/loadTracks ${EXTRA} trackDb_${USER} hgFindSpec_${USER} ${DBS}
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* create directories under this trackDb directory in the same way as they are under kent/src/hg/makeDb/trackDb, e.g. human/hg19
* create directories under this trackDb directory in the same way as they are under kent/src/hg/makeDb/trackDb, e.g. human/hg19
* don't forget to create empty trackDb.ra files in all these dirs and subdirs
* don't forget to create empty trackDb.ra files in all these dirs and subdirs, e.g.
mkdir -p human/hg19
touch human/trackDb.ra
 
* Now you can cd to usr/trackDb and do a  
* Now you can cd to usr/trackDb and do a  
   make update DBS=hg19
   make update DBS=hg19
* the tracks should now live completely separate in your sandbox and won't be part of the git source tree
* the tracks should now live completely separate in your sandbox and won't be part of the git source tree

Latest revision as of 21:18, 14 June 2012

If you want your own trackDb hierarchy whic is not in git and shows up only in your sandbox and will never appear on hgwdev there a few steps:

  • add another "sandbox-only" trackDb entry to your hg.conf, after a comma, e.g. trackDb_<user>_sandbox so the whole trackDb statement reads:
 db.trackDb=trackDb_<user>,trackDb_<user>_sandbox
  • create a directory for your own trackDb hierarchy, e.g. ~usr/trackDb
  • define the variable USER in the makefile and set it to <user>_sandbox e.g.
 USER=max_sandbox
  • you need to instruct loadTables to read the right sql file and modify the makefile to find the right scripts

The final makefile in ~/usr/trackDb should look like this:

 USER=maxSandbox
 EXTRA=-sqlDir=~kent/src/hg/lib
 REALTRACKDBDIR=~kent/src/hg/makeDb/trackDb
 update:
         $(REALTRACKDBDIR)/loadTracks ${EXTRA} trackDb_${USER} hgFindSpec_${USER} ${DBS}
         $(REALTRACKDBDIR)/checkMetaDb alpha metaDb_${USER} ${DBS}
  • create directories under this trackDb directory in the same way as they are under kent/src/hg/makeDb/trackDb, e.g. human/hg19
  • don't forget to create empty trackDb.ra files in all these dirs and subdirs, e.g.

mkdir -p human/hg19 touch human/trackDb.ra

  • Now you can cd to usr/trackDb and do a
 make update DBS=hg19
  • the tracks should now live completely separate in your sandbox and won't be part of the git source tree