File Changes for hiram

v238_preview to v238_base (2010-08-10 to 2010-08-17) v238

• src/cdnaAli/g2cCheck/makefile
  • lines changed 7, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/blastToPsl/makefile
  • lines changed 2, context: html, text, full: html, text
    properly clean everything during clean target
  • lines changed 1, context: html, text, full: html, text
    fixup test target to use compile and to clean up after test
  • lines changed 8, context: html, text, full: html, text
    properly compile target for test target and cleanup after
• src/hg/blastToPsl/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    properly compile target for test target and cleanup after
• src/hg/embossToPsl/makefile
  • lines changed 4, context: html, text, full: html, text
    fixing test target in fixed makefiles
  • lines changed 6, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/estOrient/makefile
  • lines changed 13, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/fishClones/makefile
  • lines changed 11, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/genePredHisto/makefile
  • lines changed 1, context: html, text, full: html, text
    properly clean everything during clean target
  • lines changed 13, context: html, text, full: html, text
    fixup test target to use compile and to clean up after test
• src/hg/genePredHisto/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    properly use ../testBinary in test makefiles
• src/hg/genePredSingleCover/makefile
  • lines changed 1, context: html, text, full: html, text
    properly clean everything during clean target
  • lines changed 11, context: html, text, full: html, text
    fixup test target to use compile and to clean up after test
• src/hg/genePredSingleCover/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    properly use ../testBinary in test makefiles
• src/hg/genePredToMafFrames/makefile
  • lines changed 1, context: html, text, full: html, text
    properly clean everything during clean target
  • lines changed 11, context: html, text, full: html, text
    fixup test target to use compile and to clean up after test
• src/hg/hgChroms/makefile
  • lines changed 8, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/lib/ensGtp.sql
  • lines changed 2, context: html, text, full: html, text
    need 24 characters not just 23 for other name
  • lines changed 3, context: html, text, full: html, text
    longer names for ensembl proteins first seen in mm9
• src/hg/lib/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    can remove the loader symlink after the custom track test is done to keep source tree cleaner
• src/hg/lib/wigDataStream.c
  • lines changed 7, context: html, text, full: html, text
    use hAllocConn instead of sqlConnect
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 6, context: html, text, full: html, text
    update note about lifting Ensembl EF2 sequence to sacCer2 coordinates
  • lines changed 39, context: html, text, full: html, text
    done with all organisms for v59
  • lines changed 19, context: html, text, full: html, text
    finished the ce9 ensGenes
  • lines changed 269, context: html, text, full: html, text
    finished with the broken bits
  • lines changed 850, context: html, text, full: html, text
    starting ensembl v59 update
• src/hg/makeDb/hgTomRough/makefile
  • lines changed 8, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/mouseStuff/simpleChain/makefile
  • lines changed 6, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/nci60/makefile
  • lines changed 3, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/overlapSelect/makefile
  • lines changed 5, context: html, text, full: html, text
    fixing test target in fixed makefiles
  • lines changed 8, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/pslCDnaFilter/makefile
  • lines changed 5, context: html, text, full: html, text
    fixing test target in fixed makefiles
  • lines changed 8, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/pslDiff/makefile
  • lines changed 2, context: html, text, full: html, text
    fixing test target in fixed makefiles
  • lines changed 7, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/pslFilterPrimers/makefile
  • lines changed 7, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/pslMap/makefile
  • lines changed 4, context: html, text, full: html, text
    fixing test target in fixed makefiles
  • lines changed 12, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/pslPairs/makefile
  • lines changed 10, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/pslPartition/makefile
  • lines changed 2, context: html, text, full: html, text
    properly clean everything during clean target
  • lines changed 1, context: html, text, full: html, text
    fixup test target to use compile and to clean up after test
  • lines changed 2, context: html, text, full: html, text
    fixing test target in fixed makefiles
  • lines changed 7, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/pslQuickFilter/makefile
  • lines changed 10, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/pslSwap/makefile
  • lines changed 2, context: html, text, full: html, text
    fixing test target in fixed makefiles
  • lines changed 9, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/sage/makefile
  • lines changed 16, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/snp/snpValid/makefile
  • lines changed 11, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/spideyToPsl/makefile
  • lines changed 3, context: html, text, full: html, text
    fixing test target in fixed makefiles
  • lines changed 6, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/uniqSize/makefile
  • lines changed 7, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/updateStsInfo/makefile
  • lines changed 11, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/utils/automation/ensGeneScaffolds.pl
  • lines changed 1, context: html, text, full: html, text
    allow scaffold names of ^Scaffold for macEug1
• src/inc/common.mk
  • lines changed 1, context: html, text, full: html, text
    adding -lcrypto to -lssl
• src/lib/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    can remove fetchUrlTest at end of tests and during clean
• src/product/COPYRIGHT
  • lines changed 1, context: html, text, full: html, text
    no need to mention a version or date stamp
• src/product/README.cvs.access
  • lines changed 75, context: html, text, full: html, text
    irrelevant files since changing to git
• src/product/README.install
  • lines changed 1, context: html, text, full: html, text
    point to updateHtml.sh instead of the rsync to fetch htdocs
  • lines changed 157, context: html, text, full: html, text
    updated to eliminate references to a CDROM
• src/product/README.local.cvs.source
  • lines changed 146, context: html, text, full: html, text
    irrelevant file since git introduction
• src/product/ex.InstallExample
  • lines changed 128, context: html, text, full: html, text
    the makefile and ex.InstallExample are no longer relevant
• src/product/ex.MySQLUserPerms.sh
  • lines changed 9, context: html, text, full: html, text
    fixup permission grant statements to use FILE properly
• src/product/ex.cvsup.pl
  • lines changed 183, context: html, text, full: html, text
    irrelevant files since changing to git
• src/product/ex.fixupGbdb.sh
  • lines changed 30, context: html, text, full: html, text
    fixup gbdb no longer relevant in 2010
• src/product/makefile
  • lines changed 144, context: html, text, full: html, text
    the makefile and ex.InstallExample are no longer relevant
• src/product/scripts/README
  • lines changed 18, context: html, text, full: html, text
    remove references to CVS commands
• src/product/scripts/beta.cvsup.pl
  • lines changed 210, context: html, text, full: html, text
    no longer required in git world
• src/product/scripts/browserEnvironment.txt
  • lines changed 3, context: html, text, full: html, text
    remove references to CVS commands
• src/product/scripts/dbTrashCleaner.sh
  • lines changed 58, context: html, text, full: html, text
    contents have been subsumed into trashCleaner.csh
• src/product/scripts/kentSrcUpdate.sh
  • lines changed 23, context: html, text, full: html, text
    update to git commands
• src/product/touchVersion.sh
  • lines changed 10, context: html, text, full: html, text
    irrelevant file since removal of makefile
• src/xenoAli/dynAlign/makefile
  • lines changed 11, context: html, text, full: html, text
    fixing makefiles to not leave garbage around