2e15b699069d147795f3b4bcdf50aa9d099be9ff
max
  Thu Mar 6 02:31:47 2014 -0800
moving the phoneHome business into cgiApoptosis.c/.h to make it callablefrom cart.c. We need to call it from cart.c as otherwise
cgiApoptosisSetup (originally: phoneHome) will be called after mysql
connections are opened. This leads to "mysql server has gone away" if
any CGI is not faster than the child process forked here. The child will
close all mysql connections of the parent process. With the new setup,
the childi is forked before any mysql connections are opened. Ideally
this would be all done in cheapcgi, but cheapcgi is not in the hg/lib
part of the code.

diff --git src/hg/lib/makefile src/hg/lib/makefile
index a0669a5..1078b8b 100644
--- src/hg/lib/makefile
+++ src/hg/lib/makefile
@@ -10,31 +10,31 @@
     axtLib.o bactigPos.o hgBam.o baseMaskCommon.o bdgpExprLink.o bdgpGeneInfo.o \
     bed.o bed5FloatScore.o bed5Pval.o bed6FloatScore.o bed8Attrs.o bed12Source.o \
     bed12wSeq.o bedCart.o bgiGeneInfo.o bgiGeneSnp.o bgiSnp.o bioImage.o \
     blastTab.o blastzNet.o blatServers.o borf.o borkPseudoHom.o botDelay.o\
     cart.o cartDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cdsSpec.o \
     ccdsInfo.o ccdsNotes.o ccdsGeneMap.o celeraCoverage.o \
     celeraDupPositive.o cgapSage/cgapSage.o cgapSage/cgapSageLib.o cgh.o chainCart.o \
     chainDb.o chainLink.o chainNet.o chainNetDbLoad.o \
     chicken13kInfo.o chromBins.o chr18deletions.o \
     chromGraph.o chromGraphFactory.o chromInfo.o chromInserts.o chromKeeper.o \
     clonePos.o codeBlast.o codeBlastScore.o cogs.o cogsxra.o columnInfo.o \
     contigAcc.o coordConv.o \
     cnpIafrate.o cnpIafrate2.o cnpLocke.o cnpRedon.o cnpSebat.o cnpSebat2.o \
     cnpSharp2.o cnpSharpCutoff.o cnpSharpSample.o cnpSharp.o \
     cpgIsland.o cpgIslandExt.o ctgPos.o ctgPos2.o \
-    bedDetail.o \
+    bedDetail.o cgiApoptosis.o \
     customFactory.o customPp.o customTrack.o cutter.o cv.o cytoBand.o \
     dbDb.o dbRIP.o dbSnpRs.o defaultDb.o delConrad2.o delHinds2.o \
     dgv.o dgvPlus.o dless.o dnaMotifSql.o dnaMarkovSql.o dnaProbe.o \
     dv.o dvBed.o dvXref2.o \
     easyGene.o ec.o ecCode.o ecAttribute.o ecAttributeCode.o \
     encode/encodeErge.o encode/encodeErgeHssCellLines.o \
     encode/encodeHapMapAlleleFreq.o encode/encodeIndels.o encode/encodePeak.o \
     encode/encodeRegionInfo.o encode/encodeRegionInfoCustom.o encode/encodeRna.o \
     encode/encodeStanfordPromoters.o encode/encodeStanfordPromotersAverage.o \
     encode/pairedTagAlign.o encode/peptideMapping.o encode/tagAlign.o  \
     encode/wgEncodeGencodeAttrs.o encode/wgEncodeGencodeExonSupport.o \
     encode/wgEncodeGencodeTag.o  \
     encode/wgEncodeGencodePdb.o encode/wgEncodeGencodePubMed.o \
     encode/wgEncodeGencodeRefSeq.o encode/wgEncodeGencodeGeneSource.o encode/wgEncodeGencodeTranscriptSource.o \
     encode/wgEncodeGencodeTranscriptSupport.o encode/wgEncodeGencodeTranscriptionSupportLevel.o \