b87243c823ae619a0f382db4236df99216f3f1e8
braney
  Mon Dec 13 10:38:39 2021 -0800
some knownGene cleanup

diff --git src/hg/utils/otto/knownGene/buildCgap.sh src/hg/utils/otto/knownGene/buildCgap.sh
index 6ad271c..e55ec22 100755
--- src/hg/utils/otto/knownGene/buildCgap.sh
+++ src/hg/utils/otto/knownGene/buildCgap.sh
@@ -1,17 +1,19 @@
 #!/bin/sh -ex
-
+cd $dir
+{
 mkdir -p $dir/cgap
 cd $dir/cgap
 
-wget --timestamping -O Mm_GeneData.dat "ftp://ftp1.nci.nih.gov/pub/CGAP/Mm_GeneData.dat"
-hgCGAP Mm_GeneData.dat
+wget --timestamping -O $cgapFile "ftp://ftp1.nci.nih.gov/pub/CGAP/$cgapFile"
+hgCGAP $cgapFile
 
 cat cgapSEQUENCE.tab cgapSYMBOL.tab cgapALIAS.tab|sort -u > cgapAlias.tab
 hgLoadSqlTab -notOnServer $tempDb cgapAlias $kent/src/hg/lib/cgapAlias.sql ./cgapAlias.tab
 
 hgLoadSqlTab -notOnServer $tempDb cgapBiocPathway $kent/src/hg/lib/cgapBiocPathway.sql ./cgapBIOCARTA.tab
 
 cat cgapBIOCARTAdesc.tab|sort -u > cgapBIOCARTAdescSorted.tab
 hgLoadSqlTab -notOnServer $tempDb cgapBiocDesc $kent/src/hg/lib/cgapBiocDesc.sql cgapBIOCARTAdescSorted.tab
 
 echo "BuildCgap successfully finished"
+} > doCgap.log 2>&1