4389d5f48220ed09aff243f8ff13b064e7dc7e0b
braney
  Wed Feb 22 17:32:10 2012 -0800
moving various pieces of code to build the omim table into one place #6943
diff --git src/utils/omim/checkOmim.sh src/utils/omim/checkOmim.sh
index 17ac302..61581c7 100755
--- src/utils/omim/checkOmim.sh
+++ src/utils/omim/checkOmim.sh
@@ -1,30 +1,30 @@
 #!/bin/sh
 
 #	Do not modify this script, modify the source tree copy:
 #	src/utils/omim/checkOmim.sh
 #	This script is used via a cron job and kept in $HOME/bin/scripts/
 
 # set EMAIL here for notification list
-EMAIL="fanhsu@soe.ucsc.edu"
+EMAIL="braney@soe.ucsc.edu"
 # set DEBUG_EMAIL here for notification of potential errors in the process
-DEBUG_EMAIL="fanhsu@soe.ucsc.edu"
+DEBUG_EMAIL="braney@soe.ucsc.edu"
 
 #	cron jobs need to ensure this is true
 umask 002
 
-WORKDIR="/hive/groups/gsid/medical/omim/auto"
+WORKDIR="/hive/data/outside/otto/omim"
 export WORKDIR
 
 #	this is where we are going to work
 if [ ! -d "${WORKDIR}" ]; then
     echo "ERROR in OMIM release watch, Can not find the directory:
     ${WORKDIR}" \
 	| mail -s "ERROR: OMIM watch" ${DEBUG_EMAIL}
     exit 255
 fi
 
 cd "${WORKDIR}"
 
 ftppass=`cat ftp.pwd`
 ftppass2=`cat ftp2.pwd`
 
@@ -97,33 +97,33 @@
 get genemap
 get mim2gene.txt
 get morbidmap
 bye" > ftp.omim.rsp
 
 # download the new data file
 ftp -n -v -i grcf.jhmi.edu  < ftp.omim.rsp > ftp.log
 
 # build the new OMIM track tables for hg18
 mkdir -p hg18
 cd hg18
 
 ln -s ../genemap ./genemap
 ln -s ../mimAV.txt ./mimAV.txt
 ln -s ../mim2gene.txt ./mim2gene.txt
-ln -s ../../script1.pl ./script1.pl
+ln -s ../../parseGeneMap.pl ./parseGeneMap.pl
 
 ../../buildOmimTracks.csh hg18
 cd ..
 
 # build the new OMIM track tables for hg19
 mkdir -p hg19
 cd hg19
 
 ln -s ../genemap ./genemap
 ln -s ../mimAV.txt ./mimAV.txt
 ln -s ../mim2gene.txt ./mim2gene.txt
-ln -s ../../script1.pl ./script1.pl
+ln -s ../../parseGeneMap.pl ./parseGeneMap.pl
 
 ../../buildOmimTracks.csh hg19
 
 fi