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
@@ -1,129 +1,129 @@
 #!/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`
 
 #	create ftp response script for the ftp connection session
 rm -f ftp.omim.rsp
 echo "user anonymous ${ftppass}
 cd OMIM
 ls
 bye" > ftp.omim.rsp
 
 
 #	reorganize results files
 rm -f prev.release.list
 rm -f ls.check
 cp -p release.list prev.release.list
 rm -f release.list
 
 #	connect and list a directory, result to file: ls.check
 ftp -n -v -i grcf.jhmi.edu  < ftp.omim.rsp > ls.check
 
 #	fetch the release directory names from the ls.check result file
 grep "genemap" ls.check |grep -v key|sort > release.list
 chmod o+w release.list
 
 #	verify we are getting a proper list
 WC=`cat release.list | wc -l`
 if [ "${WC}" -lt 1 ]; then
     echo "potential error in OMIM release watch,
 check release.list in ${WORKDIR}" \
 	| mail -s "ERROR: OMIM watch" ${DEBUG_EMAIL}
     exit 255
 fi
 
 #	see if anything is changing, if so, email notify, download, and build
 
 diff prev.release.list release.list  >release.diff
 WC=`cat release.diff | wc -l`
 if [ "${WC}" -gt 1 ]; then
     echo -e "New OMIM update noted at:\n" \
 "ftp://grcf.jhmi.edu/\n"`comm -13 prev.release.list release.list`"/" \
     | mail -s "OMIM update watch" ${EMAIL}
 
 FN=`cat release.diff |grep omim-|sed -e 's/omim-/\tomim-/'|cut -f 2`
 
 today=`date +%F`
 mkdir -p $today
 cd $today
 
 # prepare ftp2 download response file
 echo doing ftp2 ...
 
 #	create ftp response script for the ftp2 connection session
 rm -f ftp2.omim.rsp
 echo "user omimftp3 ${ftppass2}
 cd OMIM
 get mimAV.txt
 get geneMap2.txt
 bye" > ftp2.omim.rsp
 
 # download the new mimAv.txt data file
 ftp -n -v -i grcf.jhmi.edu  < ftp2.omim.rsp > ftp2.log
 
 # prepare ftp download response file
 echo doing ftp ...
 
 rm -f ftp.omim.rsp
 echo "user anonymous ${ftppass}
 cd OMIM
 binary
 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