ebd704b803fed9f990e2c8aeda1338a7054f8316
braney
  Wed Feb 22 17:43:49 2012 -0800
more moving things around #6943
diff --git src/utils/omim/checkOmim.sh src/utils/omim/checkOmim.sh
deleted file mode 100755
index 61581c7..0000000
--- src/utils/omim/checkOmim.sh
+++ /dev/null
@@ -1,129 +0,0 @@
-#!/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 $HOME/bin/scripts/
-
-# set EMAIL here for notification list
-EMAIL="braney@soe.ucsc.edu"
-# set DEBUG_EMAIL here for notification of potential errors in the process
-DEBUG_EMAIL="braney@soe.ucsc.edu"
-
-#	cron jobs need to ensure this is true
-umask 002
-
-WORKDIR="/hive/data/outside/otto/omim"
-export WORKDIR
-
-#	this is where we are going to work
-if [ ! -d "${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 ../../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 ../../parseGeneMap.pl ./parseGeneMap.pl
-
-../../buildOmimTracks.csh hg19
-
-fi
-