1e87a5e306cb4602fb6781077be0265db2d58c4f
hiram
  Wed Dec 1 11:29:46 2021 -0800
update scripts for new location refs #28331

diff --git src/hg/utils/otto/grcIncident/README.txt src/hg/utils/otto/grcIncident/README.txt
index 5595286..8159237 100644
--- src/hg/utils/otto/grcIncident/README.txt
+++ src/hg/utils/otto/grcIncident/README.txt
@@ -1,52 +1,52 @@
 
 Thu Oct 21 11:17:52 PDT 2021
 
 The cron job is daily at 09:33
 
-33 09 * * * /hive/data/outside/grc/incidentDb/runUpdate.sh makeItSo
+33 09 * * * /hive/data/outside/otto/grcIncidentDb/runUpdate.sh makeItSo
 
 Tue Sep  3 10:48:30 PDT 2019
 
 Create the directory:
    /gbdb/<db>/bbi/grcIncidentDb
 
 Add the new work directory to the list in runUpdate.sh:
 
 for D in GRCh37 GRCh38 GRCm38 Zv9 MGSCv37 GRCz10 GRCz11 Gallus_gallus-5.0 GRCg6a
 ...
 
 Need to get the refSeq.chromNames.tab file established in the new
 directory:
 
   hgsql -e 'select * from chromAlias;' galGal6 \
      | grep -i refseq | cut -f1,2 | sort > refSeq.chromNames.tab
 
 And add the command in the set of commands there: e.g.:
 
 ./grcUpdate.sh GRCg6a galGal6 GRCg6a_issues chicken/GRC/Issue_Mapping \
   > GRCg6a/log/${YM}/${DS}.txt 2>&1
 
 You can verify the issues.gff3 file name at the NCBI FTP directory:
 
-   ftp://ftp.ncbi.nlm.nih.gov/pub/grc/chicken/GRC/Issue_Mapping/
+   https://ftp.ncbi.nlm.nih.gov/pub/grc/chicken/GRC/Issue_Mapping/
 
 run the runUpdate.sh (optionally just the new one to avoid other issues)
 
 Will need to add the symlink, e.g.:
 
-/gbdb/galGal6/bbi/grcIncidentDb/galGal6.grcIncidentDb.bb -> /hive/data/outside/grc/incidentDb/GRCg6a/GalGal6.grcIncidentDb.bb
+/gbdb/galGal6/bbi/grcIncidentDb/galGal6.grcIncidentDb.bb -> /hive/data/outside/otto/grcIncidentDb/GRCg6a/GalGal6.grcIncidentDb.bb
 
 And run the hgBbiDbLink command:
 
 hgBbiDbLink galGal6 grcIncidentDb "/gbdb/galGal6/bbi/grcIncidentDb/galGal6.grcIncidentDb.bb"
 
 Add the verification log check at the end of runUpdate.sh:
 
 WC=`tail --quiet --lines=1 ${TOP}/GRCg6a/log/${YM}/${DS}.txt ${TOP}/GRCh37/log/${YM}/${DS}.txt ${TOP}/GRCh38/log/${YM}/${DS}.txt ${TOP}/GRCm38/log/${YM}/${DS}.txt ${TOP}/GRCz10/log/${YM}/${DS}.txt ${TOP}/GRCz11/log/${YM}/${DS}.txt ${TOP}/Gallus_gallus-5.0/log/${YM}/${DS}.txt ${TOP}/MGSCv37/log/${YM}/${DS}.txt ${TOP}/Zv9/log/${YM}/${DS}.txt | grep SUCCESS | wc -l`
 
 And change the expected count:
 
 if [ "${WC}" -ne 9 ]; then
     ${ECHO} "WC: ${WC} <- should be nine" 1>&2
 
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