8a0a3fdc82e2a1362e24e91a2f5de0ee9c1931fe
hiram
  Thu Oct 21 11:17:30 2021 -0700
scripts for the GRC Incident otto job no redmine

diff --git src/hg/utils/otto/grcIncident/README.txt src/hg/utils/otto/grcIncident/README.txt
new file mode 100644
index 0000000..1ea4ba2
--- /dev/null
+++ src/hg/utils/otto/grcIncident/README.txt
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+
+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/
+
+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
+
+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
+
+######################################################################
+OBSOLETE:
+
+To start a new one:
+
+hgsql -e 'create database tmpIncidentGRCh38;' tmpIncidentGRCh37
+
+And a table in the target db, after the file is established
+in the genomewiki::
+
+hgBbiDbLink hg38 grcIncidentDb "http://genomewiki.ucsc.edu/images/7/7f/Hg38.grcIncidentDb.bb"
+