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# Procedure for building ncbiRefSeq gene tracks on all reasonable assemblies
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# Working in directory:

mkdir -p /hive/data/inside/ncbiRefSeq/2020-03-20
cd /hive/data/inside/ncbiRefSeq/2020-03-20

# extract list of equivalent refseq<->ucsc assemblies,
# and format a list of commands to run:

hgsql -e 'select destination,source from asmEquivalent where sourceAuthority="refseq" and destinationAuthority="ucsc";' hgFixed \
  | awk '{printf "./updateOne %s %s\n", $1, $2}' > update.run.list

# that makes a list of 147 commands:
wc -l update.run.list
#  147

# Where the 'updateOne' script is from this source code directory:
#	~/kent/src/hg/makeDb/doc/ncbiRefSeq/updateOne

cp -p ~/kent/src/hg/makeDb/doc/ncbiRefSeq/updateOne ./

# Run the procedures, 5 at a time:

time (~/kent/src/hg/utils/automation/perlPara.pl 5 update.run.list) \
    >> update.log 2>&1

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# No, not really
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# what actually happened is that I did make the run.list as described
# above, but then:
# I did an exhaustive search through all database browsers on hgwdev to
# get a picture of where they stood with their absence or presence of
# existing ncbiRefSeq.  There were a whole list of those that were first
# timers, never had this track before.  So, I ran those up first, just as
# above, but with a selective list.  That required a batch edit of
# the trackDb source tree to turn on that new track for those browsers.

# To scan databases on hgwdev for the presence of a database table,
# using the periodic table status scans:

grep -l -w ncbiRefSeq /hive/users/hiram/mysql50/dev50/2020/03-08/*.status.tab \
   | sed -e 's#.*/##; s/.status.tab//;'

# that makes a database list of any that have that ncbiRefSeq table

# Then, for those browsers that had the existing track, I discovered that
# two of them already had the most up to date version.  With this in mind
# another selective list was used to run updates on those browsers that
# needed an update.

# Then archive versions of all existing and previous versions of this track
# were dumped to GTF files and symlinked into:

/usr/local/apache/htdocs-hgdownload/goldenPath/archive/<db>/ncbiRefSeq
# and:
/usr/local/apache/htdocs-hgdownload/goldenPath/<db>/bigZips/genes/ncbiRefSeq.gtf.gz

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