e8d1fff44e0f7ecd4629cfcc2ac671d6af78d8ae
hiram
  Thu Apr 30 12:54:54 2026 -0700
add an ottoRequest table interactive CGI viewer and verify lift.over URL links for email are valid refs #31811

diff --git src/hg/utils/otto/userRequests/README.txt src/hg/utils/otto/userRequests/README.txt
index 1bebf62f56c..f847635fefa 100644
--- src/hg/utils/otto/userRequests/README.txt
+++ src/hg/utils/otto/userRequests/README.txt
@@ -66,32 +66,31 @@
                - when it detects 'status=4' state, it will construct the
                - symlinks to get all the files ready for pushing and it
                - makes the entries in liftOverChain and quickLiftChain tables.
                - and then it sets 'status=5'
                - the 'status=5' states are detected by the 
                - ottoRequestPush.py cron job - which does the business of
                - getting the GenArk assembly hub.txt files built and everything
                - pushed out to hgdownload by using the 'make' commands built
                - into the source tree doc/*AsmHub/ directories.
                - TBD: add to ottoRequestPush.py the ability to push the
                -      UCSC database browser files.
                - Finally, watches for 'status=6' which was set by
                - ottoRequestPush.py upon push completion, now it will
                - use galaxyCleanup.py to release the galaxy history and WF
                - data, it will send out confirmation finished email and sets
-               - 'status=8' to indicate completion.  TBD: expand the email
-               - message to include links to the download fles.
+               - 'status=8' to indicate completion.
 
 ############################################################################
 ###  4.
 ottoRequestAlign.sh - given an 'id' number in the ottoRequest table, this
                     - will generate the arguments to: 'kegAlignLastz.sh' 
                     - to get the alignment started in galaxy.
                     - Uses the hgcentraltest.genark table and the file
                     - dbDb.name.clade.tsv to determine full assembly ID
                     - names and 'clades' for the kegAlignLastz.sh script:
                     - primate - mammal - other - and this will decide which
                     - assembly will be target and query by checking their
                     - respective N50 sizes.  Also uses the file:
           dbDb.name.clade.tsv - to map the UCSC database names into
                           - GenArk 'clades' to make the selection:
                           - primate - mammal - other