584b69eff038b10c2176d2b9299c356af21288cc
hiram
  Wed Apr 22 16:30:53 2026 -0700
initial scripts to run the galaxy workflow based off of the ottoRequest table entries refs #31811

diff --git src/hg/utils/otto/userRequests/README.txt src/hg/utils/otto/userRequests/README.txt
new file mode 100644
index 00000000000..adf58d08f0c
--- /dev/null
+++ src/hg/utils/otto/userRequests/README.txt
@@ -0,0 +1,29 @@
+
+Method of operation:
+
+ottoRequest.py - otto user cron job running each minute to watch the
+               - ottoRequest table in hgcentral - when new entries are
+               - detected it marks the table entry as pending and sends
+               - out notification emails.  TBD: use the 'ottoRequestAlign.sh'
+               - script to generate the arguments to 'kegAlignLastz.sh'
+
+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
+
+TBD:  run the kegAlignLastz.sh with the generated arguments to get the
+alignment started.
+
+
+workflowMonitor.sh - after the galaxy WF has started, this script can
+                   - check the status of the job and if it is done, then
+                   - then the processing of the results will take place to
+                   - construct the chain files.
+
+File: dbDb.name.clade.tsv - used to map the UCSC database names into
+                          - GenArk 'clades' to make the selection:
+                          - primate - mammal - other