a77bab60dc03de789c241d97692ba1f672dfddab
max
  Mon Sep 14 07:30:12 2026 -0700
uniprot otto: use the miniprot in /cluster/bin/x86_64

max built the current miniprot into /cluster/bin/x86_64/miniprot, which is the
right home for it: shared, on the PATH the cluster nodes already use, and
maintained with the rest of the kent binaries rather than by this pipeline.

Dropped the copy I had built under the otto directory, so there is only one.
Both were 0.18-r281; checked that otto can run the system one.

refs #38300

diff --git src/hg/utils/otto/uniprot/doUniprot src/hg/utils/otto/uniprot/doUniprot
index 8676593dab5..34cfc56281f 100755
--- src/hg/utils/otto/uniprot/doUniprot
+++ src/hg/utils/otto/uniprot/doUniprot
@@ -1011,31 +1011,31 @@
 #   augustus   - ab initio prediction, present almost everywhere, so it is the last resort.
 # Each entry is (name, glob relative to the hub directory). Globs, not constructed names,
 # because the files under bbi/ carry the full asmId with its assembly-name suffix while the
 # hub directory is named with the short accession.
 # Several globs per source, because the layouts differ: a GenArk assembly keeps its gene
 # models under bbi/ and its CAT genes in a contrib collection, while hs1 is a hub assembly
 # that keeps them in /gbdb/hs1/<trackName>/ like a classic assembly does.
 genArkGeneSources = [
     ("catGenes",   ["contrib/*/catGenes.bb", "catLiftOffGenesV1/*.bb"]),
     ("ncbiRefSeq", ["bbi/*.ncbiRefSeq.bb", "ncbiRefSeq/ncbiRefSeq.bb"]),
     ("ncbiGene",   ["bbi/*.ncbiGene.bb"]),
 ]
 # Augustus is deliberately not in that list. It is an ab initio prediction, so mapping
 # UniProt through it stacks its errors on top of ours; aligning the proteins straight to
 # the genome with miniprot is better and much faster than the old BLAT protein search.
-miniprotBin = "/hive/data/outside/otto/uniprot/bin/miniprot"
+miniprotBin = "/cluster/bin/x86_64/miniprot"
 miniprotThreads = 16
 
 def miniprotVersion():
     " version string of the miniprot binary we are using "
     proc = subprocess.Popen([miniprotBin, "--version"], stdout=PIPE, encoding="utf8")
     return proc.communicate()[0].strip()
 
 dbIsHubCache = {}
 
 def genArkHubDir(db):
     """ return the hub directory of a hub assembly, or None for a classic db.
     dbDb.nibPath is "hub:<dir>" for these, e.g.
     hub:/gbdb/genark/GCF/029/289/425/GCF_029289425.2 for a GenArk assembly.
     """
     if db not in dbIsHubCache: