4fdac1a09cb6a154a2f739885b02fc8f0e40a00d
hiram
  Mon Sep 9 09:57:59 2019 -0700
first instance of hub is complete refs #23734

diff --git src/hg/makeDb/doc/VGP/README.txt src/hg/makeDb/doc/VGP/README.txt
index e5795f9..690b857 100644
--- src/hg/makeDb/doc/VGP/README.txt
+++ src/hg/makeDb/doc/VGP/README.txt
@@ -1,108 +1,108 @@
 
 ################################################################
 ### VGP project information
 ################################################################
 
 For naming scheme if the assembly names:
 
  https://github.com/VGP/vgp-assembly/blob/master/VGP_specimen_naming_scheme.md
 
 
 The one letter prefix [abfmrs] corresponds to one of:
 
 prefix  class
 
 a       amphibians
 b       birds
 f       fishes
 m       mammal
 r       reptiles
 s       sharks and relatives
 
 ################################################################
 ###  Building the VGP assembly hubs
 ################################################################
 
 Working in the directory hierarchy:
 
    /hive/data/genomes/asmHubs/VGP
 
 The ucscNames directory contains the built assembly hubs:
 
    /hive/data/genomes/asmHubs/VGP/ucscNames
 
 The building of each hub was managed from the directory:
 
    /hive/data/genomes/asmHubs/VGP/cheapParasol
 
 Adjusting the script in that directory:
 
    /hive/data/genomes/asmHubs/VGP/cheapParasol/runOneJob
 
 to run steps one at a time, or multiple steps to build
 the hubs.  Using the list of jobs to run:
 
    /hive/data/genomes/asmHubs/VGP/cheapParasol/build.run.list
 
 And giving that list to the perlPara.pl script to run five
 of them at once and keep five jobs running until finished:
 
    time (./perlPara 5 build.run.list) > variousStep.log 2>&1
 
 Broken steps were fixed up and run manually, one step
 at a time.
 
    time (./runOneJob GCA_004027225.1_bStrHab1_v1.p) > GCA_004027225.1_bStrHab1_v1.p.log 2>&1
 
 The runOneJob script writes a shell script for the steps it
 is running into the work directory:
 
    VGP/ucscNames/<asmId>/steps.<stepStart>-<stepEnd>.sh
 
 And when that script is run, it leaves a log file in that
 work directory:
 
    VGP/ucscNames/<asmId>/<asmId>.<stepStart>-<stepEnd>.log
 
 ################################################################
 ###  Generating index pages for the VGP assembly hubs
 ################################################################
 
 After the hubs were finished building successfully,
 The scripts in VGP/ucscNames  build the necessary
 index.html pages and the genomes.txt file:
 
-./mkHubIndex.pl > hubIndex.html
-chmod 775 hubIndex.html
+./mkHubIndex.pl > index.html
+chmod 775 index.html
 
 ./mkAsmStats.pl > asmStatsVGP.html
 chmod 775 asmStatsVGP.html
 
 ./mkGenomes.pl > genomes.txt
 
 The 'chmod 775' allow those .html pages to run their 'include'
 commands.
 
 ################################################################
 ###  adjusting the common names
 ################################################################
 
 Some of the common names from the assembly report files were
 not specific enough.  The 'commonNames.txt' file was used
 to fix up the imprecise names:
 
 GCF_900634415.1_fCotGob3.1      Channel bull blenny
 GCA_901765095.1_aMicUni1.1      tiny Cayenne caecilian
 GCA_901699155.1_bStrTur1.1      European turtle dove
 
 The scripts use that file to correct the names.
 
 The hub.txt file is:
 
 hub VGP
 shortLabel VGP
 longLabel Vertebrate Genome Project assemblies
 genomesFile genomes.txt
 email hclawson@ucsc.edu
-descriptionUrl hubIndex.html
+descriptionUrl index.html