b5e48086053aea919ca5aa06918d0c0f68d66a20
hiram
  Mon Jul 29 18:59:16 2019 -0700
adding the .txt files and a README to describe the process refs #23734

diff --git src/hg/makeDb/doc/VGP/README.txt src/hg/makeDb/doc/VGP/README.txt
new file mode 100644
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--- /dev/null
+++ src/hg/makeDb/doc/VGP/README.txt
@@ -0,0 +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
+
+./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
+