26db090072511b54c477fb9824d24aaeae349a13
hiram
  Mon Oct 13 12:38:56 2025 -0700
document chromAlias procedure refs #36461

diff --git src/hg/makeDb/doc/asmHubs/README.chromAlias.txt src/hg/makeDb/doc/asmHubs/README.chromAlias.txt
new file mode 100644
index 00000000000..b6cd4be7562
--- /dev/null
+++ src/hg/makeDb/doc/asmHubs/README.chromAlias.txt
@@ -0,0 +1,82 @@
+
+To add custom alias names to any GenArk genome:
+
+1. go to the 'chromAlias' build directory for the assembly.
+   For example in:
+
+cd /hive/data/genomes/asmHubs/genbankBuild/GCA/044/165/215/GCA_044165215.1_HG00097_hap1_hprc_f2/trackData/chromAlias
+
+2. Create or add to any existing customNames.tsv file there:
+
+   head customNames.tsv 
+# genbank       hprcV2
+CM094060.1      HG00097#1#CM094060.1
+CM094061.1      HG00097#1#CM094061.1
+CM094062.1      HG00097#1#CM094062.1
+CM094063.1      HG00097#1#CM094063.1
+
+   The first column name needs to match the first column name in
+   the existing chromAlias.txt file there:
+
+   head GCA_044165215.1_HG00097_hap1_hprc_f2.chromAlias.txt
+# genbank       assembly        hprcV2  ncbi    ucsc
+CM094060.1      HG00097#1#h1tg000005l   HG00097#1#CM094060.1    1       chr1
+CM094061.1      HG00097#1#h1tg000007l   HG00097#1#CM094061.1    2       chr2
+CM094062.1      HG00097#1#h1tg000012l   HG00097#1#CM094062.1    3       chr3
+CM094063.1      HG00097#1#h1tg000001l   HG00097#1#CM094063.1    5       chr5
+
+   This customNames.tsv file can have any number of additional columns.
+   The title name is also necessary to be in the source code script:
+
+     src/hg/utils/automation/aliasTextToBed.pl
+
+   If the name you want to use is not in this list, add it to
+   this source file:
+
+my %nameLabels = (
+   "assembly" => "Assembly",
+   "genbank" => "GenBank",
+   "ncbi" => "NCBI",
+   "refseq" => "RefSeq",
+   "ucsc" => "UCSC",
+   "ensembl" => "Ensembl",
+   "xenbase" => "Xenbase",
+   "chrNames" => "chrNames",
+   "chrN" => "chrN",
+   "VEuPathDB" => "VEuPathDB",
+   "hprcV2" => "HPRCv2",
+   "custom" => "custom"
+);
+
+3.  With customNames.tsv in place, run the existing script in
+    this directory:
+
+    ./doChromAlias.bash
+
+    This will regenerate the chromAlias.txt and chromAlias.bb files with
+    this new column.  If it fails it will show errors, success finishes
+    with the output:
+++ grep -c -v '^#' GCA_018504665.2_NA21309_pat_hprc_f2.chromAlias.txt
++ export aliasCount=95
++ aliasCount=95
+++ grep -c -v '^#' test.chromAlias.bed
++ export testCount=95
++ testCount=95
++ '[' 95 -ne 95 ']'
++ '[' 95 -ne 95 ']'
++ exit 0
+
+    Since this is most likely already an existing
+    GenArk assembly hub, the symLinks are already in place to make these new
+    files get out.  The 'otto' process overnight will get the chromAlias.bb
+    file out to its /gbdb/genark/ location.  The alias names will function
+    on the RR the next day.
+
+4.  To get the files out to hgdownload, run the 'make sendDownload' command
+    in the respective source tree 'clade' grouping:
+
+    cd ~/kent/src/hg/makeDb/doc/primatesAsmHub
+    time (make sendDownload) >> send.down.log 2>&1
+
+5. All of the other files you see generated in this chromAlias/ directory
+   are made for the testing and verification that everthing is correct.