3030fb4a9c489593d8286b7bb469ebda3c575ad6
gperez2
  Wed Jun 10 12:56:44 2026 -0700
Documenting the release 2 archive step in the Varaico makedoc and fixing a hardcoded hg38 path in the description page example, refs #37658

diff --git src/hg/makeDb/doc/hg38/varaico.txt src/hg/makeDb/doc/hg38/varaico.txt
index 49e068c2cfc..4592f1a2711 100644
--- src/hg/makeDb/doc/hg38/varaico.txt
+++ src/hg/makeDb/doc/hg38/varaico.txt
@@ -1,18 +1,33 @@
 # May 21 2025 - Johannes
 # have a look at this config file and edit paths/API keys if necessary:
 export AMELIE2_CONFIG_JSON=/hive/users/jbirgmei/amelie2/src/scripts/config.json
 
 # then run the pipeline to create hg19 and hg38 bigbeds:
 /cluster/home/jbirgmei/opt_rocky9/miniconda3/envs/amelie2/bin/amelie2 workflow final_out --partition hg19,hg38
 
 # move bigbeds to track version directory:
 mkdir /hive/users/jbirgmei/TRACK_VERSIONS/v5_20260527
 cp -r /hive/users/jbirgmei/amelie2/data/out/None/full/hg* /hive/users/jbirgmei/TRACK_VERSIONS/v5_20260527
 
+# archive the previous release (release 2, "release 2 (20251110)") to the
+# download archive before copying in the new files:
+for db in hg19 hg38; do
+    mkdir /hive/data/genomes/$db/bed/varaico.v2_20251110
+    cp /hive/data/genomes/$db/bed/varaico/varaico.bb \
+       /hive/data/genomes/$db/bed/varaico.v2_20251110/$db.varaico.v2_20251110.bb
+    cp /hive/data/genomes/$db/bed/varaico/varaicoSuppl.bb \
+       /hive/data/genomes/$db/bed/varaico.v2_20251110/$db.varaicoSuppl.v2_20251110.bb
+    mkdir -p /usr/local/apache/htdocs-hgdownload/goldenPath/archive/$db/varaico/v2_20251110
+    ln -s /hive/data/genomes/$db/bed/varaico.v2_20251110/$db.varaico.v2_20251110.bb \
+          /usr/local/apache/htdocs-hgdownload/goldenPath/archive/$db/varaico/v2_20251110/$db.varaico.v2_20251110.bb
+    ln -s /hive/data/genomes/$db/bed/varaico.v2_20251110/$db.varaicoSuppl.v2_20251110.bb \
+          /usr/local/apache/htdocs-hgdownload/goldenPath/archive/$db/varaico/v2_20251110/$db.varaicoSuppl.v2_20251110.bb
+done
+
 # copy bigbeds:
 cp /hive/users/jbirgmei/TRACK_VERSIONS/v5_20260527/hg19/normalized_variants.hg19.bb /hive/data/genomes/hg19/bed/varaico/varaico.bb
 cp /hive/users/jbirgmei/TRACK_VERSIONS/v5_20260527/hg38/normalized_variants.hg38.bb /hive/data/genomes/hg38/bed/varaico/varaico.bb
 cp /hive/users/jbirgmei/TRACK_VERSIONS/v5_20260527/hg19/normalized_variants_supplements.hg19.bb /hive/data/genomes/hg19/bed/varaico/varaicoSuppl.bb
 cp /hive/users/jbirgmei/TRACK_VERSIONS/v5_20260527/hg38/normalized_variants_supplements.hg38.bb /hive/data/genomes/hg38/bed/varaico/varaicoSuppl.bb
 
 # finally, create symlinks from /gbdb/$D/bbi/varaico{Suppl,}.bb to /hive/data/genomes/$D/bed/varaico/varaico{Suppl,}.bb