e6bafe04b348ec643f503c1600ab336c56870214
gperez2
  Tue Jul 14 18:01:27 2026 -0700
Adding the mouseDevTimecourse bigWig signal composite for mm10,
including its track description page, build scripts, and makedoc
documentation, using Claude, refs #37001

diff --git src/hg/makeDb/scripts/mouseDevTimecourse/downloadBigwigs.sh src/hg/makeDb/scripts/mouseDevTimecourse/downloadBigwigs.sh
new file mode 100755
index 00000000000..25425161f3c
--- /dev/null
+++ src/hg/makeDb/scripts/mouseDevTimecourse/downloadBigwigs.sh
@@ -0,0 +1,49 @@
+#!/bin/bash
+# Download the 312 ENCODE bulk RNA-seq bigWigs for the mouse developmental
+# time course into /hive/data/outside/woldlab/mouseDevTimecourse/mm10/bigwig/.
+# Reads URLs from Diane's biosample TSV (#36998 attachment).
+#
+# Designed to be safely restartable: skips files that already exist.
+# Run inside screen so it survives session disconnects:
+#   screen -dmS bigwig_download ~/kent/src/hg/makeDb/scripts/mouseDevTimecourse/downloadBigwigs.sh
+
+set -u
+
+TSV=/hive/data/outside/woldlab/mouseDevTimecourse/mm10/ENCSR574CRQ_biosample.tsv
+DEST=/hive/data/outside/woldlab/mouseDevTimecourse/mm10/bigwig
+LOG=/hive/data/outside/woldlab/mouseDevTimecourse/mm10/download_bigwigs.log
+
+mkdir -p "$DEST"
+: > "$LOG"
+
+echo "$(date) start" | tee -a "$LOG"
+echo "TSV: $TSV"   | tee -a "$LOG"
+echo "DEST: $DEST" | tee -a "$LOG"
+
+# Extract URLs from columns 7 (signal_of_unique_reads) and 8 (signal_of_all_reads),
+# skip the header line. One URL per output line.
+URLS=$(awk -F'\t' 'NR>1 {print $7; print $8}' "$TSV")
+TOTAL=$(echo "$URLS" | wc -l)
+echo "$TOTAL URLs to fetch" | tee -a "$LOG"
+
+i=0
+for URL in $URLS; do
+    i=$((i + 1))
+    NAME=$(basename "$URL")
+    OUT="$DEST/$NAME"
+    if [ -s "$OUT" ]; then
+        echo "[$i/$TOTAL] skip (exists): $NAME" >> "$LOG"
+        continue
+    fi
+    echo "[$i/$TOTAL] fetching: $NAME" >> "$LOG"
+    curl -sSL -o "$OUT.partial" "$URL"
+    rc=$?
+    if [ $rc -eq 0 ]; then
+        mv "$OUT.partial" "$OUT"
+    else
+        echo "[$i/$TOTAL] FAILED rc=$rc: $URL" >> "$LOG"
+        rm -f "$OUT.partial"
+    fi
+done
+
+echo "$(date) done" | tee -a "$LOG"