ec8d25d5bd0eac0a4f5172603e704106cbf6c66b max Sun Oct 4 06:37:38 2026 -0700 methbase2 otto: ssh to hgdownload as the invoking user, not as qateam, refs #34246 diff --git src/hg/utils/otto/methbase2/methbaseDownload src/hg/utils/otto/methbase2/methbaseDownload index 88bc53891f4..8f39723590a 100755 --- src/hg/utils/otto/methbase2/methbaseDownload +++ src/hg/utils/otto/methbase2/methbaseDownload @@ -39,31 +39,31 @@ import os import sys import threading import time from concurrent.futures import ThreadPoolExecutor from urllib.parse import urljoin, urlparse import requests # The faceted hub. Note this is NOT the hub at .../methylation/hub.txt, which is # the older superTrack-per-study layout. methbase_hub/ is an alias for the # latest methbase_hub_/, and those dated directories are rewritten in # place, so the date in the name buys no reproducibility - prefer the alias. DEFAULT_HUB_URL = "http://smithlab.usc.edu/trackdata/methylation/methbase_hub/hub.txt" # The mirror lives on hgdownload, served as https://hgdownload.soe.ucsc.edu/hubs/ -# and reached as qateam@hgdownload. Each refresh gets its own vN directory, so +# served from hgdownload. Each refresh gets its own vN directory, so # bump this (or pass -o) when v4 is cut. Do not update the directory that is # being served: hardlink it first (cp -al v3 v4), update the copy, then swap. DEFAULT_OUT_DIR = "/mirrordata/hubs/methbase/v3" # Where that directory is served from. Rewritten bigDataUrls point here, so the # mirrored trackDb works for anyone who loads it by url, not only for a copy # sitting next to the data. Keep this and DEFAULT_OUT_DIR pointing at the same # vN directory. DEFAULT_BASE_URL = "https://hgdownload.soe.ucsc.edu/hubs/methbase/v3" DEFAULT_STRIP_PREFIX = "http://smithlab.usc.edu/methbase/data/" # trackDb settings whose value is a big binary file that lives outside the hub BIG_DATA_TAGS = frozenset([ "bigDataUrl", "bigDataIndex", "barChartMatrixUrl", "barChartSampleUrl", "linkDataUrl", "frames", "summary", "searchTrix", ])