Error parsing the tool configuration /galaxy/config/shed_tool_conf.xml

,
1

Hi,

today by restarting my Dockerized Galaxy that worked well so far, I got the following error that lets my instance stucked:

…

panel_searches\[panel_view_id\] = ToolPanelViewSearch(

                                ^^^^^^^^^^^^^^^^^^^^

File “/galaxy/lib/galaxy/tools/search/_init_.py”, line 199, in _init_

self.index = self.\_index_setup()

             ^^^^^^^^^^^^^^^^^^^

File “/galaxy/lib/galaxy/tools/search/_init_.py”, line 203, in _index_setup

return get_or_create_index(self.index_dir, self.schema)

       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

File “/galaxy/lib/galaxy/tools/search/_init_.py”, line 75, in get_or_create_index

if index.exists_in(index_dir):

   ^^^^^^^^^^^^^^^^^^^^^^^^^^

File “/galaxy/.venv/lib/python3.12/site-packages/whoosh/index.py”, line 136, in exists_in

ix = open_dir(dirname, indexname=indexname)

     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

File “/galaxy/.venv/lib/python3.12/site-packages/whoosh/index.py”, line 123, in open_dir

return FileIndex(storage, schema=schema, indexname=indexname)

       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

File “/galaxy/.venv/lib/python3.12/site-packages/whoosh/index.py”, line 421, in _init_

TOC.read(self.storage, self.indexname, schema=self.\_schema)

File “/galaxy/.venv/lib/python3.12/site-packages/whoosh/index.py”, line 632, in read

check_size("int", \_INT_SIZE)

File “/galaxy/.venv/lib/python3.12/site-packages/whoosh/index.py”, line 626, in check_size

sz = stream.read_varint()

     ^^^^^^^^^^^^^^^^^^^^

File “/galaxy/.venv/lib/python3.12/site-packages/whoosh/filedb/structfile.py”, line 191, in read_varint

return read_varint(self.read)

       ^^^^^^^^^^^^^^^^^^^^^^

File “/galaxy/.venv/lib/python3.12/site-packages/whoosh/util/varints.py”, line 102, in read_varint

b = ord(readfn(1))

    ^^^^^^^^^^^^^^

TypeError: ord() expected a character, but string of length 0 found

2025-10-12 10:41:19,037 WARN exited: gunicorn (exit status 1; not expected)

2025-10-12 10:41:20,039 INFO gave up: gunicorn entered FATAL state, too many start retries too quickly

This is the content of my shed_tool_conf.xml, all these tools were well installed (and used!) through the GUI:

<?xml version="1.0" ?> toolshed.g2.bx.psu.edu retropath2 tduigou 61f770bdfa09 toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/3.5.0+galaxy1 3.5.0+galaxy1 toolshed.g2.bx.psu.edu rp2paths tduigou 5ff2b0c02dd6 toolshed.g2.bx.psu.edu/repos/tduigou/rp2paths/rp2paths/2.1.0+galaxy1 2.1.0+galaxy1 toolshed.g2.bx.psu.edu rptools_rpcompletion tduigou e59d28e31f88 toolshed.g2.bx.psu.edu/repos/tduigou/rptools_rpcompletion/rptools_rpcompletion/6.5.0+galaxy0 6.5.0+galaxy0 toolshed.g2.bx.psu.edu rptools_rpviz tduigou 693c335d65e7 toolshed.g2.bx.psu.edu/repos/tduigou/rptools_rpviz/rptools_rpviz/6.5.0+galaxy0 6.5.0+galaxy0

Any help would be greatly appreciated. Thanks!

2

Problem vanished once restarted from scratch. Seem Galaxy doesn’t like pauses during Installation or maybe doesn’t like pauses at all.

1 Like