Hello! I am attempting to use the HaLLA service in the Galaxy server. However, even with the default settings, my job keeps failing. I tried using documents that I had previously been able to obtain a hallagram from, but even those failed.
See below for job details:
Dataset Error Report
An error occurred while running the tool halla.
Details
Execution resulted in the following messages:
Fatal error: Exit code 1 ()
Tool generated the following standard error:
Traceback (most recent call last):
File “/galaxy_venv/lib/python3.7/site-packages/pkg_resources/init.py”, line 568, in _build_master
ws.require(requires)
File “/galaxy_venv/lib/python3.7/site-packages/pkg_resources/init.py”, line 886, in require
needed = self.resolve(parse_requirements(requirements))
File “/galaxy_venv/lib/python3.7/site-packages/pkg_resources/init.py”, line 777, in resolve
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (tqdm 4.46.1 (/galaxy_venv/lib/python3.7/site-packages), Requirement.parse(‘tqdm>=4.50.2’), {‘HAllA’})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/galaxy_venv/bin/halla”, line 33, in
sys.exit(load_entry_point(‘HAllA’, ‘console_scripts’, ‘halla’)())
File “/galaxy_venv/bin/halla”, line 25, in importlib_load_entry_point
return next(matches).load()
File “/galaxy_venv/lib/python3.7/site-packages/importlib_metadata/init.py”, line 96, in load
module = import_module(match.group(‘module’))
File “/tool_deps/_conda/lib/python3.7/importlib/init.py”, line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File “”, line 1006, in _gcd_import
File “”, line 983, in _find_and_load
File “”, line 967, in _find_and_load_unlocked
File “”, line 677, in _load_unlocked
File “”, line 728, in exec_module
File “”, line 219, in _call_with_frames_removed
File “/galaxy-central/tools/halla/scripts/halla.py”, line 8, in
import pkg_resources
File “/galaxy_venv/lib/python3.7/site-packages/pkg_resources/init.py”, line 3242, in
@_call_aside
File “/galaxy_venv/lib/python3.7/site-packages/pkg_resources/init.py”, line 3226, in _call_aside
f(*args, **kwargs)
File “/galaxy_venv/lib/python3.7/site-packages/pkg_resources/init.py”, line 3255, in _initialize_master_working_set
working_set = WorkingSet._build_master()
File “/galaxy_venv/lib/python3.7/site-packages/pkg_resources/init.py”, line 570, in _build_master
return cls._build_from_requirements(requires)
File “/galaxy_venv/lib/python3.7/site-packages/pkg_resources/init.py”, line 583, in _build_from_requirements
dists = ws.resolve(reqs, Environment())
File “/galaxy_venv/lib/python3.7/site-packages/pkg_resources/init.py”, line 772, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The ‘tqdm>=4.50.2’ distribution was not found and is required by HAllA
cp: cannot stat ‘halla_output/hallagram.pdf’: No such file or directory
cp: cannot stat ‘Halla_Results.zip’: No such file or directory
