conda path problem

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conda path problem

Matthias Bernt
Dear list,

now that I got conda working I got a new error when installing tools
(bot when installing via the web interface and via the galaxy-tools
ansible role). There seems to be an update write on a nonexistent file
...../_condarc

I guess an important point is that I needed to redefine the conda path
in galaxy.ini (since I got warnings that the path name was to long).
Maybe there are still some hard coded paths around?

Best,
Matthias

Uncaught exception in exposed API method:
Traceback (most recent call last):
   File
"/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/decorators.py",
line 282, in decorator
     rval = func( self, trans, *args, **kwargs )
   File
"/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py",
line 502, in install_repository_revision
     payload )
   File
"/gpfs1/data/galaxy_server/galaxy-dev/lib/tool_shed/galaxy_install/install_manager.py",
line 706, in install
     install_options
   File
"/gpfs1/data/galaxy_server/galaxy-dev/lib/tool_shed/galaxy_install/install_manager.py",
line 805, in __initiate_and_install_repositories
     return self.install_repositories(tsr_ids, decoded_kwd,
reinstalling=False)
   File
"/gpfs1/data/galaxy_server/galaxy-dev/lib/tool_shed/galaxy_install/install_manager.py",
line 852, in install_repositories
     tool_panel_section_mapping=tool_panel_section_mapping )
   File
"/gpfs1/data/galaxy_server/galaxy-dev/lib/tool_shed/galaxy_install/install_manager.py",
line 910, in install_tool_shed_repository
     [self._view.install_dependencies(r) for r in new_requirements]
   File
"/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/views.py",
line 59, in install_dependencies
     return
self._dependency_manager._requirements_to_dependencies_dict(requirements,
**{'install': True})
   File
"/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/__init__.py",
line 148, in _requirements_to_dependencies_dict
     dependencies = resolver.resolve_all(resolvable_requirements, **kwds)
   File
"/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/resolvers/conda.py",
line 171, in resolve_all
     is_installed = self.install_all(conda_targets)
   File
"/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/resolvers/conda.py",
line 126, in install_all
     return_code = install_conda_targets(conda_targets, env,
conda_context=self.conda_context)
   File
"/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/conda_util.py",
line 405, in install_conda_targets
     conda_context.ensure_channels_configured()
   File
"/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/conda_util.py",
line 136, in ensure_channels_configured
     self.save_condarc(conda_conf)
   File
"/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/conda_util.py",
line 198, in save_condarc
     raise Exception(message)
Exception: Failed to update write to path
[/gpfs1/data/galaxy_server/galaxy-dev/database/dependencies/_condarc]
while attempting to update conda configuration, please update the
configuration to override the condarc location or grant this application
write to the parent directory.

--

-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
[hidden email], www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------


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