[galaxy-dev] conda path problem

[Matthias Bernt]

Dear list,






Best,
Matthias

Uncaught exception in exposed API method:
Traceback (most recent call last):

    rval = func( self, trans, *args, **kwargs )

    payload )

    install_options

    tool_panel_section_mapping=tool_panel_section_mapping )

    [self._view.install_dependencies(r) for r in new_requirements]

    dependencies = resolver.resolve_all(resolvable_requirements, **kwds)

    is_installed = self.install_all(conda_targets)

    conda_context.ensure_channels_configured()

    self.save_condarc(conda_conf)

    raise Exception(message)


--

-------------------------------------------
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,
m.be...@ufz.de, www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703

Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------

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? File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/decorators.py", line 282, in decorator File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py", line 502, in install_repository_revision File "/gpfs1/data/galaxy_server/galaxy-dev/lib/tool_shed/galaxy_install/install_manager.py", line 706, in install 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 File "/gpfs1/data/galaxy_server/galaxy-dev/lib/tool_shed/galaxy_install/install_manager.py", line 910, in install_tool_shed_repository 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 File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/resolvers/conda.py", line 171, in resolve_all 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 File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/conda_util.py", line 136, in ensure_channels_configured File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/conda_util.py", line 198, in save_condarc 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. Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus

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