galaxy startup errors and warnings

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galaxy startup errors and warnings

Matthias Bernt
Dear list,

I get two messages where I do not know how to continue:

The first seems to be severe:

tool_shed.util.common_util WARNING 2017-04-10 07:37:39,800 The URL
https://toolshed.g2.bx.psu.edu/repository/get_repository_dependencies?owner=devteam&changeset_revision=08a01b2ce4cd&name=column_maker
raised the exception:
<urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify
failed (_ssl.c:661)>

tool_shed.galaxy_install.migrate.check DEBUG 2017-04-10 07:37:39,800 The
main Galaxy tool shed is not currently available, so skipped tool
migration 1 until next server startup


What could I do to debug this?

The other one seems to be easy to fix:

galaxy.tools.deps.resolvers.conda WARNING 2017-04-10 07:33:27,435 Conda
install prefix
'/gpfs1/data/galaxy_server/galaxy-dev/database/dependencies/_conda' is
65 characters long, this can cause problems with package installation,
consider setting a shorter prefix (conda_prefix in galaxy.ini)

My idea would be to setup a symbolic link which leads to a shorter
prefix. Are there better suggestions?

Could somebody give me a pointer to understand the reason for the
potential problems?

Best,
Matthias


--

-------------------------------------------
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
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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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