Dear
Youssef,
Thanks for answering, the target permissions have
not changed and are defined via NFS4 ACLs:
A::OWNER@:rwaDxtTnNcCy
A::GROUP@:rwaDxtTnNcy
A:fdi:galaxy@AD.DKFZ-HEIDELBERG.DE:rwaDxtTnNcy
A:fdig:W190-galaxy-admins@AD.DKFZ-HEIDELBERG.DE:rwaDxtTnNcy
In this case the galaxy user (i.e. the user
starting the process) has full access to the
share.
In our instance the "user directories" are just
symbolic links to the target folders mention
above.
When I try to import data from a user
directory/NFS4 share into a data library we get
the following error:
"You do not habe any files in your user directory.
Use FTP to upload there." (I attached a
screenshot)
We still use galaxy.ini to configure our instance,
in the galaxy.yml I find the following parameter:
# For security reasons, users may not import any
files that actually
# lie outside of their `user_library_import_dir`
(e.g. using symbolic
# links). A list of directories can be allowed
by setting the
# following option (the list is
comma-separated). Be aware that *any*
# user with library import permissions can
import from anywhere in
# these directories (assuming they are able to
create symlinks to
# them).
#user_library_import_symlink_whitelist: null
Would implementing this solve my issue?
Cheers,
Christopher
On 11/26/18 4:36 PM,
Youssef GHORBAL wrote:
Hello,
What
do you mean exactly "doesn't work anymore" ?
Do current links no longer appear in
data-library ? Do new soft-links can no longer
be made available into data-library ? Do you
have any error messages ?
By
the way the symlink permissions are not
valuable, you need to check the target
permissions (/galaxy-clients/w190_galaxy/ for
instance)
Youssef Ghorbal
IIS / DSI
Institut Pasteur
-----------------------
Dear all,
We implemented a system using
soft-links to link user-directories to
NFS shares in order to import/link
datasets that are larger than 2GB
(through links to data-libraries) and
provide our users with longer term
storage space for their analyses.
This worked fine for Galaxy version
17.09...and stopped working for
Version 18.05.
An example can be seen here in the
folder (the path to this folder will
vary between installations):
/opt/galaxy/galaxy/database/files
lrwxrwxrwx 1 galaxy
W190-htseq-bioinf 28 Sep 11 12:37
christopher.previti@dkfz-heidelberg.de
-> /galaxy-clients/w190_galaxy/
Setting the proper rights allows users
to link files from the nfs data-share
make available under /galaxy-clients
(in this case the share is called
"w190_galaxy")
directly into a data-library (with the
approriate rights).
Would anybody have an idea why this
doesn't work anymore in v18.05?
Is it a galaxy.ini configuration
issue?
Thanks for any advise you could
provide!
Christopher
--
Dr. Christopher Previti
Genomics and Proteomics
Core Facility
High Throughput Sequencing (W190)
Bioinformatician
German Cancer
Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661
christopher.previti@dkfz.de
www.dkfz.de
Management
Board: Prof. Dr. Michael
Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537
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--
Dr. Christopher Previti
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician
German
Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661
christopher.previti@dkfz.de
www.dkfz.de
Management Board:
Prof. Dr. Michael Baumann, Prof. Dr. Josef
Puchta
VAT-ID No.: DE143293537
Vertraulichkeitshinweis:
Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert
ist.
Sie kann vertrauliche und/oder nur für
den/die Empfänger bestimmte Informationen
enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein,
kontaktieren Sie bitte den Absender und
löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der
Informationen in dieser Nachricht ist
untersagt.