This is bizarre...our production server is on 16.04 and the old UI is no
On 03/01/2017 06:03 PM, D K wrote:
> Hi Hans,
> I'm running 16.10. If I'm not mistaken, the old Data Library interface
> is still accessible in the Admin menu isn't it? I have the same issue
> when navigating to a Data Library either from the Admin or Shared Data
> links. I also tried this in 16.07 with the same result. If it makes a
> difference, I'm using PostgreSQL and Apache.
> On Tue, Feb 28, 2017 at 11:47 PM, Hans-Rudolf Hotz <hrh(a)fmi.ch
> <mailto:email@example.com>> wrote:
> Hi Daniel
> Just double checking which version of galaxy are you running? In
> other words: are you still using the old Data Library interface?
> (if I remember correctly, the old UI was deprecated in 15.10)
> We had similar issues with the old UI.
> The new one works fine and is very fast. E.g. we have a 'MISEQ'
> folder with more than 100 sub folders and a HISEQ folder with more
> than 600 sub folders. Each containing up to 100plus fastq and text
> Regards, Hans-Rudolf
> On 03/01/2017 12:13 AM, D K wrote:
> I've noticed that the more files / folders (think hundreds of
> each with 20+ fastq files) I add to a Shared Data Library, the
> and longer it takes to initially navigate the folder structure
> clicking on the specific Shared Data Library). Just opening up the
> Shared Data Library can take several minutes and often the
> browser times
> out. Is there a way to speed this up?
> If it's relevant, when I add shared data, it's linked rather
> than copied
> into Galaxy. Any suggestions would be greatly appreciated
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Dear galaxy developers,
Is it expected that the virtualenv in .venv/ does include the python
binary but does not include the python shared libraries?
Some more details:
I have installed galaxy on CentOS 6.8 which includes the required python
2.7 only via software collections. For the installation of galaxy I have
enabled the software collection by calling "source
/opt/rh/python27/enable" (which sets PATH, LD_LIBRARY_PATH, MANPATH,
XDG_DATA_DIRS, and PKG_CONFIG_PATH).
Currently I was trying to run the ansible role ansible-galaxy-tools from
https://github.com/galaxyproject/ansible-galaxy-tools which runs
"/home/galaxy/galaxy/.venv/bin/python manage_bootstrap_user.py ..."
and gives me
/home/galaxy/galaxy/.venv/bin/python: error while loading shared
libraries: libpython2.7.so.1.0: cannot open shared object file: No such
file or directory.
This python call would work if I again "source /opt/rh/python27/enable".
But then the venv python binary is used with the library of the system.
Intuitively I would expect that the library and binary belong together.
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,
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
Like Matthias (http://gmod.827538.n3.nabble.com/Fatal-Error-while-uploading-a-File-with-...) I can't upload a file with special characters.
My test file is : Frédéric.txt
The database itself seems to be ok, I can see that the insertion is ok in "history_dataset_association" :
id history_id dataset_id create_time update_time copied_from_history_dataset_association_id hid name info
328 1 330 2017-03-01 08:13:56 2017-03-01 08:14:05 NULL 293 Frédéric.txt uploaded txt file 1 line
But until I change Frédéric.txt to Frederic.txt within the name column, my history is broken.
Errors are the same as described by Matthias.
galaxy.web.framework.decorators ERROR 2017-03-01 09:14:18,321 Uncaught exception in exposed API method:
Traceback (most recent call last):
File "/softs/bioinfo/galaxy-prod/lib/galaxy/web/framework/decorators.py", line 284, in decorator
rval = _format_return_as_json( rval, jsonp_callback, pretty=trans.debug )
File "/softs/bioinfo/galaxy-prod/lib/galaxy/web/framework/decorators.py", line 317, in _format_return_as_json
json = safe_dumps( rval, **dumps_kwargs )
File "/softs/bioinfo/galaxy-prod/lib/galaxy/util/json.py", line 67, in safe_dumps
dumped = json.dumps( obj, allow_nan=False, **kwargs )
File "/usr/local/lib/python2.7/json/__init__.py", line 251, in dumps
File "/usr/local/lib/python2.7/json/encoder.py", line 209, in encode
chunks = list(chunks)
File "/usr/local/lib/python2.7/json/encoder.py", line 431, in _iterencode
for chunk in _iterencode_list(o, _current_indent_level):
File "/usr/local/lib/python2.7/json/encoder.py", line 332, in _iterencode_list
for chunk in chunks:
File "/usr/local/lib/python2.7/json/encoder.py", line 390, in _iterencode_dict
UnicodeDecodeError: 'utf8' codec can't decode byte 0xe9 in position 2: invalid continuation byte
I have read a lot of threads about this kind of error (mostly from stackoverflow)
It is related to Galaxy or it's related to my python installation ?
For a production server, it means that I will have to update manually the database each time a user try to upload such a file (find his id, find the broken history and the file name to correct !)
I'm running Galaxy 17.01 with a mysql (5.7.11-4, UTF-8) database.
I've modified lib/galaxy/datatypes/binary.py (for XLS datatypes) and lib/galaxy/jobs/runners/__init__.py (truncate the job name for PBS-PRO)
# On branch release_17.01
# Your branch is ahead of 'origin/release_17.01' by 3 commits.
# Changed but not updated:
# (use "git add <file>..." to update what will be committed)
# (use "git checkout -- <file>..." to discard changes in working directory)
# modified: lib/galaxy/datatypes/binary.py
# modified: lib/galaxy/jobs/runners/__init__.py
Thanks in advance!
Bioinformatics Research Engineer
BIOGEMMA - Upstream Genomics Group
Centre de Recherche de Chappes
Tel : +33 (0)4 73 67 88 54
Fax : +33 (0)4 73 67 88 99
E-mail : frederic.sapet(a)biogemma.com<mailto:firstname.lastname@example.org>
I've noticed that the more files / folders (think hundreds of folders each
with 20+ fastq files) I add to a Shared Data Library, the longer and longer
it takes to initially navigate the folder structure (after clicking on the
specific Shared Data Library). Just opening up the Shared Data Library can
take several minutes and often the browser times out. Is there a way to
speed this up?
If it's relevant, when I add shared data, it's linked rather than copied
into Galaxy. Any suggestions would be greatly appreciated