Thanks, I will try this tomorrow.
Fenglou
On 20 February 2014 22:32, Nate Coraor wrote:
> Hi Fenglou,
>
> In similar instances, I've simply compiled my own version of Python 2.7
> and placed it in a cluster-wide filesystem, then used the
> environment_setup_file option in universe_wsgi.ini to
Hi Turner,
In universe_wsgi.ini, set 'use_pbkdf2 = False' in the '[app:main]' section.
You probably do not need to make any changes to PostgreSQL's configuration
unless your database is running on a different host from your Galaxy server.
For proftpd.conf, the most important bits are these:
# D
Thanks, Nate! Got it to run after playing with the postgresql url, table was
created, and I began populating it with my admin account. I also prepared the
database for ftp by creating a user for lookup. As for proftpd, I have it
installed, but am not quite sure what do now. How must I edit the p
Hi Fenglou,
In similar instances, I've simply compiled my own version of Python 2.7 and
placed it in a cluster-wide filesystem, then used the
environment_setup_file option in universe_wsgi.ini to ensure this version
is used when jobs run.
--nate
On Thu, Feb 20, 2014 at 3:31 PM, Fenglou Mao wro
Hi Turner,
You should be connecting to the database that Galaxy is using, specified in
the database_connection option in universe_wsgi.ini. If you have not yet
started Galaxy at least once, then the tables will not have been created
yet. Once you run Galaxy and the tables have been created, you sh
Hi Sarah,
This looks a lot like a transient filesystem error. If you attempt to
reinstall the repository, do you get the same error?
--nate
On Thu, Feb 20, 2014 at 10:48 AM, Sarah Diehl wrote:
> Hi everyone,
>
> I just updated our local Galaxy installation to the latest dist version
> and also
Hi Geert,
Thanks for letting us know - I've added the folllowing Trello card for this and
we'll get it fixed asap.
https://trello.com/c/65DOL7PL/160-repository-package-libpng-owned-by-devteam-on-main-tool-shed-bug
Greg Von Kuster
On Feb 20, 2014, at 5:10 PM, Geert Vandeweyer
wrote:
> Hi Bj
Hi Bjoern & devteam members,
I tried to install R_3_0_2 iuc version from the main toolshed, but got
an error from the package_libpng from the devteam. I checked between the
working tool_dependency from the testtoolshed and the failing one from
the main.
working:
type="download_by_url">http:
Thanks for the answer. I am talking to our sysadmin to upgrade cluster nodes
from CentOS 5 to CentOS 6.
Fenglou
On Feb 20, 2014, at 2:18 PM, Dannon Baker wrote:
> Got it. We dropped the simplejson egg during the last release (and any you
> find are holdovers from previous versions of galaxy
Got it. We dropped the simplejson egg during the last release (and any you
find are holdovers from previous versions of galaxy) in favor of the stdlib
module. The relevant module from your find would have been
simplejson-2.1.1, and the rest are unrelated.
If possible, I'd *really* recommend upda
Hello Nikos,
This is a known issue after the recent tool migrations. The ticket is
here: https://trello.com/c/h9LSdfdS
The root cause of the error is a missing fortran library. If you click
on the "eye" for the associated log dataset, and scroll down through the
full report down to the "Warn
It is a little complicated here, The Galaxy server itself is running CentOS
6 with python 2.6, but the cluster nodes are running CentOS 5 with python
2.4. Mose jobs are running in the cluster nodes.
My questions is:
if there is a json module in galaxy-dist/eggs, why Galaxy is not picking it
up? If
The json module is included in python's standard library since python 2.6,
which is the minimum version of python Galaxy currently supports. Are you
using a python version older than that?
___
Please keep all replies on the list by using "rep
I just upgraded our galaxy server to the latest version, and I got this
error in many of the tools:
Traceback (most recent call last): File "./scripts/set_metadata.py", line
14, in ? import json ImportError: No module named json
And a "find" command below give many a few json eggs, please help. W
Hi,
I'm not experienced with postgres and ftp and am thus having difficulties
setting up an ftp server on my local Galaxy instance, but it is essential as
our files are all over 2GB. The admin support page
(https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP) is a little
fuzzy on th
Hi,
I'm not experienced with postgres and ftp and am thus having difficulties
setting up an ftp server on my local Galaxy instance, but it is essential as
our files are all over 2GB. The admin support page
(https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP) is a little
fuzzy on t
Attempting to run a workflow with the tool XY_Plot_1 results in an error when
trying to display the workflow steps. The local dep_value variable is
undefined.
The XY_Plot_1 tool has contains a repeat with a DataToolParameter "input" and 2
ColumnListParameter "xcol", "ycol" dependent on the
Hi everyone,
I just updated our local Galaxy installation to the latest dist version and
also did the tool migration steps (./scripts/migrate_tools/0009_tools.sh).
However, the package galaxy_utils gave me an error and I don't have the
slightest idea what happened. So any help to figure out the
Hi Peter,
Regarding youyr previous question about why the more usefule log resutls are
not returned for display in the Tool Shed, the reason is that our use of
fabric's local command for installing tool dependnecies restricts us from
bewing able to capture that information. We are currently wo
Hi Bjoern,
No, I'm not compressing the results. However, Dannon pointed out the
problem:
My first guess is that it's likely this is due to 'debug = True'
being set in your universe_wsgi.ini. If you set this to false and
restart, the entire request will no longer be loaded into memory
Hi Michael,
are you compressing the results during download?
Cheers,
Bjoern
Dear all,
We run our Galaxy server in a virtual machine with less than 1GB RAM.
When I'm trying to download results via the Download button in the
corresponding history entry that are larger than 1GB, the results fil
My first guess is that it's likely this is due to 'debug = True' being set
in your universe_wsgi.ini. If you set this to false and restart, the
entire request will no longer be loaded into memory.
-Dannon
___
Please keep all replies on the l
Dear all,
We run our Galaxy server in a virtual machine with less than 1GB RAM.
When I'm trying to download results via the Download button in the
corresponding history entry that are larger than 1GB, the results file
is loaded into memory. This leads to the galaxy process being killed,
due to mem
Hello,
Hi,
Compilation/installing works now. Using this R from the commandline no
longer complains about missing X. With regards to cairo, I don't think
I explicitly need it, but as I understood it, it was used in case
there was no X11 server on the system?
Not sure, I will add it if anyon
Hi,
Compilation/installing works now. Using this R from the commandline no
longer complains about missing X. With regards to cairo, I don't think I
explicitly need it, but as I understood it, it was used in case there
was no X11 server on the system?
would you add it to the main toolshed? Th
On Thu, Feb 20, 2014 at 9:59 AM, Peter Cock wrote:
> On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster wrote:
>> Your installation recipe for mira attempts to download a binary and if that
>> fails, it echoes an error, but still performs actions..
>
> Ah - I can see that now, I need a fall back
if a tool failed we all really benefit from seeing as much as we can - as
securely as we can.
Can we safely expose them somewhere protected?
On Thu, Feb 20, 2014 at 8:59 PM, Peter Cock wrote:
> ,
>
> On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster wrote:
> > Hi Peter,
> >
> > On Wed, Feb 19, 20
,
On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster wrote:
> Hi Peter,
>
> On Wed, Feb 19, 2014 at 9:33 PM, Greg Von Kuster wrote:
>>>
>>> In any case, we have a fix for out move_directory_files which
>>> Dave is now committing. So your tests should pass with tonight's
>>> run - Let's hope!
>>
>
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