,
On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
On Wed, Feb 19, 2014 at 9:33 PM, Greg Von Kuster g...@bx.psu.edu 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 -
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 p.j.a.c...@googlemail.comwrote:
,
On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster g...@bx.psu.edu wrote:
On Thu, Feb 20, 2014 at 9:59 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Your installation recipe for mira attempts to download a binary and if that
fails, it echoes an error, but still performs set_environment
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?
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
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
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
___
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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
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
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
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
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,
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
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
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. Why
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?
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Please keep all replies on the list by using
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?
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
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
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 dannon.ba...@gmail.com wrote:
Got it. We dropped the simplejson egg during the last release (and any you
find are holdovers from
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 di...@ie-freiburg.mpg.dewrote:
Hi everyone,
I just updated our local Galaxy installation to the latest
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
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
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:
#
Thanks, I will try this tomorrow.
Fenglou
On 20 February 2014 22:32, Nate Coraor n...@bx.psu.edu 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
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