I have some problems with the download of genome files by the data
manager. I tried to download some genome files from the UCSC server with
the data manager of galaxy ( name: data_manager_fetch_genome_all_fasta,
revision: cca219f2b212), but it fails because of a timeout. Our galaxy
server is in an internal network without connection to the Internet. To
access the Internet we are required to go trough a http-proxy before any
web-services can be accessed.
manages the download of the file. Line 183 shows the problem. Here the
FTP item from the python ftplib module tries to establishes the
connection to the UCSC ftp server. This connection fails. So here is my
How can i download data by the data manager with a http-proxy?
We're having problems adding files to data libraries.
We'd like to create links to files instead of copying them into Galaxy. We can create links if there aren't spaces in the paths. Also, we can copy files into libraries even if there are spaces in the paths.
Unfortunately, we cannot create links to files when their paths contain spaces.
The job standard error and miscellaneous information are:
Miscellaneous information:uploaded RAW file Traceback (most recent call last): File "/share/galaxy/working/002/2615/set_metadata_hnsR90.py", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/home/galaxy/Galaxy/galaxy-dist
Job Standard Error
Traceback (most recent call last):
File "/share/galaxy/working/002/2615/set_metadata_hnsR90.py", line 1, in <module>
from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()
File "/home/galaxy/Galaxy/galaxy-dist/lib/galaxy_ext/metadata/set_metadata.py", line 80, in set_metadata
filename_out = fields.pop( 0 )
IndexError: pop from empty list
We've set allow_library_path_paste = True in galaxy.ini.
We've also tried adding "" or '' around the path and get the following error message:
Invalid paths: "home/galaxy/Galaxy/galaxy-dist/"/share/projects/2014 Test""
Any help or suggestions would be great.
Proteomics Center of Excellence
Hi Björn, Eric, all,
I'm trying to get ipython running on our instance. Without the proxy, e.g.
http://myserver:8080 it works fine. However, with the proxy in front (e.g.
http://myserver/galaxy) I get this firefox error
"11:28:37.793 Cross-Origin Request Blocked: The Same Origin Policy
disallows reading the remote resource at
(Reason: CORS request failed).1 <unknown>"
or on chrome "xhr" request "cancelled".
Do you happen to know the correct apache settings to overcome this?
I tried a few things, but I ended up with ipython starting, but with a
message "cannot connect to websocket".
I am new to maintaining the galaxy server at my institute and a user
emailed me that they get the following error message when trying to view
"Either you are not allowed to view this history or the owner of this
history has not made it accessible."
Is there a way to modify access privileges of the users' histories?
Thanks for any advice!
I get this error on cluster creation:
Error creating volume: EC2ResponseError: 400 Bad Request
InvalidParameterValueVolume of 2048GiB is too large for volume type
standard; maximum is 1024GiB
Is there a way to get a volume that big for galaxy?
I have this tool that creates a collection by discovery datasets.
It always worked fine, but this time I had 3 Histories, where I ran
the tool on three different datasets.
When it finished, the collections were empty.
The datasets, that should be in the collections however, were there.
Is that known?
Is that fixed in 15.07?
cloudlounch at launch.usegalaxy.org doesn't work for me anymore.
Some hours ago I still was able to start a cluster, but now it seems
that the launcher can't connect to my amazon anymore?
No machnie get's started.
But I'm still able to fetch key pair and placement.
Any suggestions what to try?
Already: Reloaded page, Restarted PC.
I am trying to run metaphlan on the Galaxy public website, but even a 25MB file cannot be uploaded for analysis. It says the size is too large. And to run metaphlan on local it is just a nightmare because there is absolutely no tutorial of how to install all the prerequisites for material and metaphlan itself. Please see if you can extend the upload file size to atleast 1GB on the galaxy public server of size or atleast have a tutorial for running metaphlan locally.
The Galaxy "Variant Annotator" tool uses this loc file :
This file is available in tool-data/ directory and completed but the
dropdown menu of "Variant Annotator" tool is empty.
#This is a sample file distributed with Galaxy...
oviAri1 oviAri1 Ovis:oviAri1 /bank/Galaxy/oviAri1/current/flat/picard_index/oviAri1.dict
oviAri1.dict oviAri1.fa oviAri1.fa.fai
Could you please tell me where does my mistake ?
INRA - LGC - SIGENAE
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
We am attempting to build a local galxay server and we are looking for
The plan is to purchase a decdicated server to host galaxy and
communicate with our IBM System x3755 120 node computer cluster running
TORQUE/Maui resource manger and scheduler. Do you have an recomendations
on the configuration and adequate hardware for the server. The server
will only act as a gateway to users, but will not do any computational
If anyone has had experience with this kind of setup, could you offer
any further suggestions?