Running jobs as real user and extra_file_path
by Louise-Amélie Schmitt
Hi everyone,
I just wanted to ask how the extra_file_path is handled in case of job
running as the real user since the file_path is only writable by the
galaxy user. Any clue?
Thanks,
L-A
2 years, 6 months
Upload issue in local installation
by Batsal Devkota
I installed galaxy locally in a linux server. However, I cannot upload the files (no matter how small, I have tried few kb size fasta files). When I try to upload, the link to the file shows up in the History and gets a new number (purple box). When I click on the link I get 'Dataset is uploading' forever.
In the terminal window where I start galaxy, I get the following error report:
92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /root/tool_menu HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /history HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:33 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:40 -0400] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://redhat:8080/root/tool_menu" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /tool_runner/upload_async_create HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /tool_runner/upload_async_message HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /history HTTP/1.1" 200 - "http://redhat:8080/tool_runner/upload_async_message" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:34:04 -0400] "POST /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:34:08 -0400] "POST /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
The last line keeps going for ever... writes new line every 4 secs.
I am stuck and don't know where to look. Please help.
Batsal.
3 years, 9 months
filtering a <param> of type 'data' so only one type is available
by Dan Tenenbaum
Hi,
I have a tool wrapper with a <param> of type="data".
Currently, this renders as a text box with a drop down list that has
52 items in it (the number of things I have in my history, I guess).
I'd like to filter this list so that only some items in the history
(in my case any item whose name ends with '.rda') are shown in this
dropdown.
It seems like maybe the 'format' parameter to the 'param' tag is what
I want, but:
1) I tried format="rda" and that didn't seem to change anything.
2) "rda" is not in the datatypes.conf file which the documentation
suggests is required?
(.rda is an extension used for serialized R objects.)
The tool I'm working on only accepts rda files as input and the reason
I'm asking for this is that it is all too easy to accidentally feed it
a file of some other type. If the dropdown could be filtered so that
only items which will work with the tool are shown, that would be
great.
Is there a way to do that?
Thanks,
Dan
5 years
Workflow param error leads to template error
by Paul-Michael Agapow
Looking for pointers on what might be causing this problem:
A user had a moderately complicated workflow that when run under certain parameter values results in a traceback that ends:
Module workflow_run_mako:232 in render_body
>> for ic in oc.input_step.module.get_data_inputs():
AttributeError: 'WorkflowStep' object has no attribute 'module'
After some puzzling, I realized one of the parameters was outside the allowed range (a max on an integer param) and that Galaxy was trying to render "run.mako" flagging up the error but erroring out. Why Galaxy tries to call this non-existent member is unclear to me. Any insight or places I should start exploring?
Galaxy version: various (started with an 6-month old one, upgraded to latest production to see if it would fix error, it didn't)
Hosting OS: CentOS 6
------
Paul Agapow (paul-michael.agapow(a)hpa.org.uk)
Bioinformatics, Health Protection Agency (UK)
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5 years, 2 months
user specific access/options
by Jennifer Jackson
Hi Petr,
I am going to forward your email to the galaxy-dev list so that the
development community can offer comments/suggestions.
Best,
Jen
Galaxy team
On 8/30/11 2:27 AM, Petr Novak wrote:
> Hi everybody,
> I am developing the application on Galaxy server. One of the requirement
> is to create user specific list of options. Is it possible to access
> somehow $__user_email__ in <options> tag or in <conditional> ?. I did
> not found documentation how to used cheetah in galaxy tool xml files but
> from files provided with galaxy, cheetah is used only in <command> and
> <config> tag. Is that rigth? If it can be used in any part of xml
> definition file it would make much easier to generate xml dynamicaly
> based on the $__user_email__
> Does anybody have an idea how to manage this problem?
> Petr Novak
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
5 years, 6 months
Default value for data_column not working?
by Peter Cock
Hi all,
I'm trying to write a new tool working with tabular data (specifically
a Reciprocal Best Hits (RBH) tool using BLAST style tabular output).
I want the user to be able to choose a column number (from one of the
input files), but I have a default column in mind. However, Galaxy
doesn't seem to obey the default column number:
<inputs>
<param name="a_vs_b" type="data" format="tabular" label="Hits
from querying A against B" description="Tabular file, e.g. BLAST
output" />
<param name="b_vs_a" type="data" format="tabular" label="Hits
from querying B against A" description="Tabular file, e.g. BLAST
output" />
<param name="id1" type="data_column" data_ref="a_vs_b"
multiple="False" numerical="False" value="1" label="Column containing
query ID" help="This is column 1 in standard BLAST tabular output" />
<param name="id2" type="data_column" data_ref="a_vs_b"
multiple="False" numerical="False" value="2" label="Column containing
match ID" help="This is column 2 in standard BLAST tabular output"/>
<param name="score" type="data_column" data_ref="a_vs_b"
multiple="False" numerical="False" value="12" label="Column containing
containing score to rank on" help="The bitscore is column 12 in
standard BLAST tabular output"/>
</inputs>
I've tried giving the default column value numerically (as shown), and
also using value="c2" etc. Regardless, Galaxy just defaults to the
first column.
Is this a bug, or am I doing something wrong?
Thanks,
Peter
5 years, 6 months
history item status not updating
by Robert Baertsch
I submitted a workflow that in turn submits a drm job to sun grid engine.
The queue had an error (probably due to a problem with automount).
Traceback (most recent call last):
File "/inside/depot4/galaxy/lib/galaxy/jobs/runners/__init__.py", line 60, in run_next
method(arg)
File "/inside/depot4/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 169, in queue_job
external_job_id = self.ds.runJob(jt)
File "/inside/depot4/galaxy/eggs/drmaa-0.4b3-py2.7.egg/drmaa/__init__.py", line 331, in runJob
_h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate)
File "/inside/depot4/galaxy/eggs/drmaa-0.4b3-py2.7.egg/drmaa/helpers.py", line 213, in c
return f(*(args + (error_buffer, sizeof(error_buffer))))
File "/inside/depot4/galaxy/eggs/drmaa-0.4b3-py2.7.egg/drmaa/errors.py", line 90, in error_check
raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))
DeniedByDrmException: code 17: error: no suitable queues
When the sysadmin cleared the error, the job started running normally after being in an error state for 10 minutes.
The cool thing is that galaxy kept running without a problem.
galaxy.jobs.runners.drmaa DEBUG 2013-06-27 14:51:22,968 (10481/4767487) state change: job is running
galaxy.jobs.runners.drmaa DEBUG 2013-06-27 15:00:23,628 (10481/4767487) state change: job is queued and active
galaxy.jobs.runners.drmaa DEBUG 2013-06-27 15:00:27,751 (10481/4767487) state change: job is running
However in the history panel, the job shows as queued but not running, even if I refresh the history panel.
Is this normal or should the status change to running?
I'm using this version of straight galaxy:
changeset: 10162:f295092476c7
branch: stable
parent: 10160:2efb1083676b
user: Dannon Baker <dannonbaker(a)me.com>
date: Sat Jun 15 09:08:09 2013 -0400
summary: Fix reports import issue reported by Lance, https://trello.com/card/bug-in-reports-webapp-imports/506338ce32ae458f6d1...
-Robert Baertsch
UC Santa Cruz
5 years, 6 months
registration problem
by Wesley Schaal
Galaxy-Dev,
I have a new galaxy installation under Linux. It's running as an Apache proxy (subdirectory) with authentication through galaxy (not apache).
When trying to register a new user (which will be the administrator), the registration page declare success ("Now logged in as foo") but I am still just an anonymous user. If I try to login, it appears to succeed but I'm still anonymous. If I purposely enter the wrong password, the system complains as it should but I never get proper credentials.
If I take away the Apache proxy configuration and run on the internal server, the problem goes away: I can login as expected and get the correct environment. The error is clearly here but I feel like I've followed the procedure written on the wiki. Specifically,
Apache
-----------
RewriteEngine on
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy(.*) http://localhost:8082$1 [P]
# 8080 and 8081 are busy
Galaxy
---------
[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /galaxy
[app:main]
filter-with = proxy-prefix
cookie_path = /galaxy
Any idea of what might be wrong? Don't know if it matters but I'm using a MySQL database. I can see new users and it seems to work well enough to complain when bad passwords are entered.
--
Wes
5 years, 7 months
Blast+: new feature filter/mask... by taxid before job in one task
by Berner, Thomas
Hi guys,
We recently installed NCBI BLAST + to our local Galaxy instance and now we need to provide the possibility to filter/mask ... by taxon id (taxid) using the command line option (-window_masker_taxid) of BLAST (cf. http://www.ncbi.nlm.nih.gov/books/NBK1763/) before the job will be performed in one task.
However searching in the documentation and the mailing list, I did not find anything about this.
So it would be great to provide the possibility to subselect by taxid (e.g. NCBI BLAST server http://blast.ncbi.nlm.nih.gov/Blast.cgi) by changing the BLAST integration.
We believe this could be of common interest. It would be great if anybody could comment on this.
Thanks a lot, Thomas
5 years, 8 months
