Hi,
I'm not sure if this is related or not but I'm also noticed a
similar problem where the program is not found in the path, but it
exists. I have it submitted as an issue , but it could be related here
so mentioned here. The problem started when I recently upgraded my
Galaxy installation(It wa
I haven't added any such delay after DrmCommunicationException however I have
thought about increasing it in the job monitor function itself (site specific
change, not suggesting it in the blessed galaxy repo).
https://bitbucket.org/galaxy/galaxy-central/src/cb8d6a29ea22/lib/galaxy/jobs/runners
On Jan 18, 2012, at 5:28 PM, Matt Shirley wrote:
> Hi all. I'm sorry if this has been answered before, but I've searched and
> cannot find a solution other than "add SAMtools to your PATH", which I
> already have done. I can invoke samtools from BASH while logged in as the
> "galaxy" user I set
On Jan 16, 2012, at 8:31 AM, Peter Cock wrote:
> On Mon, Jan 16, 2012 at 1:20 PM, graham etherington (TSL)
> wrote:
>> Hi Nate,
>> We are getting quite large discrepancies between 'Size on disk' and
>> 'Usage' numbers, so I've run the scripts/set_user_disk_usage.py script.
>> When I run it, some
On Jan 19, 2012, at 10:49 AM, Sarah Maman wrote:
> Hi Brad, Hi Christopher,
>
> Thanks a lot.
> I'm talking to Open LDAP. I have changed
>
> RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e
> to
> RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e
>
> But I always have the same message /(Acce
Hi Leon,
Jen is correct. As far as the FTP directory, we use the MaxStoreFileSize
directive in ProFTPd to limit the size of any single file uploaded.
--nate
On Jan 17, 2012, at 10:22 PM, Jennifer Jackson wrote:
> Hi Leon,
>
> I can let you know that there is a hard limit of 50G per file allo
On Jan 16, 2012, at 5:22 AM, Louise-Amélie Schmitt wrote:
> Hello,
>
> We want to move Galaxy's jobs from our small TORQUE local install to a big
> cluster running PBS Pro.
>
> In the universe_wsgi.ini, I changed the cluster address as follows:
> default_cluster_job_runner = pbs:///
> to:
> de
Hi Hans,
We're releasing a distribution today. If this is still the case with that
distribution, let me know. There were branches that weren't showing up under
newer versions of Mercurial. Hopefully this is all resolved in the latest.
--nate
On Jan 17, 2012, at 4:11 AM, Hans-Rudolf Hotz wro
Hey Ed,
This is a neat approach. You could possibly also do this in the Galaxy
database by associating users and groups with roles that match project names.
A select list or history default that allowed users to select their "current"
project/role would remove the single-project-per-user limi
Hi,
is it possible to restrict the number of concurrent jobs for a single
user in a local instance of galaxy? I see that in the public site
this feature is implemented, but I don't find documentation about
how to implement this locally. I think it's not possible through
pbs because all users subm
David,
This is the approach recommended on the wiki for performance:
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
Would be nice if your alternative approach using virtual hosts were similarly
documented.
chris
On Jan 19, 2012, at 10:01 AM, David Hoover wrote:
> Why do you need to
Hello Sarah,
Sarah Maman wrote, On 01/19/2012 10:49 AM:
> I'm talking to Open LDAP. I have changed
>
> RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e
> to
> RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e
>
> But I always have the same message /(Access to Galaxy is denied
> Galaxy is conf
Why do you need to create a proxy? The way I have ours set up is within a
virtual host:
AuthName "Helix Systems"
AuthType Basic
AuthBasicProvider ldap
AuthzLDAPAuthoritative off
AuthLDAPUrl ldaps://helixdrive.nih.gov/ou=Users,ou=helix.nih.gov,o=scb?uid
AuthLDAPBindD
Hi Brad, Hi Christopher,
Thanks a lot.
I'm talking to Open LDAP. I have changed
RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e
to
RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e
But I always have the same message /(Access to Galaxy is denied
Galaxy is configured to authenticate users via
You're absolutely right, sorry, I did misread your email as two separate
issues. Workflow parameters are currently unavailable via the API.
Instead of making actions settable at runtime and directly available through
the API, I will probably implement parameters via API as the path forward her
We also ran into this. Our local server configuration was case-sensitive and
the LDAP uid key was converted to upper-case, so we used:
RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e
which fixed the problem. We found the solution by searching for
'AUTHENTICATE_uid', it appears to be a re
Hi Sarah:
I don't know what kind of LDAP you're talking to... I'm talking to Active
Directory and this configuration works in that situation.
Order allow,deny
allow from all
AuthType Basic
AuthName "NEB Credentials"
AuthBasicProvide
Hello,
I'm trying to install galaxy on a apache server,and i have the same
error message than David HOOVER when i tried to generate the
authentification files. Thanks to David Hoover who gives me some helpful
explanation.
When i read the thread on gmod, it seems,that the problem is solved
(
Hi Ross,
Yeah, it was probably a merging issue. I confess I didn't double-check
in Bitbucket. *slaps hand*
Actually hg behaved strangely this time, and didn't report all failed
merges so I had to look for the conflicting files manually. Hopefully
there will be no remaining error.
Sorry for
Hi, L-A,
2012/1/19 Louise-Amélie Schmitt :
> Hi Ross
>
> Thanks a million, I hg-pull'ed it solved the problem!! Please push it to
> galaxy-dist? ;)
Glad to hear it works - thanks for reporting back.
> I ran in another little bug though, but nothing serious, you might even have
> already spotted
Hi Jeremy
Thank you very much for your help. I will look into your suggestions.
Regards, Hans
On 01/18/2012 10:08 PM, Jeremy Goecks wrote:
it works fine on the public server
Good, this narrows down the problem to installing the -central script on your
instance b/c main's copy of the scrip
Hi Ross
Thanks a million, I hg-pull'ed it solved the problem!! Please push it to
galaxy-dist? ;)
I ran in another little bug though, but nothing serious, you might even
have already spotted it by now:
In lib/galaxy/web/framework/__init__.py the line 873 made the whole
thing crash due to a wr
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