Le 29/08/2011 18:54, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
Le 29/08/2011 15:52, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
Hello everyone,
These questions are a bit silly but I'm really ignorant when it
comes to security. Sorry about that.
Why use API keys instead of us
Hi,
There is a 'set_metadata_externally' setting in universe_wsgi.ini file. What
is involved in this step? Is it run for every dataset/output being generated in
the galaxy?
--
Thanks,
Shantanu.
___
Please keep all replies on the list by
Shantanu Pavgi wrote:
>
> Hi,
>
> There is a 'set_metadata_externally' setting in universe_wsgi.ini file. What
> is involved in this step? Is it run for every dataset/output being generated
> in the galaxy?
Hi Shantanu,
Metadata is always detected/set on all job outputs. This setting simpl
I just changed it and ran into an error, so I modified the line and it
now works fine:
$__app__.security.encode_id( '%s' % $input1.id )
What was the 'file.' originally for?
Le 24/08/2011 15:00, Louise-Amélie Schmitt a écrit :
Thanks a lot!
I found another way to do it but it is awfully more
On Aug 30, 2011, at 9:16 AM, Nate Coraor wrote:
> Shantanu Pavgi wrote:
>>
>> Hi,
>>
>> There is a 'set_metadata_externally' setting in universe_wsgi.ini file.
>> What is involved in this step? Is it run for every dataset/output being
>> generated in the galaxy?
>
> Hi Shantanu,
>
> Metad
Louise-Amélie Schmitt wrote:
> I just changed it and ran into an error, so I modified the line and
> it now works fine:
> $__app__.security.encode_id( '%s' % $input1.id )
> What was the 'file.' originally for?
On the API side, a library or history's "contents" are all identified by
ID, so:
ht
Shantanu Pavgi wrote:
>
> On Aug 30, 2011, at 9:16 AM, Nate Coraor wrote:
>
> > Shantanu Pavgi wrote:
> >>
> >> Hi,
> >>
> >> There is a 'set_metadata_externally' setting in universe_wsgi.ini file.
> >> What is involved in this step? Is it run for every dataset/output being
> >> generated in
Le 30/08/2011 16:51, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
I just changed it and ran into an error, so I modified the line and
it now works fine:
$__app__.security.encode_id( '%s' % $input1.id )
What was the 'file.' originally for?
On the API side, a library or history's "contents"
Louise-Amélie Schmitt wrote:
> Le 30/08/2011 16:51, Nate Coraor a écrit :
> >Louise-Amélie Schmitt wrote:
> >>I just changed it and ran into an error, so I modified the line and
> >>it now works fine:
> >>$__app__.security.encode_id( '%s' % $input1.id )
> >>What was the 'file.' originally for?
> >O
This is probably a question for our sys admin but when I run tools such as
GATK I get an error java command not found. I can execute java from the command
line and it works. Further I can grab the drmaa submission script (ie
galaxy_job_id.sh) and qsub it from the command line and it finds JAVA.
Yes, your java path is not set, because you are using an non-login shell.
Indeed, you should be talking to your sysadmins.
George Marselis, systems administrator
Building #2, Level 4, room 4327
Computational Bioscience Research Center, KAUST
Land: +966-2-808-2944, Mobile: +966-56-321-7713, S
Le 30/08/2011 18:00, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
Le 30/08/2011 16:51, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
I just changed it and ran into an error, so I modified the line and
it now works fine:
$__app__.security.encode_id( '%s' % $input1.id )
What was the '
How do I set my path in a non login shell?
From: George Marselis [mailto:george.marse...@kaust.edu.sa]
Sent: Tuesday, August 30, 2011 9:40 AM
To: Chorny, Ilya; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Tools requiring java can't find java
Yes, your java path is not set, because you ar
The following has a bit of advice on that:
http://www.admon.org/difference-between-login-shell-and-non-login-shell/
chris
On Aug 30, 2011, at 1:03 PM, Chorny, Ilya wrote:
> How do I set my path in a non login shell?
>
> From: George Marselis [mailto:george.marse...@kaust.edu.sa]
> Sent: Tues
Gah, wrong link, apologies (the other one is okay, if a bit wonky):
http://www.linuxfromscratch.org/blfs/view/cvs/postlfs/profile.html
chrus
On Aug 30, 2011, at 1:12 PM, Chris Fields wrote:
> The following has a bit of advice on that:
>
> http://www.admon.org/difference-between-login-shell-and
August 30, 2011 Galaxy Development News Brief
http://galaxyproject.org/wiki/News%20Briefs/2011_08_30
Source: http://getgalaxy.org
new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r 949e4f5fa03a
What's New
ISMB/ECCB, BOSC, and 3DSIG 2011 Slides
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