Hi Jan
This is brilliant - it is always the simple solutions you overlook -
thank you very much!
May I just add a modified version, in case you use external
authentication. There is no point to create a cookie, since you need to
provide userid (not the e-mail) and password each time. So a
Hi Robert
Have you looked at the Download or Export option? - you get this
option, when you click on the triangle next to the names of you workflows.
Regards, Hans
On 03/27/2012 08:36 PM, Robert Chase wrote:
Hello,
We are going to migrate to a new instance of the galaxy server. Our
Hi,
I managed to run a local Tool Shed and add a repository.
On the same machine, a local galaxy is running, and configured for using
this local toolshed.
In the Admin menu of Galaxy, I can see my local Toolshed listed under
'Search and Browse tool sheds'.
However, when I click on my
Dear Galaxy Dev,
Now I have another problem with the Galaxy sample tracking data
transfer. Galaxy is not able to transfer the datasets but when it
attempts to associate the datasets with the library and folder
specified in the sequencing request I get this:
2012-03-28 13:07:02,706 -
Hi,
after thinking more about this and also trying to get Apache use NIS (I failed
with that :-( )
I just came up with an idea for a different solution:
I don't use NIS for login into galaxy but when starting jobs I consult a mapping file (or the
database) to map email addresses to know
Jemma,
It looks like the boto package is not installed on your system. Try:
sudo apt-get install python-boto
Dave B.
On 3/18/12 8:19 PM, Jemma Wu wrote:
Dear Galaxy developers,
This is the first time that I installed Galaxy on a Debian Lenny 64 bit
server. I got an error of “ImportError:
Dear Galaxy Dev,
The malformed library folder error on the latest galaxy-dist I am
gettting (shown below) right after data transfer I am pretty sure is a
bug and regression.
I was just able to do the exact same sample tracking setup on one of
my other Galaxy servers which is an older galaxy-dist
Hi Rob
I don't know what exactly you mean by new server. Assuming you are
just talking about different hardware:
Have you considered moving 'everything' to the new server? ie copying
the Galaxy directory tree (especially make sure you copy ~/database/ )
and connect to the same PostgreSQL
Ann,
Could you give me the value of the cleanup_jobs configuration entry in
universe_wsgi.ini?
Thank you,
Dave B.
On 3/21/12 4:35 PM, Ann Black wrote:
Hello -
I have noticed on our local install, that the job scripts as well as
stdout/err in our cluster_files_directory is not getting
Hi,
I'm running these tools on a cluster..
Alban
Emil Bouvier wrote:
Alban,
Are you running these tools on a cluster, or on a local system?
Dave B.
On 3/19/12 6:55 AM, Alban Lermine wrote:
Hi,
I have the same error message for multiple tools (GFFtoBED,
BEDtoBIGBED,BAMtoSAM,...):
Hello -
Thanks much for the response. I do not find an entry in my
universe_wsgi.ini file for cleanup_jobs - should I have one?
Ann
On 3/28/12 9:45 AM, Emil Bouvier d...@bx.psu.edu wrote:
Ann,
Could you give me the value of the cleanup_jobs configuration entry in
universe_wsgi.ini?
Thank
Hi,
Try:
--no_overlap $singleOrPair.no_overlap
Best,
L-A
Le 28/03/2012 18:59, cai cai a écrit :
Hi All,
I am trying to add a tool to Galaxy, here is my xml configuration:
## Set params based on whether reads are single-end or paired.
#if $singleOrPair.readType ==
Thank you very much L-A.
It works perfectly.
Cai
2012/3/28 Louise-Amélie Schmitt louise-amelie.schm...@embl.de
Hi,
Try:
--no_overlap $singleOrPair.no_overlap
Best,
L-A
Le 28/03/2012 18:59, cai cai a écrit :
Hi All,
I am trying to add a tool to Galaxy, here is my xml
Thank you that could be very helpful to our users if we can't download them
all as one big batch. I was hoping to be able to do something to save the
users the headache of having to export and upload their workflows to the
new server.
Regards,
-Rob
On Wed, Mar 28, 2012 at 4:07 AM, Hans-Rudolf
I have a custom module/page created to get data from some SOAP-based web
services. I haven't determined the threshold yet, but for small BAM files,
Galaxy behaves just fine. However, when I get large BAM files (I've had the
same results with 10gig and 40gig files), Galaxy doesn't recognize
I am getting an error upon my local Galaxy startup which I suspect is causing
an invalid tool runner entry in my left hand menu (my tool url is:
http://localhost:8081/tool_runner/index instead of
http://localhost:8081/tool_runner?tool_id=FLASHforFASTQ)
Here is the error I get:
galaxy.tools
That did it! Silly mistake - thanks so much!!
-Original Message-
From: Dannon Baker [mailto:dannonba...@me.com]
Sent: Wednesday, March 28, 2012 2:21 PM
To: Brami, Daniel
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] toolrunner / xml parse
data format=fastqsanger
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