Hi;
My interpretation is that your BioJava tool is sending normal
information to stderr, and Galaxy interprets it as an error. The same
happened to me with OPPL-Galaxy.
This is a well known bug
(http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr). You
have two options:
- Best
On 12/22/2011 11:46 AM, liram_va...@agilent.com wrote:
Hi Hans,
Thank you for your reply.
Anyway, I tried to install Galaxy again by using the site "check-out" (hg clone
https://...) and it still cause problems.
Specifically, those were my steps:
1) I Installed galaxy in different location.
The tool shed does not handle displaying images included in tool configs like
this, nor does it properly link to other files that within the tool's
subdirectory hierarchy to which the tool config may point. This is because the
files are contained within an hg repository's internal .i files, and
The first option (wrapper) also gives one the opportunity to actually check for
errors.
Chris
On Dec 22, 2011, at 2:21 AM, "Mikel Egaña Aranguren" wrote:
> Hi;
>
> My interpretation is that your BioJava tool is sending normal information to
> stderr, and Galaxy interprets it as an error. The
We are anticipating a similar issue and decided it would be easier to just have
separate VMs where possible. I know this isn't always possible, but it is a
very easy way to both manage multiple galaxy instances and keep the various
galaxy instances completely separate.
Chris
On Dec 22, 2011,
On 12/22/2011 04:13 PM, liram_va...@agilent.com wrote:
Hi Chris,
Thank you.
Just to make sure that I fully understand:
Basically you say that there are no easy way to run two Galaxy process on the
same Linux operating system?
Hi Liram
I am sorry, but I can't leave this statement out there
Hi Hans,
Thank you for your reply.
Anyway, I tried to install Galaxy again by using the site "check-out" (hg clone
https://...) and it still cause problems.
Specifically, those were my steps:
1) I Installed galaxy in different location.
2) After run run.sh in the first time, I changed universe_
Hi Hans,
Sorry, but I not familiar with type of the database that Galaxy is running and
didn't configure any
of the Galaxy SQL features.
(In another words, I don't have a clue what is PostgreSQL or SQLite and how to
configure it... :-) )
About your suggestion:
You absolutely right. I tried to
Hi Chris,
Thank you.
Just to make sure that I fully understand:
Basically you say that there are no easy way to run two Galaxy process on the
same Linux operating system?
Thanks,
Liram
-Original Message-
From: Fields, Christopher J [mailto:cjfie...@illinois.edu]
Sent: Thursday, Decembe
Hi Hans,
Thank you again on your prompt answer. From your reply below, it is clear that
it should be possible to run multiple Galaxy servers under a single linux -
this is exactly what we are trying to do: running two galaxy servers (one
production one for test). I would think this is relative
Dear Galaxy team:
I was trying to use the Get Data - Upload File tool
yesterday. I uploaded all files through FTP. Then selected them in "Files
uploaded via FTP", selected "auto-detect" + "Mouse July 2007 (NCBI37/mm9)
(mm9)" and clicked execute. My jobs are registered, but they
No, I'm sure it's possible. I can't say how easy it is, I've never
tested it myself, but I would assume one could use virtual hosts or
something similar.
I personally just like keeping such things as separate as possible, and
having them as separate VMs makes it a little easier to distinctly
On 12/22/2011 09:57 AM, amir_ben-...@agilent.com wrote:
Hi Hans,
Thank you again on your prompt answer. From your reply below, it is clear that
it should be possible to run multiple Galaxy servers under a single linux -
this is exactly what we are trying to do: running two galaxy servers (one
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