On 11/06/2012 04:17 AM, Kevin Y wrote:
Hi,
I'm looking for documentation on what I can do inside the command
tag for tools.
I know of things like
#if str( $input ) == 'yes':
Do stuff
#end if
can I do for loops?
yes, as an example see:
~/tools/filters/catWrapper_fasta.xml
What
Hi ,
I am trying map my Chip-Seq data with Bowtie for Illumina. It's been two
day and my job status is Job still waiting to run
Please help me why my job is taking too much time to run
--BONNY PATEL
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Hi
I am trying to map my Chip-Seq data using Bowtie for Illumina. It's been
two days my job status is Job is waiting to run.
Can please tell me why its taking so much time ??
regards,
-BONNY
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Hello,
The next meeting of the GalaxyAdmins group will be held on November 14 at 10 AM
Central time.
Curtis Hendrickson of the University of Alabama Birmingham's Center for
Clinical and Translational Science (UAB CCTS) will speak on Deploying Galaxy
on a shared-node cluster at UAB.
The
Hi galaxy devs,
We are in the final stages of deploying a new Galaxy instance. We
downloaded the galaxy-dist version a month ago aprox. We realized that,
when launching a job and deleting it in the middle of the execution
(hitting the Delete button in the history bar) will output the following
Hi galaxy devs,
We are in the final stages of deploying a new Galaxy instance. We
downloaded the galaxy-dist version a month ago aprox. We realized that,
when launching a job and deleting it in the middle of the execution
(hitting the Delete button in the history bar) will output the following
That sounds perfectly reasonable. I'll make the change.
Thanks, Juan!
-Scott
- Original Message -
Hi galaxy devs,
We are in the final stages of deploying a new Galaxy instance. We
downloaded the galaxy-dist version a month ago aprox. We realized
that, when launching a job and
Hi Juan,
Thanks for reporting this, it is indeed a bug. The fix below isn't quite
correct (if there is an external metadata job, we do actually want to terminate
it) but I'll take care of it.
For reporting bugs in the future, certainly feel free to message this list or
you can also file an
Hi Alan,
I'm CC'ing the Galaxy-Dev list on my response to your question.
I talked with Jen Jackson on this. Her suggestion is that the symlink is
most likely the problem somehow - this time. When in doubt, getting rid of
these good place to start. So recommended starting solution to try - use
On Oct 29, 2012, at 9:23 PM, Todd Oakley wrote:
I changed the name of this thread, to go in a related by new direction:
I wonder if the Galaxy developers and community have any opinions on what is
the best way to organize tools into repositories. We've developed a large
number of tools
Yes, primer3 is available as a command line tool, it was just an example,
the one I'm actually after is optimus primer..
I'm sure there are several web-tools out there that would be nice to get to
Galaxy...
Any Ideas??
Regards,
Franco
On 5/11/12 11:18 PM, Peter Cock
Subject: Re: [galaxy-dev] Cannot run Galaxy : socket.gaierror: [Errno -2]
Name or service not known
From: n...@bx.psu.edu
Date: Mon, 5 Nov 2012 12:07:59 -0500
CC: yj...@hotmail.com; galaxy-...@bx.psu.edu
To: paul.bod...@biotek.uio.no
On Nov 5, 2012, at 5:39 AM, Paul Boddie wrote:
Hi,
I wonder if it's a known problem. I had a quick look through the mailing list,
but didn't see any relevant messages:
An extraction of a workflow from a history breaks on the bwa step:
Error - type 'exceptions.ValueError': invalid literal for int() with base 10:
'False'
URL:
This is a pre-migration bwa. I've not updated this Galaxy instance, yet.
Here is a paste of used all options:
Will you select a reference genome from your history or use a built-in index?
history
Select a reference from history 3: StaphAureus_USA300_FPR3757 .fasta
Is this library
Got this in the latest pull of galaxy central...Ideas?Traceback (most recent call last):
File "./scripts/set_metadata.py", line 24, in ?
import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers
File
Well, lib/galaxy/datatypes/registry.py hasn't changed in over two months. Out
of curiousity,
I tried downloading a fresh copy of galaxy-central (without any initial
configuration or database,
either) and didn't encounter the same problem. I even tried messing with that
line of code and
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