On 11 July 2013 04:31, Saket Choudhary wrote:
> Apologies if my previous suggestion confused you :
> http://dev.list.galaxyproject.org/error-while-writing-to-pdf-in-python-tp4660463p4660464.html
>
>
> You may first generate the pdf :
>
> input_file = sys.argv[1]
> output_file = sys.argv[2
Apologies if my previous suggestion confused you :
http://dev.list.galaxyproject.org/error-while-writing-to-pdf-in-python-tp4660463p4660464.html
You may first generate the pdf :
input_file = sys.argv[1]
output_file = sys.argv[2]
#txt_in = options.exp_data # + '.txt' ## NOT REQUIRED
On Wed, Jul 10, 2013 at 8:03 PM, Björn Grüning
wrote:
> Hi VJ,
>
> you only can have one tag in a tool, afaik. You can try to
> write it with cheetah and concatenate several shell commands with && or
> you can extend your python script to call your java tool at first step.
>
> Cheers,
> Bjoern
>
Hi VJ,
you only can have one tag in a tool, afaik. You can try to
write it with cheetah and concatenate several shell commands with && or
you can extend your python script to call your java tool at first step.
Cheers,
Bjoern
> Hi,
>
>
> I am trying to integrate a tool into galaxy. The tool
Hi,
Are any of the following tools available in galaxy?
1) IDRhttp://www.uwencode.org/software/hotspot
2) Hotspot https://sites.google.com/site/anshulkundaje/projects/idr
3) Wiggler https://code.google.com/p/align2rawsignal/
4) PhantomPeakQualTools
Regards,
Vijayalakshmi.
Hi Galaxy,
When I try to process my exome data bam files using DepthOfCoverage under GATK
tools (on the main instance), the program seems to keep running forever
without ever completing. There is no error message output but the program
never ends after going for several days! Could it be som
Hi,
I am trying to integrate a tool into galaxy. The tool runs in two parts -
1) Computes correlation and provides an ouput 'txt' file (Java) 2)
Takes the previously ouput txt file and outputs a 'pdf' file. (Python)
I am having trouble with the second tool. If I provide a sample 'txt' file
Hi Huayan,
Your external website should accept a parameter "GALAXY_URL" and use this value
as e.g. the content of the attribute (use a sensible
default when not starting at Galaxy and this value is not provided). Your
webpage should post back to GALAXY_URL with a parameter named "URL" which
c
Hi,
Are any of the following tools available in galaxy?
1) IDRhttp://www.uwencode.org/software/hotspot
2) Hotspot https://sites.google.com/site/anshulkundaje/projects/idr
3) Wiggler https://code.google.com/p/align2rawsignal/
4) PhantomPeakQualTools
Regards,
Vijayalakshmi.
Hi, Ross,
I appreciate you taking the time to answer my inquiry. I did know about
the options that technically should not be set on a production server (i.e.
debug), although I have to admit I did not fully understand the
implications of this (i.e. "your Galaxy process may run out of memory if
it
On Wed, Jul 10, 2013 at 1:38 PM, Himanshu Gupta wrote:
> Hello everyone,
>
> I had been using an old galaxy build, downloaded in 2010, on my local server
> and now I am updating it to latest build. I had made some changes as per our
> need. Along with the output file I have added a piece of code w
After 1 year of using the same share string at the launch page *
https://biocloudcentral.herokuapp.com/launch, *the program no longer loads
my application; I. The instance loads, but my galaxyData folder is empty. I
am not sure if the problem has occurred because Galaxy has moved something
or wheth
Hello everyone,
I had been using an old galaxy build, downloaded in 2010, on my local
server and now I am updating it to latest build. I had made some changes as
per our need. Along with the output file I have added a piece of code which
was making us able to download the stderr file as well in ca
On Tue, Apr 30, 2013 at 4:30 PM, Peter Cock wrote:
> On Thu, Apr 25, 2013 at 3:36 PM, Peter Cock wrote:
>>
>> OK, I've updated to the latest galaxy-central default branch. Here's
>> the slightly revised test for ncbi_makeblastdb.xml,
>>
>> ...
>
> In the absence of any fresh feedback, I've filed
Hi,
A follow up to my own question.
When I setup up the Galaxy instance from Cloudman the GATK tools were not
included automatically. Something most have gone wrong during the upgrade
process from Mercurial.
Based on Dan Blankenberg's advice, I was able to got the GATK tools to show
up in Galaxy b
Hi All,
I've setup the Galaxy application on a standard NFS mount without the
'noac' option and then the galaxy datasets on a enabled 'noac' NFS
mount. I updated the universe configuration to reflect the updated
locations. The performance however to the 'noac' mount is really poor,
something
You have two options:
(1) set the number of workers in the LocalJobRunner;
(2) Galaxy can use many different computing clusters, all of which have queuing
systems that you can control.
See this page for more details on both options:
http://wiki.galaxyproject.org/Admin/Config/Performance/Cluste
On Wed, Jul 10, 2013 at 12:39 PM, Tim-Christoph Roloff
wrote:
> Hi Peter,
>
> I thought about that but the user is expected to choose individual
> fold-change and p-value for each of the selected contrasts. I currently
> don't see how I would be able to connect the selected items in the
> multi-s
Hi Peter,
I thought about that but the user is expected to choose individual
fold-change and p-value for each of the selected contrasts. I currently
don't see how I would be able to connect the selected items in the
multi-select column picker with these values. Any suggestions on that?
Than
Is it possible to create a queue system for separate jobs.
I have a module which roughly consumes all CPUs on our machine and if another
user decides to run the same module with other data it should wait till all
other runs are finished to prevent overloading.
Is there a setting for this?
Jas
On Wed, Jul 10, 2013 at 11:26 AM, Ido Tamir wrote:
> Hi,
> I grabbed some xml files from Hannons website for his fastx toolkit (improved
> over galaxys default version).
> Then I created a repository, uploaded the xml files,
> but the toolshed complains that it could not find the tools for
> crea
On Wed, Jul 10, 2013 at 11:23 AM, Tim-Christoph Roloff
wrote:
> Hi,
>
> I am working on a tool that allows to filter on a selected set of contrasts.
> The contrast names are read from the second column of a history item. In
> order to allow selection of individual filters for each contrast, I am u
Hi,
I grabbed some xml files from Hannons website for his fastx toolkit (improved
over galaxys default version).
Then I created a repository, uploaded the xml files,
but the toolshed complains that it could not find the tools for
creating metadata in the xml files.
Could somebody please tell me
Hi,
I am working on a tool that allows to filter on a selected set of contrasts. The contrast
names are read from the second column of a history item. In order to allow selection of
individual filters for each contrast, I am using the tag. Now I would like
to make sure that the user selects e
Ricardo,
You can configure galaxy such that it will allow users to permanently delete
and purge datasets from their own histories. After deleting by pressing the
cross...select 'include deleted datasets' from the history menu. There you can
undelete but also purge immediately from disk.
So i
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