On Thu, Oct 6, 2011 at 4:48 AM, Duddy, John wrote:
> One of the things we’re facing is the sheer size of a whole human genome at
> 30x coverage. An effective way to deal with that is by compressing the FASTQ
> files. That works for BWA and our ELAND, which can directly read a
> compressed FASTQ, b
On Tue, Sep 6, 2011 at 5:12 PM, Nate Coraor wrote:
> Peter Cock wrote:
>> On Tue, Sep 6, 2011 at 5:00 PM, Nate Coraor wrote:
>> > Peter Cock wrote:
>> >> On Tue, Sep 6, 2011 at 3:24 PM, Nate Coraor wrote:
>> >> > Ideally, there'd just be a column on the dataset table indicating
>> >> > whether t
Hello,
I'm trying to write a wrapper for the intersectBed tool from the
BEDTools suite. The difficulty lies in the possible combinations of
input and output data formats. Input can be either bed or bam. When the
input is bed, the output is also bed. However, when the input is bam the
output c
Hi all,
I've got some Python applications that I've hooked into Galaxy, which
use the Python logging module for output. To capture this output in my
Galaxy history I've created a wrapper that adds a logging.FileHandler
to the root logger, which uses an Galaxy tool output argument as file
to write
Ok, I found the problem myself. I was totally searching in the wrong
place for the error. It was simply a syntax problem. The output
definition should be like follows:
I was closing the data tag too early.
On 10/06/2011 11:40 AM, Sarah Diehl wrote:
Hello,
I'm trying to write a wrapp
Hi,
The scatterplot tool is broken in the distributed version. It works on the
main Galaxy server, but on our local installation it gives this error:
An error occurred running this job:Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing
I'd be up for that something like that, although I have other tasking in the
short term after I finish my parallelism work. I'd rather not have Galaxy do
the compression/decompression, because that will not effectively utilize the
distributed nature of many filesystems, such as Isilon, that our
We want to use CloudMan to provision and control a cluster with our own
VM image (with Galaxy front-end as well). Our plan was to make the VMs
for both our internal Eucalyptus cloud as well as EC2. Will CloudMan
work with Eucalyptus? If not, how much would our effort have be in order
to extend
On Thu, Oct 6, 2011 at 3:48 PM, Duddy, John wrote:
> I'd be up for that something like that, although I have other tasking
> in the short term after I finish my parallelism work. I'd rather not have
> Galaxy do the compression/decompression, because that will not
> effectively utilize the distribu
As I understand it, Isilion is built up from "bricks" that have storage and
compute power. They replicate files amongst themselves, so that for every IO
request there are multiple systems that could respond. They are interconnected
by an ultra fast fibre backbone.
So, depending on your topology
On Thu, Oct 6, 2011 at 5:02 PM, Duddy, John wrote:
> As I understand it, Isilion is built up from "bricks" that have storage
> and compute power. They replicate files amongst themselves, so
> that for every IO request there are multiple systems that could
> respond. They are interconnected by an u
GZIP files are definitely our plan. I just finished testing the code that
distributes the processing of a FASTQ (or pair for PE) to an arbitrary number
of tasks, where each subtask extracts just the data it needs without reading
any of the file it does not need. It extracts the blocks of GZIPped
Got another problem with the bug reporting tool:
"POST /dataset/report_error HTTP/1.1" 500 -
"http://galaxy.hpc.ufl.edu/dataset/errors?id=775"; "Mozilla/5.0 (compatible;
MSIE 9.0; Windows NT 6.1; Trident/5.0)"Error - : local variable 'dataset_id' referenced before
assignmentURL: http://galaxy.h
Hi Andrey,
CloudMan does not currently support eucalyptus but I am looking into it now
so the support is coming (sorry but I don't have a timeline yet, still
working on setting up the infrastructure).
Enis
On Thu, Oct 6, 2011 at 5:13 PM, Andrey Tovchigrechko wrote:
> We want to use CloudMan to p
Hello Florent,
Thanks for your comments and suggestions - see my inline comments.
On Oct 4, 2011, at 11:42 PM, Florent Angly wrote:
> Hi Greg,
>
> I have a few additional comments and questions though:
> 1/ In the universe_wsgi.ini file, maybe the tool_config_file parameter could
> be renamed
John,
I've been following this message thread, and it seems it's gone in a direction
that differs from your initial question about the possibility for Galaxy to
handle automatic editing of the datatypes_conf.xml file when certain Galaxy
tool shed tools are automatically installed. There are so
That would all be terrific. Thanks Greg!
Florent
On 07/10/11 10:15, Greg Von Kuster wrote:
Hello Florent,
Thanks for your comments and suggestions - see my inline comments.
On Oct 4, 2011, at 11:42 PM, Florent Angly wrote:
Hi Greg,
I have a few additional comments and questions though:
1/ I
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