On Thu, Oct 6, 2011 at 4:48 AM, Duddy, John jdu...@illumina.com 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
On Tue, Sep 6, 2011 at 5:12 PM, Nate Coraor n...@bx.psu.edu wrote:
Peter Cock wrote:
On Tue, Sep 6, 2011 at 5:00 PM, Nate Coraor n...@bx.psu.edu wrote:
Peter Cock wrote:
On Tue, Sep 6, 2011 at 3:24 PM, Nate Coraor n...@bx.psu.edu wrote:
Ideally, there'd just be a column on the dataset
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
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:
outputs
data name=output format=bed
change_format
when input=intype.bed value= format=bam/
/change_format
/data
/outputs
I
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
On Thu, Oct 6, 2011 at 3:48 PM, Duddy, John jdu...@illumina.com 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
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,
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 - type
'exceptions.UnboundLocalError': local variable 'dataset_id' referenced before
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 atovt...@jcvi.orgwrote:
We want to
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
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