Hello Ross,
Thanks for the reply..
i copied the source directory to tool-data/shared/jars
now it works for the fastqc..
I tried the same for GATK copied the source directory t the location
tool-data/shared/jars
but it gives ERROR as mentioned below..
# ERROR
---
Hi, Sridar,
Why use the FastQC directory -tool-data/shared/jars would make it easy to
simply copy the way the current FastQC tool does this - the source for
FastQC xml and python wrappers are easy to find in the central repository
on bitbucket?
However, to do it properly so it's easy to autoinsta
Dear Developers,
I am using java jar files for softwares like fastqc, GATK. For running
these tools i install the softare and set path in bash_profile file.
My doubt is i placed the jar files in galaxy dist folder (
galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc
)
is this enough to cal
Dear Developers,
Could you please tell me the possibilities of using the R package
cummeRband for visualization of RNA-seq data in galaxy??
Thanks
Sridhar
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Please keep all replies on the list by using "reply all"
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Hello Carl,
Thanks for the reply.
My file 9094 line its cuffdiff output..
After clicking the draw button it keep on shows rendering..
Thanks
Sridhar
On Thu, Jul 11, 2013 at 7:37 PM, Carl Eberhard wrote:
> Hello, Sridhar
>
> How large is the file you're trying to plot?
>
> The scatterplot visua
Thank you for your quick response. However, I have checked and bedtools are
indeed in the galaxy path. When reviewind the log, I get the following:
galaxy.jobs.runners.local DEBUG 2013-07-09 16:59:15,937 execution
finished: grep -v '^#'
/usr/local/galaxy/galaxy-dist/database/files/000/dataset_5
I had migrated BWA tool while at release_2013.02.08 revision. It was working
fine, however, it fails to run with following warning message after updating
Galaxy to release_2013.06.03.
{{{
Building dependency shell command for dependency 'bwa'
galaxy.tools WARNING 2013-07-11 17:16:28,429 Failed
Hi,
I suggest you make a search in the tool shed:
http://toolshed.g2.bx.psu.edu/
I made a quick search, and found at least something named "IDR" there.
Good luck!
Regards
// Samuel
On 07/10/2013 07:45 PM, vijayalakshmi wrote:
Are any of the following tools available in galaxy?
_
You can use the minwidth attribute in the tool config for this
purpose, it will hide the history if the main panel is less than a
certain width. See the UCSC Get Data tool as an example.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, Jul 11, 2013 at 12:00 AM, Peng Li
Here's a cloud image that the Galaxy team often uses for workshops:
http://wiki.galaxyproject.org/CloudWorkshop
Good luck,
J.
On Jul 11, 2013, at 1:28 PM, Maddhi, Srinivas wrote:
> Hi Max,
>
>
> An alternative approach, in case that becomes necessary, would be to set
> up your own temporary i
Hi Max,
An alternative approach, in case that becomes necessary, would be to set
up your own temporary instance of Galaxy in the Amazon Web Services (AWS)
Cloud as described at http://wiki.galaxyproject.org/CloudMan.
Another Cloud-based option: if interested in installing Galaxy on an
auto-scali
Hi,
We would like to use Galaxy to introduce genomic analysis in our introductory
graduate genetics course. Would anyone be willing to let us "borrow" a server
for two hours (9-11 am Boston time, Sept 25)?
The students will be uploading ~1M 30-bp reads, running QC and trimming
barcodes, usi
Dear All
I develop one data display tool for my local galaxy instance, I want to make
the history panel and tools panel auto hidden while I load this tools since
I need more room to show the data, does anyone has any clue for this? Like
change the tools xml or add a JS function to operate father
Hi Galaxy-devs,
When adding files to a data library (as admin), I have to choose the
genome corresponding to my dataset, but the drop-down list is not
sorted, making it a tad annoying to scroll. In addition, by default, the
homIni20 genome is selected, which seems a bit anthropocentric ;)
I
I tried the following in the xml: (it is modified that it is not a valid xml as
I cannot deposit everything here yet….)
the following somehow ignores the amount of jobs as when I run 2 the second one
runs immediately after the first one in the history panel and in the terminal
top I can see it a
Hello, Phillip
I haven't been able to replicate this yet (https://trello.com/c/LdLlJDo9).
Do you see any errors in your log near or after "GET /history/list
HTTP/1.1"?
Shane Sturrock worked around this problem by updating his universe_wsgi.ini
file (if I understand his procedure):
1. Make a backu
I'm trying to setup a virtualenv with JPype via tool_dependencies.xml. I've
verified that JPype is available from PyPI via pip, however, when Galaxy tries
to install the dependency, it's not finding a distribution.
JPype 0.5.4.2 https://pypi.python.org/pypi/JPype
Here is the snippet from my
Hello, Sridhar
How large is the file you're trying to plot?
The scatterplot visualization doesn't do well with large datasets (more
than ~10,000 points). I'm working to provide some form of pagination, but
it may take some time.
If your file is large, filtering or splitting up your data may help
Hi guys,
I just thought I'd check in again. None of the researches that want
to run out genotyping program can do so until I figure this out. Any
help or advice at all would be greatly appreciated.
Thanks,
Greg
On Mon, Jul 8, 2013 at 8:43 AM, greg wrote:
> Hi guys,
>
> Any thoughts on this?
Hi,
First of all, I apologize for interrupting into this discussion, but I have
exactly the same problem and did not find a solution yet. And no: prefix and
cookies are set properly in our particular setting (as "/")! This is not the
cause...
I think that the problem occurred with the May
Sorry forgot,
root cause = A message body writer for Java type, class
com.github.jmchilton.blend4j.galaxy.beans.History, and MIME media type,
application/json, was not found
On 11 July 2013 11:37, Eric Kuyt wrote:
> Hello all,
>
> I'm trying to implement blend4j in a java application. for thi
Hello all,
I'm trying to implement blend4j in a java application. for this I cloned
the source, fetched the dependencies and added a maven assembly plugin to
assemble a jar file with dependencies.
This jar I put in my classpath.
Now fetching histories works, but creating a new one fails. Online
Dear Developers,
I could see the visualize icon in the History page below the output file..
Actually i am trying to plot the graph between the column 4 and 8 from the
output..
I tried using the visualize option, But takes long time to and i could'nt
get the plot..
Please suggest , how to get the
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