Hi Galaxy Users,
I'm interested in integrating microarray and NGS data.
My problem concerns the uploading of an affybatch object
in Galaxy (I have a local instance of galaxy, but exacly
the same problem is present in http://main.g2.bx.psu.edu)
After processing the upload, the only message in the
Hi Ivan,
> In particular the data which I'm trying to upload are
> created with rexpression (incidentally, is it still
> supported or novel versions are attended?), because
Unfortunately, rexpression is not supported at present- the source is
readily available from bitbucket but the original auth
On Nov 8, 2011, at 6:34 PM, Andrew Warren wrote:
> Hi Nate,
>
> I am running in daemon mode so this out of paster.log.
>
> The job gets submitted to the PBS queue normally but the error shows up in
> history panel right away (also the working directory shows up during the
> cufflinks run):
Hi
On Nov 8, 2011, at 10:42 PM, Greg Von Kuster wrote:
> James,
>
> In addition to Ross's comments, consider that the base class of all Galaxy
> datasets ( library datasets, etc ) is the DatasetInstance class, whose
> get_file_name() method leverages the file_name property from the Dataset
> clas
Hi Dan,
Thanks for your response, but I'm still confused.
When I edit the workflow there are two different kind of "Reference
genome" fields. One where I can use a drop down menu to select a
reference genome, like in "Unified Genotyper" tool, where you are
correct the only option is hg_g1k_v37 in
Hi Carlos,
In the cases where the Editor is showing a text box instead of the dropdown,
you enter the unique id from the .loc file, in the case of the public Galaxy
server this would be 'hg_g1k_v37', in the case of your local instance, this
would be the id that you have assigned; this text box
Thanks a lot for your time!, I get it now and I should be able to run
my workflow.
On Wed, Nov 9, 2011 at 11:13 AM, Daniel Blankenberg wrote:
> Hi Carlos,
> In the cases where the Editor is showing a text box instead of the dropdown,
> you enter the unique id from the .loc file, in the case of th
On Oct 5, 2011, at 10:01 AM, Nikolai Vazov wrote:
> Hi,
>
> I can't find out how to use the dropdown "User type" which is displayed after
> I select User > Register in the start page of Galaxy. Do I have to define the
> types myself? Are they pre-set? The dropdown menu just says "Select one", b
I successfully pushed updates to my gmap and mothur toolshed repositories
yesterday,
but got an error when I tried to push changes to defuse.
% hg push
pushing to http://jjohn...@toolshed.g2.bx.psu.edu/repos/jjohnson/defuse
searching for changes
abort: HTTP Error 404: Not Found
I also tried u
I have an application that needs to return a zip file.
I attempted to follow the instructions to add a "zip" datatype, with no
success.
It appears to me that Galaxy insists on generating the output file name
and I can't get it to generate one with a ".zip" extension.
The documentation on the w
I have a diff for a bug that's been present in at least the last two releases
of galaxy-dist when python 2.6(.5) is used, which doesn't have SMTPError in
smtplib:
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -607,7 +607,7 @@ def send_mail( frm, to, subject, body, config
Hi Jim,
Thanks for sending your archive.
I can successfully clone your defuse repository, but I have not tried pushing
anything to it - I don't want to write to your repository. I noticed that your
last change set removed the defuse directory. Did you do that by uploading a
new tarball that
Hi all,
Most of our playing around with Galaxy has been in getting it working
on our local cloud, but now for the first time I'm configuring a
non-cloud local install of galaxy-dist (set up as per
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server)
So I have some naive questio
Thank you for the offer Nate. I ended up writing a tool to do the
exporting instead. Less elegant, but it does the job. It solves my
probelm to use Galaxy as a CLI workflow driver.
Best regards
Martin Dahlö
---
Bioinformatic support
martin.da...@scilifelab.uu.se
+46 18 611 59 59
+46 706 70 79 55
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