Hi Florian,
I am fairly certain that this exact issue is still open, and so have
opened a bitbucket ticket to track progress:
http://bitbucket.org/galaxy/galaxy-central/issue/718/unsorted-bam-files-and-import-into-data
If this has been corrected already, one of us will send an update tomorrow.
Hello again,
The link is not a Galaxy Main public instance share link, which would
start with: http://main.g2.bx.psu.edu
Having the datatype as BED and the database as hg19 would (for all of
the cases I can think of) bring up the "View at UCSC" link, if the
instance is set up to have "displa
Hi Dev Team,
Do you have any plan to integrate PolyPhen2 to Galaxy? I feel, it would be good
if you can, as this extends the functionality of NGS analysis and (definetly)
it would be value addition to Galaxy as well.
Let me know your comments.
Best,
Raj
Thi
Hi Luobin,
To display at UCSC, the datatype has to be a UCSC display type and the
database has to be a UCSC genome browser. Often, small changes can be
made to tune a dataset to help it fit into these requirements. Other
times, a dataset will need to be transformed into another type or it
can
Hi,
I'm writing you because i'm trying to install galaxy in a server running
suse behind a proxy, so i have to build the eggs like if the server were
offline, in the guide says that i should execute the
command ./scripts/make_egg_packager.py but i get the following error, and i
don't really under
Hi Nathan,
I am going to move your question over to the galaxy-...@bx.psu.edu
mailing list to see if anyone in the development community has feedback.
Galaxy-user is mostly a Q & A list for scientists working with tools on
the main Galaxy public server.
http://wiki.g2.bx.psu.edu/Mailing%20Li
Yves;
> I am currently investigating if Galaxy Cloudman can help us in analyzing
> large NGS datasets.
>
> I was first impressed by the simple setup, the autoscaling and
> useability of Galaxy Cloudman but soon ran into the EBS limit of 1 TB L
>
> I thought to be clever and umounted the /mnt/ga
Hi Nate,
That's good to hear. Just letting you know that testing on my local install of
galaxy, if the following stars align:
-Google Chrome 17 / Firefox 10 (Mac os x)
-Nginx as galaxy's front end web server
-Nginx's optional upload module installed
HTML uploading of large files to galaxy (teste
Thats it! Consider this resolved, and total operator error. I tried using the
'Input Dataset' step, and am no longer having issues.
Thanks for the help Dannon.
From: Petit III, Robert A.
Sent: Tuesday, February 14, 2012 3:49 PM
To: galaxy-dev@lists.bx
Workflow is beginning directly with a tool.
An example test workflow I've been trying is, I have 20 fasta files, and the
workflow has only the FASTA-to-Tabular tool.
Thanks,
Robert
From: Dannon Baker [dannonba...@me.com]
Sent: Tuesday, February 14, 2012 3
I hadn't had a chance to follow up again yet, but in your workflow, are you
using an Input Dataset step, or do you have the workflow beginning directly
with a tool?
-Dannon
On Feb 14, 2012, at 3:26 PM, Petit III, Robert A. wrote:
> Here's the latest. I have tested this on Chrome, Firefox, and
Here's the latest. I have tested this on Chrome, Firefox, and IE.
I've tried the latest revisions of galaxy-central (71031bf3105c) and
galaxy-dist (26920e20157f) straight out of the box (hg clone, sh run.sh, go to
localhost:8080). I am still running into same issue. All is well with 19 or
le
Hi Carlos,
Not every tool form parameter will properly display when previewing the tool in
the tool shed because the tool shed doesn't have access to some Galaxy
components (e.g., a Galaxy history ) that are required for some tool parameter
types. When I get a chance, I'll take a closer look,
Perfect-- it works now. I will email to Galaxy-Dev next time
Thank you,
-CB
On 2/14/12 11:50 AM, "Dannon Baker" wrote:
>Sure, I'm happy to help, though in the future it's probably best to mail
>galaxy-dev (cc'd for ticket tracking) directly as there are several of us
>that may be able to answe
Hi,
I have a local instance of Galaxy, but I found there is no "Display at UCSC
Main" link for some datasets that can be viewed in GeneTrack or displayed
by Ensemble, what has been wrong?
Thanks,
Luobin
___
Please keep all replies on the lis
Hi,
I'm currently developing my first Galaxy tool. I'm working on a
wrapper for R's library cummeRbund[1]. I got to the point where the
tool although incomplete on functionality, I think is ready to be
uploaded to the Toolshed. I was able to do so. I also made sure I
could then install it on my lo
Hi,
Based on your previous questions, I'm going to guess that you're trying to add
multiple tools, run both on an input dataset in series, and see the results in
the History. Is this the case? If you're referring to how to combine these
into one process, take a look at the Galaxy workflow cap
Sure, I'm happy to help, though in the future it's probably best to mail
galaxy-dev (cc'd for ticket tracking) directly as there are several of us that
may be able to answer and get a response out sooner.
That said, your problem is likely due to a permissions issue with the new tool
snapshot(sn
Hi Jorrit,
There was a permissions issue with the new tool snapshot(snap-b28be9d5) created
yesterday that I've fixed, it should work next time you start an instance.
Thanks!
-Dannon
On Feb 14, 2012, at 10:37 AM, Jorrit Boekel wrote:
> Dear list,
>
> I am trying to deploy Galaxy as an enviro
Paul:
I was about to suggest the same - great idea!
++
brad
On Feb 14, 2012, at 11:08 AM, Dannon Baker wrote:
> Hi Paul,
>
> Thanks for this suggestion, it would definitely make sense to create a
> reference to the actual workflow inputs in the new history. I'll see what I
> can do!
>
> -Da
Hi Paul,
Thanks for this suggestion, it would definitely make sense to create a
reference to the actual workflow inputs in the new history. I'll see what I
can do!
-Dannon
On Feb 14, 2012, at 11:05 AM, Paul Gordon wrote:
> Hi all,
>
> I have noticed that when I run a workflow with output to
Hi all,
I have noticed that when I run a workflow with output to a new history, the
data sets used as input to the workflow do not become part of the new
history. Unfortunately, if a job fails in the workflow, the "rerun"
interface for the job can't access the original dataŠit needs to be manuall
Dear list,
I am trying to deploy Galaxy as an environment for proteomics tools in
amazon's EC2 cloud, probably/preferably via Cloudman. I have used both
the biocloudcentral portal and a manual approach to set up
cloudman/galaxy, but run into the same error message which seems to
start with a
Good point, Nate! I will move galaxy out of my documentroot then.
Best,
Huayan
On Tue, Feb 14, 2012 at 1:21 AM, Nate Coraor wrote:
> On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote:
>
>> Hi Nate.
>>
>> I am ok now.
>>
>> The code I copied from wiki was using galaxy_dist, while my folder name is
Can you confirm that the following lines are in your datatypes_conf.xml file?
--
--
If so, the other issue is that you'll need to restart Galaxy in order for the
changes to take hold. Apologies for not mentioning
Thon,
Not currently, though the question comes up often enough that I'll try and bump
it up my list.
Instead of interlacing and deinterlacing a better workaround for now might be
to use the API to execute over all these samples.
-Dannon
On Feb 13, 2012, at 8:46 PM, Anthonius deBoer wrote:
First, thanks. I just created a new user, and I am ready to go with that
user.
FYI, the reset of the datatypes_conf.xml did not do the trick: following
error appears on the custom builds page: NoConverterException:
"Conversion from 'fasta' to 'len' not possible"
Thanks,
Joachim
On 02/13/2012
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