Il 2013-10-11 17:21 Sytchev, Ilya ha scritto:
On 9/12/13 10:35 AM, "Peter Cock" wrote:
On Thu, Sep 12, 2013 at 2:01 PM, Mathieu Bahin
wrote:
Hi all,
We have been developing our own Galaxy instance for a while now. We
have a
cluster on which the job are sent to be executed, it is managed
t
Il 2014-04-09 22:18 John Marmaduke Eppley ha scritto:
As far as I can figure out, the parameter map for running a workflow
via the API is supposed to look like this:
{'blastn': {'param': 'evalue', 'value': '1e-06’}}
This doesn’t seem to allow for multiple parameters to a single tool.
Is there a
Hi all,
I've just skimmed Greg's latest blog post which is about
the REST API for the ToolShed:
http://gregvonkuster.org/galaxy-tool-shed-restful-api/
I would be interested in automating pushing updates to the
ToolShed, which I currently do manually by uploading a
tar-ball. Is it possible yet to
Hi Peter,
This is not yet available, but we'll certainly implement it. I've created this
Trello card for it.
https://trello.com/c/fykf8IPO/197-enhance-api-to-enable-tar-archive-uploads
Thanks!
Greg Von Kuster
On Apr 10, 2014, at 7:50 AM, Peter Cock wrote:
> Hi all,
>
> I've just skimmed G
(Moved to galaxy-dev mailing list because it concerns server admin rather than
Galaxy usage.)
If everything worked fine with a human build but not for PF3d7, then my guess
is that the len file for PF3d7 isn’t correctly formatted. Right now, the file
parser is very unforgiving—no extra spaces or
This is implemented by the web browser.
http://en.wikipedia.org/wiki/File_select
File tool parameters are rendered by tool_form.mako in such a way that
the web browser takes over and allows users to select files. One is
very constrained about how customized one can make this as a security
mechani
This is tricky and has changed in the last few releases. If you have
are developing against the latest revision of galaxy-central this is
all handled via Backbone MVC code. In particular checkout the render
method of static/scripts/mvc/dataset/hda-base.js about 100 lines down.
The class of each of
Ah, yes. That seems to have been added a couple months ago. The BioTeam
appliance just missed that update by a week or two. I’ll go bug them. Thanks.
FWIW, I am using bioblend, and I got my example from the bioblend documentation:
http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html
On Wed, Apr 9, 2014 at 9:55 AM, Alexandre Defelicibus
wrote:
> Hi all,
>
> I have some doubts about how to configure a LWR server on Linux.
> I have read the LWR documentation, however how to configure the LWR is not
> clear to me.
>
> This is my scenario:
>
> On my Galaxy server I have some tools
Hi Nicola,
Perchance, do you know what type of validator I can put to ensure that the
string input is does not consist of only whitespace? Such a string is
still invalid for my tool, but counts as a string.
--
Ravi Sanka
ICS Sr. Bioinformatics Enginee
Hi Ravi,
for that you need a regex validator:
https://bitbucket.org/galaxy/galaxy-central/src/tip/lib/galaxy/tools/parameters/validation.py#cl-27
e.g.
.*\S
Best,
Nicola
Il giorno gio, 10/04/2014 alle 10.20 -0400, Sanka, Ravi ha scritto:
> Hi Nicola,
>
> Perchance, do you know what type of va
Hello,
I am testing the example_watch_folder.py script on my local instance of
Galaxy (Feb.10 distribution). I have set up a simple workflow with the
Fasta-to-Tabular tool. It takes a single input fasta file. Works in Galaxy
UI.
I have created input and output folders and followed the steps her
Hello,
I just updated to Feb.10 and also noticed that Trackster is not working. I
too get the blank screen. Could you please tell me how to manually update
the vis packed files? I do not know what these are.
Thanks in advance,
Liisa
___
Pl
Thanks for the help John. I am using a slightly older version of Galaxy.
However, I was hoping that the change of colour may help me understand the name
change in the history.
For example when you upload a file i.e. test.txt, "test.txt" appears in the
history. However, if you want the history
Python code in galaxy tools can import all sorts of modules. Is there a way to
add an extra path to the sys.path so that I can include some other python
modules that way? I.e. in some galaxy python config file?
I'd like to say in my tool code
HTMLReportModule = __import__(html_template)
15 matches
Mail list logo
