You can do so / allowing them to, by using the galaxy ftp solution.
That way users can link or provide files in their email subdirs. You have to
sort out how to set the users/rights properly on your linux box though.
But see the galaxy ftp solution pages, it might be of help.
Alex
Hi there
I've got a workflow that uses BioPerl's bp_genbank2gff3 to convert
Genbank to GFF3, then hands the GFF3 to Extract features to filter to
only genes, before moving on. The workflow JSON is at
http://pastebin.com/zHWsC6YT. Step 4 - the Genbank2GFF runs fine, and if
I view the output in the
Hi,
I don't want dowload the output files which Galaxy generates, because I
don't want to have them in double in my disk.
I saw, that the output files are in file_path an I found them.
But they have a .dat extension !
In your mailing-list archive I haven't found a solution to transform these
On May 19, 2012, at 10:09 AM, Peter van Heusden wrote:
Hi there
As I adapt Galaxy to the needs of the particular workflows I'm
implementing, I invariably end up tweaking the existing code,
especially the tool definitions and the datatypes config file. These
tweaks are often minor - e.g.
Hi,
I think I found the solution to my problem by googling it instead of just
searching through the dev mailing list. I found this post very useful for
debugging tips on cheetah template:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-March/004817.html
Then I read on the galaxy wiki:
Is it possible to create visualizations via the API yet? Can't seem to
find an example.
Ayton
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists,
Hi,
I've successfully configured a local galaxy instance to submit jobs to our
local cluster, but have a question regarding setting PBS options such as the
number of nodes and processors to use. I've followed the guide here:
Hi there
Because my Galaxy workflows tend to sprawl outside the viewable space in
my browser, I've written a script that, when given a workflow JSON file
as input, writes out a graphviz dot format graph of the workflow. By
default the graph treats datasets as nodes and analyses as edges (unlike
Thanks for the reply. Ideally, I would have a cron job run that would monitor a
directory and automatically add the new files to a particular library. I do not
want the end users to have to deal with this. Does anyone have a working
solution or ideas for implementation? This is the main
Yes, you can set these things for each tool independently.Check the file"universe_wsgi.ini"and check the section:[galaxy:tool_runners]There you can set the -pe options for GSUB in the same way you can do on the command line...Here's an example of my setup:gatk_variant_select = drmaa://-V -pe smp
Excellent! Thanks for the reply.
-J
-- Jason Greenbaum, Ph.D.
Manager, Bioinformatics Core | jgb...@liai.org
La Jolla Institute for Allergy and Immunology
- Original Message -
From: Anthonius deBoer thondeb...@me.com
To: J. Greenbaum jgb...@liai.org
Cc:
Thanks for sharing Peter.
FWIW, there is already code in Galaxy to generate SVG from a workflow. See the
gen_image function in web/controllers/workflow.py I think this code is used
when workflows are included in the tool shed as well.
If your code is better in some way(s), please consider a
Peter,
I'm not ignoring you. However, there are others on the Galaxy team that are
more familiar with the API and can provider better answers. I expect they'll
chime in soon to address your questions.
Best,
J.
On May 20, 2012, at 5:39 PM, Peter van Heusden wrote:
Hi Jeremy
I'm need this
Hi, Ciara,
AFAIK new tools always require a server restart at present, but an
already loaded tool can have updates to the tool XML re-read using the
'Reload a tool's configuration' option from the administrative menu if
your login is listed as an administrator in the config file.
Restarting
I didn't know that. Thanks for the reply! Now I have a new set of
questions. First, how do I list myself as an admin? Should I just literally
add my login detail in the config file? Second, my colleague would like to
be able to edit and view the changes that he has made in his tools, even if
I am
15 matches
Mail list logo
