Hey Galaxy-dev’s,
I’m completely new to galaxy, but I am tasked with a small scale deployment
project.
I am looking for an alternate option to upload data to galaxy. All data from
our sequencers is stored on a NAS, which is accessible by the galaxy server. I
would like to make it so that the u
Libraries can help manage access and data doesn't need to be copied into
Galaxy:
https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles?highlight=%28directory%29%7C%28library%29
On 8 April 2015 at 18:12, De Smet Matthias
wrote:
> Hey Galaxy-dev’s,
>
>
> I’m completely new to
Hello Carlos,
I think we have had reports of problems installing say the newest
tophat tool on older Galaxy versions because it uses newer features
the older Galaxy and tool shed install code doesn't know how to
handle. I see the cummerbund wrapper is using some stuff added over
the last 18 mont
Yeah - I am with you on this. It is definitely less than ideal that any
exception will cause that to happen.
Here is a commit that I believe should fix the problem:
https://github.com/galaxyproject/galaxy/commit/87e19aa4d708d6c719b396867f431d94c92077c5
Do you have a working run-as-real user setu
I had my own use case for this a few weeks ago and I couldn't figure
out anyway to configure this right now - I was hoping Dan might
respond to your question with some crazy trick though. For now I have
created a Trello card for the implementation of this feature - please
vote for it:
https://trel
Hi Zhaozhen,
the --config_file argument needs to point to galaxy.ini config so the
script can load the database.
Galaxy continues to support Python 2.6 and 2.7, I am sorry that this script
required 2.7 (or you could `pip install argparse`) - we will look into
improving it.
Martin, Galaxy Team
Hi Davids,
For some a somewhat more complex example, have a look at the GenomeSpace
importer tools under tools/genomespace in the distribution. They always create
at least 1 dataset, but can create any number of files, of any type of
datatype. In this tool, it will use the filetype declared by
John,
Looks good.
I’m afraid I can’t test this on our main install any more, but I do have a VM
somewhere at home which will let me test in a reasonable amount of time. I
could probably look at that by the end of the week. Sorry I can’t do it
straight away.
Cheers,
DT
From: John Chilton [ma
Hi Rui,
(cc’d back to list)
One of the nice things about tool Data Tables is that it allows us to have
multiple ‘.loc’ files as the source for the content for a single data table —
so we can have many ‘all_fasta.loc’ files, but one ‘all_fasta’ tool data table,
with merged contents, and a tool
On Wednesday, March 25, 2015, Björn Grüning
wrote:
> Hi all!
>
> We are proud to present you the next release of Galaxy Docker.
>
> https://github.com/bgruening/docker-galaxy-stable
> https://registry.hub.docker.com/u/bgruening/galaxy-stable/
>
> A few highlights:
>
> * based on Galaxy 15.03, wit
On Wednesday, March 25, 2015, Björn Grüning
wrote:
> Hi all!
>
> We are proud to present you the next release of Galaxy Docker.
>
> https://github.com/bgruening/docker-galaxy-stable
> https://registry.hub.docker.com/u/bgruening/galaxy-stable/
>
> A few highlights:
>
> * based on Galaxy 15.03, wit
Hi all,
I just imported a workflow and noticed the following glitch with the
red message shown to the user about missing tools - the escaped HTML
is show to the user (ampersand lt semi-colon etc).
Specifically, I imported
http://www.myexperiment.org/workflows/4601.html from Bjoern.
Using the cur
Marten has added this to an existing issue - over zealous
over escaping due to a security fix:
https://trello.com/c/oX6i51Mn/2298-back-off-over-escaping
Thanks,
Peter
On Wed, Apr 8, 2015 at 5:13 PM, Peter Cock wrote:
> Hi all,
>
> I just imported a workflow and noticed the following glitch wit
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