On Mon, Aug 26, 2013 at 12:27 PM, Carlos Borroto
wrote:
> Hi,
>
> I'm interested in developing a tool that would allow easy interaction
> with the Galaxy API. I started coding and this[1] is what I have so
> far.
>
> [1]https://github.com/cjav/galaxy-api-tools
>
Second effort session on this proj
Folks,
First, I wanted to thank you for making the datacache available
(http://wiki.galaxyproject.org/Admin/Data%20Integration;
rsync://datacache.g2.bx.psu.edu). It's a great resource.
However, what is the best way to stay abreast of changes to what's in
datacache, and understand how these ind
Hi Simon,
it's just a guess but can you try the attached patch if you have a
reproducible case. It is not tested, but at least it should point you in
the right direction. If its working, I will create a pull request.
Cheers,
Bjoern
> My optimism was short lived. I think I've hit a galaxy bug in
Hey Srinivas,
I have no insights here, I am sorry. My knowledge of LDAP is rather limited.
-John
On Wed, Sep 18, 2013 at 9:10 AM, Maddhi, Srinivas
wrote:
> Another galaxy + nginx + LDAP user here.
>
>
> Iry,
>
> I have it working as well with help from Galaxy Wiki docs and mailing list
> arch
Hi Simon,
thank you very much for your comments!
> I can see man years of effort being spent on solving this problem within
> Galaxy. I was going to title this email "Danger, Will Robinson", but I
> didn't want to be disrespectful.
> I think the path being embarked upon, tool dependency pack
Feature request received.
The following changeset demonstrates how one could implement this
https://github.com/jmchilton/galaxy-central/commit/b500a24bc1aa94bef48db20a7cc1f3d68855b7fd
First step is to create a new dynamic job destination, this is
demonstrated in job_conf.xml in the above changes
my galaxy instance:
parent: 10587:1f34ec186fcf
Pack script.
branch: stable
commit: 3 modified, 91 unknown
update: (current)
testtoolshed.g2.bx.psu.edu:
parent: 10592:ea0c57f1cdf0 tip
Fix for unicode values in rst_to_html.
branch: d
On Thu, Sep 19, 2013 at 5:15 PM, Björn Grüning
wrote:
> Hi Peter and Carlos,
>
>> On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto
>> wrote:
>> > I did an extra test. Started with a clean 'galaxy-dist'. This time
>> > both repositories fail with the same error. I guess before something
>> > was ca
It would be useful to have access $__history_id__ in the same way as one
accesses $__user_id__. I am running a local instance of galaxy and have
modified the following file to achieve this:
lib/galaxy/jobs/__init__.py
At line ~694:
incoming['__user_name__'] = user_name
+ if job.hist
Hi,
Could somebody point me to the place where I can create a ticket for the
following feature:
- We want to have tools available only to users who provided a licence for this
tool.
- To prevent very long email lists (see example on dev-only tools), I'd like to
have a group 'have_licence'
-
Hi Samuel, everyone,
There is now a Vimeo channel containing all 25 taped talks from GCC2013:
https://vimeo.com/channels/581875
We're still figuring out how to best use Vimeo. Please do let us know if
you have any suggestions for how to improve the site. Look for more
content here going forwa
If I might chime in, I am a bit worried about all the automatic installation
going on in galaxy, and it seems that the trend is to enhance this.
A small R or python script calling into well known libraries that come from
well known repositories (bioconductor etc… ) I can check.
(Of course I insta
Jeremy
First of all, thanks for all your efforts, and for updating the cuffdiff, etc,
wrappers.
However, it's a little frustrating to us that a non-backward compatible change
in the supported version of the cuffdiff executable was not reflected in a new
version number for the cuffdiff (and oth
Jeremy
Thanks for the super-quick response. That should resolve things nicely.
We can hack the old wrapper back in, using a hard-coded path to the old
cuffdiff.
We can pull your new wrapper, and install the new cuffdiff.
Then we should have backward and forward compatibility.
Shantanu suggests
> I know the general versioning problem is address through the tool-shed
> mechanism, but for the remaining core wrappers, can maintainersplease update
> wrapper version numbers when making changes?
Not bumping wrapper versions is an oversight, not deliberate.
>
> For this wrapper set, how wo
Hi everyone,
I am posting this position description for a Part Time - Galaxy (BioLinux)
Server Administrator / Python Programmer.
We are a really great company in an interesting space. Please check out
this video for a good overview of what we do.
(We also have some full time openings that range
> We can hack the old wrapper back in, using a hard-coded path to the old
> cuffdiff.
You could also use Managed Tool Dependencies for multiple versions of cuffdiff:
http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
> Shantanu suggests it might be a better world if we create a tool
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