Hi Derrick,
The wiki page to which you refer describes the manual way that the Galaxy admin
can install tool dependencies (using a manual process). The tool shed
automatically does everything to install repositories, tools, tool
dependencies, datatypes, and other repository contents. If you h
Dear Galaxy community,
I have noticed that since I have upgraded to the latest galaxy distribution
(October 5th, b5bda7a5c345), the "search tools" function in the left frame
doesn't seem to work properly. For example, in previous distributions, if I
typed "fastx", it would display all the tool
Alex,
This is definitely an issue, but it is not currently high priority for the
Galaxy team.
We expect to move the Velvet wrappers to the tool shed in the near future, and
from there others can enhance the wrappers as needed. In the meantime,
community contributions to the Galaxy code base,
I'm having the same issue. I started a brand new cloudman instance to
see if the problem was something I had done, but I got the same error.
Is the tool shed working for anyone?
-Josh
On Mon, Oct 8, 2012 at 1:13 PM, Joel Rosenberg wrote:
>
> (Apologies if this is in duplicate, Peter Cock may hav
I'm trying to add CSRA (NCBI Compressed
Sequence Read Archive) as a new datatype for Galaxy.
I've followed the instructions on the wiki, and the module seems
to load OK. csra shows up as a datatype in the upload view.
But the upload fails, and the up
Hey Mark,
A few things, instead of printing stuff out you could use the global
variable log in the binary.py file. Maybe something like
log.warn("SNIFFING csra"). I think your logging statements will be
more likely to show up then.
I don't know why what you are doing won't work (it looks like it
I ran into this issue as well on my locally installed instance. After
some poking around, it looks like it might be a cookie issue.
Specifically, the toolshedgalaxyurl and galaxycommunitysession cookies
don't seem to be getting set by toolshed.g2.bx.psu.edu and this is
causing the server erro
Comments inline.
On Wed, Oct 10, 2012 at 2:35 PM, Mark Johnson wrote:
>
> Thanks for the quick turnaround. On the contrary, your examples are very
> helpful. I'll try your approach. I haven't upgraded Galaxy in about 6
> months, but was hoping that change had already been made. (I haven't worked
Hi,
What's happening ? or what do I need to install ? I review my python
sqlite 3 and yes it is installed
I configured my own local galaxy instance in own server, it works well, I
used proftp, postgresql, and Python 2.7
I uploaded my SOLiD colorspace and Quality data via filezilla to my galaxy
My comments inline...
On Oct 10, 2012, at 4:39 PM, John Chilton wrote:
> Comments inline.
>
> On Wed, Oct 10, 2012 at 2:35 PM, Mark Johnson
> wrote:
>>
>> Thanks for the quick turnaround. On the contrary, your examples are very
>> helpful. I'll try your approach. I haven't upgraded Galaxy in
Hi,
Can you tell me the part of the Galaxy code or method responsible for
actually copying over the data from one machine to another? i.e. it looks like
data is first copied over to the ~/galaxy-dist/database/tmp area first before
being moved on, which method copies over the data to ~/galaxy
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