Hello all,
What is the recommended URL for the main Tool Shed?
Simply http://toolshed.g2.bx.psu.edu/ itself?
I believe the URL http://usegalaxy.org/community used to
go to the main Tool Shed, but right now I am instead taken
to https://main.g2.bx.psu.edu/community/ and told:
"This link may not be
Hello all,
Either I made a typo in some old README files, or the old
URL for the Tool Shed http://community.g2.bx.psu.edu/ has
stopped working. Could this redirect to the current Tool Shed
address http://toolshed.g2.bx.psu.edu/ please?
Thanks,
Peter
__
Hi Peter,
Thanks for your message. The URL has ben changed to
http://usegalaxy.org/toolshed
On Mar 6, 2013, at 5:24 AM, Peter Cock wrote:
> Hello all,
>
> What is the recommended URL for the main Tool Shed?
> Simply http://toolshed.g2.bx.psu.edu/ itself?
>
> I believe the URL http://usegala
Hi Peter,
I've added this to the same Trello card. These URL redirects lie outside of my
control, so I'll bug the right person to get them set up.
https://trello.com/card/toolshed-galaxyproject-org-url-redirects/506338ce32ae458f6d15e4b3/697
Thanks!
On Mar 6, 2013, at 6:52 AM, Peter Cock wrot
Thanks Ira,
We'll take a look at this as soon as possible and get back to you.
Greg Von Kuster
On Mar 6, 2013, at 3:45 AM, Ira Cooke wrote:
> Hi Greg,
>
> I should probably add to this some background info about my dependencies ..
> which are a bit weird.
>
> Basically I have a bunch of re
Hi Greg,
I should probably add to this some background info about my dependencies ..
which are a bit weird.
Basically I have a bunch of repositories that all depend on a rubygem I wrote.
This gem is installed under its own gemset using rvm. Installation of this
repository is essential befo
No, rename is a completely separate and unrelated action. Back to your
original question, for counting the number of steps, can you just look at
the api/workflows/ and look at the steps dict? Anything with a tool_id
is a tool step.
-Dannon
On Tue, Mar 5, 2013 at 10:52 PM, Richard Park wrote:
Hi,
I'm trying to load an instance of Galaxy from scratch, and I'm getting
this error message after configuration and typing "./run.sh":
Traceback (most recent call last):
File "./scripts/paster.py", line 33, in
serve.run()
File
"/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescrip
Is this a fresh clone from galaxy-dist or have you pulled it from somewhere
else? It looks like your galaxy clone's lib/galaxy/datatypes/registry.py
has been altered to have an extra import, 'gmap', for gmap tools.
-Dannon
On Wed, Mar 6, 2013 at 12:08 PM, David Hoover wrote:
> Hi,
>
> I'm tryin
Dr. Taylor,
Thanks for the e-mail. I think that is a solid instinct, it makes me
nervous too, though most things do. I am responding to the list
because I think others are going to have the same concern
(hopefully!).
This whole concept puts a lot of onus on the tool developer. A
biologist who has
This is a fresh clone, from galaxy-dist, but I have a pile of patch
files to keep my local hacks straight. I forgot about the registry.py
file. Removed that, as well as the blast import. It's hard to keep
local hacks and regular updates in sync...
Thanks,
David
On 3/6/2013 12:16 PM, Dannon
I've installed the latest version of galaxy, and the admin column won't
scroll. I can't see any of the toolshed functions unless mybrowser is
expanded beyond the size of my desktop display. Is there something wrong?
David Hoover
Helix Systems Staff
On Wed, Mar 6, 2013 at 12:22 PM, John Chilton wrote:
> This whole concept puts a lot of onus on the tool developer. A
> biologist who has taken a two week course on perl could probably write
> a Galaxy tool, they probably couldn't write a secure tool for a public
> LWR. I think some experience in
> I understand that instead of having one dataset with multiple files you are
> planning to use existing datasets and combine them in a ‘collection’. My
> concerns are:
This needs to be fleshed out much more, but this is not exactly what
we are thinking. The main change is to make it possible for
On Wed, Mar 6, 2013 at 12:39 PM, James Taylor wrote:
> On Wed, Mar 6, 2013 at 12:22 PM, John Chilton wrote:
>
>> This whole concept puts a lot of onus on the tool developer. A
>> biologist who has taken a two week course on perl could probably write
>> a Galaxy tool, they probably couldn't write
Hi everyone,
I have some questions about the tool of Megablast in NGS:Mapping when I
download the needed indexes .
There are four indexes files we need for Megablast:htgs 28-Jan-2013 ,nt
28-Jan-2013,wgs 28-Jan-2013,phiX174;but there are too many types of the indexes
file in ftp://ftp.ncbi.nlm.ni
Hi everyone,
I also have this confusion between bowtie/bowtie2 and tophat/tophat2 on our
local galaxy.Have all of these we need to installed?
Actually,Map with Bowtie for Illumina and Map with Bowtie for SOLiD depend on
the bowtie-0.12.8 ,Bowtie2 just depends on bowtie2-2.0.2.If we just install
Thanks for your response.
I solved the issue. We all know the .loc files use the tab character as the
delimiter. I knew I was supposed to use tab and have been double checking,
but the problem arises when I enter tab while editing with the two IDEs I
use (mvim and Xcode). Apparently, what mvim and
Hello,
You can pick which you want to use: any of the four, in any combination.
The binary dependencies are explained in this wiki, per tool:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
And the .loc and index set-up is explained in this wiki, see the section
"Bowtie and Tophat -
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