On Wed, Aug 7, 2013 at 3:41 AM, Rodolfo Aramayo wrote:
> On Tue, Aug 6, 2013 at 11:41 AM, Peter Cock wrote:
>>
>> Looks like your BOOST is too new for BLAST 2.2.26+ (which
>> just recently became a problem on the Galaxy Tool Shed testing
>> system as well).
>>
>> In the short term I'm hoping to u
Attempting to run oasesoptimizer rev. 53e887dda799 (konradpaszkiewicz)
on Galaxy fd4113962c32+ (stable)
I get the following error:
#
error
An error occurred with this dataset: Traceback (most recent call
last): File
"/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradp
I have implemented a cool idea Brad Chapman had the recent BOSC
Codefest. It would save me tons of effort related to maintaining
separate proteomics module definitions for the tool shed and
CloudBioLinux for Galaxy-P.
I thought I would throw this out there and see if anyone has any comments:
>Fro
On Tue, Aug 6, 2013 at 11:41 AM, Peter Cock wrote:
> On Tue, Aug 6, 2013 at 5:30 PM, Rodolfo Aramayo wrote:
>> Dave,
>>
>> It did contain errors as reported by tailing the last part of the
>> INSTALLATION.log
>>
>> Thanks
>>
>> --Rodolfo
>
> Looks like your BOOST is too new for BLAST 2.2.26+ (whi
I'll leave the rsync question to the experts - worked for me, but I don't know
why it worked for me (linux/ubuntu laptop, not networked) and not for you .
About the filenames: You can download a file listing to text.txt by
.../galaxy-dist$ rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes >
On Aug 5, 2013, at 12:33 PM, Boaz Shaanan wrote:
> Hi,
>
> I think I'm running into a problem of getting my local galaxy installation
> server to start because another httpd server is currently running on the same
> computer (see attached output of run.sh). Toward the end I notice that the
> s
Hi,
1) I'd like to fetch the genome of H. salinarum NRC-1 on my local installation. Following your advice (http://wiki.galaxyproject.org/Admin/Data%20Integration
I wanted to use rsync. To begin with I tried the example in the above url, even though that's not the genome I'm interested in:
You just need something like the following in your universe_wsgi.ini.
# Tool config files, defines what tools are available in Galaxy.
# Tools can be locally developed or installed from Galaxy tool sheds.
tool_config_file = tool_conf.xml,shed_tool_conf.xml
On Aug 6, 2013, at 1:27 PM, Peter Cock
On Tue, Aug 6, 2013 at 6:22 PM, Greg Von Kuster wrote:
>
> On Aug 6, 2013, at 1:14 PM, Peter Cock wrote:
>
>> My Firefox is setup to accept cookies until the expire, but not
>> to accept third-party cookies.
>>
>> Do I need to worry about cross-site cookies for my Galaxy server
>> talking to the
On Aug 6, 2013, at 1:14 PM, Peter Cock wrote:
> My Firefox is setup to accept cookies until the expire, but not
> to accept third-party cookies.
>
> Do I need to worry about cross-site cookies for my Galaxy server
> talking to the Main (or Test) Tool Shed?
>
Yes, this must be the problem - th
On Tue, Aug 6, 2013 at 6:11 PM, Greg Von Kuster wrote:
> Hi peter,
>
> Do you have cookies blocked in your Firefox browser? Does your
> cookie_path setting work for what you've configured in your apache
> prefix?
Yes, logging into my Galaxy and using it works fine - I can close
tabs and go back
Hi peter,
Do you have cookies blocked in your Firefox browser? Does your cookie_path
setting work for what you've configured in your apache prefix? It's impossible
to tell what specifically could be causing this in your environment, but it's
definitely related to cookies.
Greg Von Kuster
O
Hi all,
I'm (finally) attempting to install a tool from the main Tool Shed into
a local Galaxy instance, using Firefox, and got the same red error
that Adam reported (below):
"Repository installation is not possible due to an invalid Galaxy URL:
None. You may need to enable cookies in your browse
On Tue, Aug 6, 2013 at 5:30 PM, Rodolfo Aramayo wrote:
> Dave,
>
> It did contain errors as reported by tailing the last part of the
> INSTALLATION.log
>
> Thanks
>
> --Rodolfo
Looks like your BOOST is too new for BLAST 2.2.26+ (which
just recently became a problem on the Galaxy Tool Shed testing
Hi Rodolfo,
There was a bug with regard to displaying the Installation status of a tool
dcependency installed into Galaxy along with a repository from the Tool Shed.
I have corrected this bug in the mentioned change set, so if you upgrade your
Galaxy code to the mentioned revision, the install
> If I share a history, it produces a url with the datasets. This is good. But
> if you click on the eyeball in this view, it shows the dataset in its raw
> form. Its as if the code path does not go through the sophisticated datatype
> logic. Is this deliberate or an oversight?
Incomplete inte
You are very welcome
So...what happened??
Thanks
--R
On Tue, Aug 6, 2013 at 9:26 AM, Greg Von Kuster wrote:
> Hello Rodolfo,
>
> The following issue is resolved in 10319:61de03c05cf6 - thank for reporting
> this.
>
> Greg Von Kuster
>
> On Aug 5, 2013, at 3:50 PM, Rodolfo Aramayo wrote:
>
>>
>
Hello Rodolfo,
The following issue is resolved in 10319:61de03c05cf6 - thank for reporting
this.
Greg Von Kuster
On Aug 5, 2013, at 3:50 PM, Rodolfo Aramayo wrote:
>
> I did and it worked well it installed Blast 2.2.26+
>
> However there are two problems:
>
> 1. On the admin page "Installe
Rodolfo,
--Dave B.
On 8/5/13 15:50:46.000, Rodolfo Aramayo wrote:
Dave,
See below
On Mon, Aug 5, 2013 at 1:55 PM, Dave Bouvier wrote:
Rodolfo,
Please keep the thread on the mailing list by using the "Reply all" option.
Apologies
You should now be able to go to the manage reposi
Hi Gerald
Have you looked into 'Data Libraries'?
http://wiki.galaxyproject.org/Admin/DataLibraries/Libraries
http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
This will allow you to access the files without data duplication.
Regards, Hans-Rudolf
On 08/05/2013 08:48 PM,
On 08/06/2013 08:17 AM, shenwiyn wrote:
Hi Hans-Rudolf,
Thank you very much for you help.Actually I want some more information
about how to configure 'smtp_server' in "universe_wsgi.ini".Could you
show me some samples to have a look please?
you need the address of your smtp server, eg:
smtp
21 matches
Mail list logo
