Hi all,
According to Galaxy, uploading files larger than 2GB will surely fail. For
this reason, uploading via FTP is recommended. Unfortunately, I cannot
download/install an FTP server for Galaxy since I am working on a remote
server. I only have access to it via Xming. Is there anyway to allow FT
Hi Xiangyu,
This question is best directed to the galaxy development list, which I've cc'd.
In general, to integrate a tool into Galaxy, you'll want to write a tool
wrapper:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax
and then upload it to the Galaxy toolshed:
http://wiki.g2.
I used bwa to align a short read file to a reference sequence. I ran it several
times, and I got different results for the runs on the same input dataset.
The fist run, it generated a ~280,000 lines "gzipped file". I checked the file
on the server, and it was actually a sam file, not gzipped.
The
Hi Greg,
I commented out sqlite line, but I missed "database_connection = " in the new
line I added in the configuration file.
It is working now.
Thank you very much for the quick reply.
Cai
--- 12年4月24日，周二, Greg Von Kuster 写道：
发件人: Greg Von Kuster
主题: Re: [galaxy-dev] Galaxy with postgre
On Apr 19, 2012, at 11:12 AM, Nate Coraor wrote:
> On Apr 19, 2012, at 10:44 AM, Peter Cock wrote:
>
>> On Thu, Apr 19, 2012 at 2:53 PM, Nate Coraor wrote:
>>> On Apr 17, 2012, at 9:04 AM, Peter Cock wrote:
>>>
Hi all,
Does anyone know what might have introduced this problem run
Hi Cal,
Did you comment out this line?
# By default, Galaxy uses a SQLite database found here
#database_file = database/universe.sqlite
Also, I assume you following reference:
> in Galaxy configuration file, use postgresql
> postgres:///galaxy_db?user=ubuntu&host=/var/run/postgresql
actually lo
Hi Paul,
The use of mercurial eggs for all tool shed mercurial related actions is now
available in our central repository in change set 7102:c8f4f73e9199. This will
be available in the dist repository with the next release, which I believe will
be coming soon. If you're tracking the central r
Hi All,
I want to use postgresql instead of sqlite, and below is how I did the settings:
I am running Galaxy under the user ubuntu, so first I create the ubuntu user
sudo -u postgres createuser -D -A -P ubuntu
Then I create the database named galaxy_db
sudo -u postgres createdb -O ubuntu galaxy_
Hello Peter,
This issue was fixed a while ago, but has not yet made it to the Galaxy dist
repository. Since the dist repository is generally 4 to 6 weeks behind the
Galaxy central repository, your local Galaxy instance will have to track the
central repository instead of the dist repository in
I am having the same problem when I use condor as the scheduler instead of sge.
Cai
--- 12年4月23日，周一, Louise-Amélie Schmitt 写道：
> 发件人: Louise-Amélie Schmitt
> 主题: [galaxy-dev] Error: Job output not returned from cluster
> 收件人: galaxy-dev@lists.bx.psu.edu
> 日期: 2012年4月23日,周一,下午5:09
> Hello every
Hi Jeremy,
So, we updated our galaxy instance and now the genomic sequences can be
displayed, when sufficiently zoomed in and also the visualization can be saved
now.
It looks really nice :-)
Thanks a lot for your help.
Regards,
Naharajan
On Apr 18, 2012, at 6:10 PM, Jeremy Goecks wrote:
>
Hello
I've encountered some problems installing and then trying to remove a
tool from the main toolshed in a local Galaxy production instance. The
tool is the tmap_wrapper but I don't think that the tool itself is the
problem.
When I tried the automated install from the toolshed, the Galaxy
Hello everyone,
I'm still trying to set up the job submission as the real user, and I
get a mysterious error. The job obviously runs somewhere and when it
ends it is in error state and displays the following message: "Job
output not returned from cluster"
In the Galaxy log I have the followi
Hi Deepthi
what do you want to use the 'dynamic_options' for?
the file provided in the tag is a pyhton script, but remember the
' tag' is deprecated see:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Ccode.3E_tag_set
Regards, Hans
On 04/21/2012 12:48 AM, Unknown wrote
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