Hi Greg,
Thanks, and sorry for the long delay in response.
To make the problem clear:
https://dl.dropboxusercontent.com/u/18352887/GalaxyToolShedToolError.ogv
The version of our Galaxy is:
*
[galaxy@galaxy galaxy-dist]$ hg summary
parent: 9944:cea3ddf6cdda tip
Upda
Hi,
i want to add new visualization tool in galaxy . can i get the required
documents ?
can u send me the details how can i add the visualization tool in galaxy .
Regards
shashi
___
Please keep all replies on the list by using "reply
Hi all,
I am trying to format the input to a java tool that I am writing. I want
to display different options to choose from based on the user input. I am
not sure how to do that.
For example, based on the input file, I want to display the chromosome
options to choose from. How do I do this?
All,
I'm attempting to configure ProFTPD to authenticate against the Galaxy
database. I appear to be able to connect to the database, but can't
authenticate a registered user via FTP.
Here are the relevant entries for the ProFTPD configuration:
[root@login002 proftpd-1.3.4d]# grep SQL etc/
On Mon, Jun 17, 2013 at 5:44 PM, Patel, Viren wrote:
> Hello. I have installed Galaxy and run it successfully. Now I am trying to
> configure it to use DRMAA job runner. I created a job_conf.xml file as
> explained in the Galaxy wiki:
>
>
>
>
> load="galaxy.jobs.runners.drmaa:DRMAA
On Jun 18, 2013, at 8:02 AM, galaxy-dev-requ...@lists.bx.psu.edu wrote:
> I have Galaxy running on a small Mac workstation. I have made a specific
> user, 'galaxy', for it. It is cleaner, but probably overkill for 1 person.
>
> Note also that you can install a daemon to start Galaxy automatically
Hello folks,
I am trying to configure an external data source and it is driving me crazy. I
keep getting the error "The remote data source application has not sent back a
URL parameter in the request." , even though it is.
My xml file is:
data_source.py $output
$__app__.config.ou
The upload_dataset parameter type is very specific to the upload tool.
You may be able to make this work but it is not a supported feature
(meaning, we can't tell you how to do it). You probably want to use a
normal data input (" wrote:
> Hi all,
>
>I have a tool written in java for which I wan
Hi all,
I have a tool written in java for which I want to upload a file as a
parameter. I have trouble figuring out how to do it. I tried writing the
xml file similar to 'tools/data-source/upload.xml' but it is not working.
*correlation.xml*
for the given BAM file
java -jar Corre
Thanks for the hint - that may be due to the fact that mercurial as
package only comes via a repository dating back to SLES 11 SP1 - there
seems to be no newer one. I just looked up the version: instead of
current v2.6.2 it's v1.0.2 (!)
On the other hand I'm glad that this reads like it does not
On Tue, Jun 18, 2013 at 10:54 AM, Sebastian Schaaf <
sch...@ibe.med.uni-muenchen.de> wrote:
> Thus, the cloning process as the LDAP user (did not want to store the
> foreign username/password explicitly in the galaxy user files) worked,
> although I get this message:
> "*** failed to import extens
Hi Saket,
First of all thanks a lot for your really quick reply. To sum it up: you
were right.
After ensuring the SSH out (works) your comments led me to the idea to
test the 'hg clone' command with a user account, which is neither root
nor galaxy. These two are local users, while my persona
You might want to ssh out and check if that is allowed. If you can ssh out,
you should be able to clone from bitbucket ssh too [ Though you might not
be able to push, depending on whether or not you own the repository]
On 18 June 2013 19:59, Saket Choudhary wrote:
> Hi Sebastian,
>
>
> I work b
Hi Sebastian,
I work behind a proxy too(In my case I have to supply a username and
password too )
I have the following thins setup in my ~/.bashrc:
export http_proxy= http://username:password@proxy-url:proxy-port/
then source it:
$ source ~/.bashrc
or maybe relogin .
and the .hgrc settings t
Hi all,
I'm currently trying to set up a galaxy-dist instance on a SLES server
within an 'encapsulated' network (hospital environment; here all
sensitive data is stored and handled). Within this network, clients are
only capable of accessing the internet via HTTP/HTTPS and FTP, using a
proxy
Hey Nikos,
Thanks for the interest in the LWR and frankly I am excited to hear
that bowtie worked properly. Some of these core NGS tools that require
implicit indices spanning multiple files are not really addressed by
the LWR currently, it only knows how to stage files that actually
appear in the
Hi
We are running the latest stable distribution on our server. We want
tophat2 (along with other tools) to be executed on another machine.
LWR is setup based on the online documentation (
http://wiki.galaxyproject.org/Admin/Config/LWR,
https://lwr.readthedocs.org/en/latest/)
Bowtie2 is working
This should now be resolved in -central. If you update again, you'll get
the changes and your instance should work fine.
-Dannon
On Tue, Jun 18, 2013 at 8:34 AM, Dannon Baker wrote:
> This is actually a bug in the current tip of galaxy-central that we should
> have resolved shortly. We should
This is actually a bug in the current tip of galaxy-central that we should
have resolved shortly. We should have an update out today, or you can
downgrade your galaxy to revision dfba9b0 (hg update -r dfba9b0).
-Dannon
On Tue, Jun 18, 2013 at 8:12 AM, Marco Ocana wrote:
> Hi,
>
> Just setup G
Hi Inbar
If you want to keep the NCBI stile fasta header, you need to change the
setting for "Output Sequence File Format:" to "NCBI style FASTA (m)".
By default, most EMBOSS tools change the fasta header format to the
"EMBOSS" style format.
Regards, Hans-Rudolf
On 06/16/2013 12:01 PM,
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