I've finally sorted this. Here is my solution in case anyone else is
getting stuck with this.
The URLs to the tool sheds in the file tool_sheds_conf.xml were http not
https.
Changing them to https and restarting galaxy seems to have resolved this
issue.
Anna
___
Thanks Martin
On 27 March 2015 at 15:20, Martin Čech wrote:
>
> This is one installable revision behind. Try selecting 'install latest
> revision' instead of updating in the repository dropdown.
>
>
Great, also sorted.
>
>> I think this has to do with your proxy configuration that is not
>>>
Hi Martin, thanks for looking at this
On 27 March 2015 at 14:51, Martin Čech wrote:
>
>
> The requested revisions are from the Test Tool Shed, which means your
> package_samtools_1_1 is also installed from the Test Tool Shed. Please
> install only from the Main Tool Shed (https://toolshed.g2.bx
p would be greatly appreciated, as I'm thinking something major has gone
wrong and that I will have to reinstall galaxy.
Many thanks
Anna
On 6 March 2015 at 16:50, Anna Terry wrote:
> Hi,
> I have a few installed tool shed repositories which are showing that
> updates are av
date is indicated as
being available) I get the same problem, so I don't think its to do with
what toolshed they are from - they are mostly the main toolshed anyway.
Kind regards
Anna
>
> thanks
>
> Martin
>
> On Thu, Mar 12, 2015 at 10:37 AM Anna Terry
> wrote:
>
>&g
Hi, can anyone help with this? TIA
On 6 March 2015 at 16:50, Anna Terry wrote:
> Hi,
> I have a few installed tool shed repositories which are showing that
> updates are available. When I click get repository updates, instead of the
> usual upate page, I get a page that simply
Hi,
I have a few installed tool shed repositories which are showing that
updates are available. When I click get repository updates, instead of the
usual upate page, I get a page that simply says
Found
The resource was found at
http://toolshed.g2.bx.psu.edu/repository/check_for_updates?galaxy_url
tps://wiki.galaxyproject.org/Admin/Config/ApacheProxy#>
RequestHeader set X-URL-SCHEME https
Many thanks for your help
Anna
On 21 January 2015 at 11:04, Anna Terry wrote:
> Hi John,
>
> Unfortunately swapping out this line for the one in the previous version
> does not work, but get this
t to do now to side this
> problem.
>
>
> On Mon, Jan 19, 2015 at 8:36 PM, John Chilton wrote:
> > Hello Anna,
> >
> > Can you try something for me -
> >
> >
> >
> https://bitbucket.org/galaxy/galaxy-central/commits/579d211c2b0fa8ef4195930cb999ed
ul.ac.uk/tool_runner'. This request has been blocked;
the content must be served over HTTPS.
Is there any way to change settings so that it points back to https? The
server should redirect to https but I guess the browser doesn't know this?
TIA
Anna
On 13 January 2015 at 16:39, Anna Te
Thanks Hans-Rudolf, will do
On 15 January 2015 at 08:24, Hans-Rudolf Hotz wrote:
> Hi Anna
>
> I am just guessing, but it might be worth checking the proxy settings of
> your local galaxy server.
>
>
> Regards, Hans-Rudolf
>
>
>
> On 01/13/2015 05:39 PM, Anna
Hi,
I am having lots of problems with the get data tools installed on our local
galaxy server, I'll start with just one.
With the UCSC Main one, I am unable to send data back to galaxy, when I
click "Send query to Galaxy" nothing happens, the button is unresponsive.
This is in contrast to when I
manage jobs
> interface. Clicking on the job id will display more details. Are there
> other things that you'd like included that aren't there?
>
> -Dannon
>
> On Wed, Jan 7, 2015 at 11:50 AM, Anna Terry
> wrote:
>
>> Hi,
>>
>> Sorry if this is a s
Hi,
Sorry if this is a stupid question, but is the job id and other queue info,
for a job that has run on a cluster available from within galaxy?
Both during and and after completion of the job.
Many thanks
Anna
___
Please keep all replies o
Deleting the newer 0.3 version of Bowtie fixes the problem with version 0.2.
On 18 December 2014 at 13:29, Anna Terry wrote:
>
> Hi again,
> I have just updated Picard, and am getting a similar error with some tools
> from that repository when I switch to older version from tool pa
old_errors, process_state, history=history, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
__check_param_values
errors = self.update_state( trans, inputs, state.inputs, incoming,
old_errors=old_errors or {}, source=source )
File '/home/galaxy/g
Hi,
I am getting an error page when I try to open the bowtie2 tool page (after
selecting older version 0.2 a54de7e658f7 from drop down on version 0.3
c1ec08cb34f9 page).
URL: http://../tool_runner/index
File
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middlewa
great, thanks
On 26 November 2014 at 16:39, bjoern.gruen...@googlemail.com <
bjoern.gruen...@gmail.com> wrote:
> I would use .bashrc. You can also try to symlib the default dir to the
> actual /bin directory. Maybe this works for you.
>
> 2014-11-26 17:36 GMT+01:00 An
ls to create metadata for BAM files, so this
> process is actually running ofter bowtie has finished.
> You need a samtools version globally accessible for Galaxy. Make sure you
> have smatools in your $PATH and than restart Galaxy.
>
> Cheers,
> Bjoern
>
> 2014-11-26 17:14 GMT+
Installed tool shed repositories
>
> uninstall -> reinstall package_samtools_0_1_18
>
>
> On 26 November 2014 at 16:55, Anna Terry wrote:
>
>> yway, I am also getting the problem with samtools filter sam or bam
>
>
>
>
>
> --
> Central Veterinary Instit
What is really weird is when running the bowtie2 tool, before it quits, I
can see samtools come up in top
On 26 November 2014 at 15:55, Anna Terry wrote:
> So I actually still have a problem,
> (I guess the setting was still there somewhere from the bash_profile)
>
> Anyway, I am
he samtools binary to
default, but still the same problem.
Any other ideas?
On 26 November 2014 at 14:01, Anna Terry wrote:
> Great, I've done it and it works.
>
> galaxy-dist/tools/samtools/default
> cd galaxy-dist/tools/samtools/default/
> cp -rs ~/galaxy-dist/tools/samtool
Hi,
I installed bowtie2 from the toolshed, but get the following error when I
run it:
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py",
line 129, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/home/galaxy/galaxy-dist/l
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