To ease the maintenance of our Dutch National galaxy, we're trying to set
up our own toolshed on a system that happens to have a nicely large MySQL
database running. We'd like to make it use that database. The setup has
been ok, until we started running the toolshed on the MySQL server for the
firs
FYI: Here are the entries in paster.log. If you notice no job_handlers are
being sent. I performed tests on both nginx reverse proxy and direct
localhost:8080 (limited to our private network on campus)
128.200.34.227 - - [11/Apr/2013:13:24:40 -0700] "GET
/tool_runner?tool_id=upload1 HTTP/1.0" 200
Howdy Galaxy Admins,
I am installing Galaxy on our HPC cluster and running into a strange issue
that I can no longer debug further. I am running the latest galaxy build as
of Tuesday April 9th.
hg clone https://bitbucket.org/galaxy/galaxy-dist/
hg update stable
When a user tries to upload
On Apr 11, 2013, at 12:39 PM, Peter Cock wrote:
> On Thu, Apr 11, 2013 at 5:02 PM, John Chilton wrote:
>> Hey Peter,
>>
>> Hopefully Nate will have some wisdom, all I have is a workaround (I
>> have fought with this on multiple forks and this is the best I have
>> come up with).
>>
>> Check ou
On Thu, Apr 11, 2013 at 5:02 PM, John Chilton wrote:
> Hey Peter,
>
> Hopefully Nate will have some wisdom, all I have is a workaround (I
> have fought with this on multiple forks and this is the best I have
> come up with).
>
> Check out a clean version of the tools branch somehow (it seems lik
Hi all,
Does anyone else see this problem with broken tool ids in the
function test script? I found this because one of my own tools
wasn't being recognised because for some reason the id was
treated as _name= [sic].
This happens on the default branch:
$ ./run_functional_tests.sh -list | grep "_
Hello, Hakeem
Although I've never used it, you might try the java_genomics_toolkit
available as a tool shed repository (or have your installation's admin
install it). It contains a tool called 'Align values in a matrix' which may
work for your needs.
Thanks,
Carl
On Tue, Apr 2, 2013 at 12:51 PM
Hey Peter,
Hopefully Nate will have some wisdom, all I have is a workaround (I
have fought with this on multiple forks and this is the best I have
come up with).
Check out a clean version of the tools branch somehow (it seems like
the working contents can get stuck in an invalid state that upda
Hello, Alexander, and thanks for the report
Do any of the bugged histories contain shared data (such as library
datasets)?
On Wed, Apr 3, 2013 at 5:27 AM, Alexander Kurze <
alexander.ku...@bioch.ox.ac.uk> wrote:
>
> Hello,
>
> I am running a local galaxy server where I have restricted the amoun
(Apologies if this comes twice - it seems I didn't press send when I wrote
the draft earlier in the week)
On Tue, Feb 19, 2013 at 5:38 PM, Peter Cock wrote:
> On Tue, Feb 19, 2013 at 5:26 PM, Nate Coraor wrote:
>> On Feb 19, 2013, at 12:18 PM, Peter Cock wrote:
>> Nate wrote:
Hi Peter,
Thanks much for the information, Geert. I've created a card for this bug in
Trello: https://trello.com/c/KLmH1nag.
On Wed, Apr 3, 2013 at 5:39 AM, Geert Vandeweyer wrote:
> Hi,
>
> In case anybody is wondering, the "set_user_disk_usage.py" script corrects
> this.
>
> Best,
>
> Geert
>
>
> On 03
Hi Sarah,
It still sounds like there is a path problem - this is why the tools are
looking in the wrong loc file. When bowtie2/tophat2 installs, it will
create a symbolic link that names itself as just "bowtie" or "tophat",
pointing to the v2 binaries.
When you run these, what do you get?
Thanks a lot Jennifer,
Restart, full paths were OK.
I don't know why but the 2nd version of Tophat (so the tophat tool
available from Galaxy) search indexs in bowtie-index.loc file and not in
bowtie2-index.loc
So, I've added my bowtie2 index paths in bowtie-index. loc file and
tophat run...
On Thu, Apr 11, 2013 at 7:54 AM, Holtgrewe, Manuel
wrote:
> Dear all,
>
> is it possible to make Galaxy use a specific extension for a given data type
> without a wrapper?
>
> I.e. can I make Galaxy use the extension .bam, .sam, .fasta etc. internally
> instead of .dat?
>
> Thanks,
> Manuel
I t
Hi Manuel,
collect your binaries in a separate location and add to PATH and your
cluster. If you want to ship your tool in the toolshed, the installation
and PATH will be automatically added once you installed it from the
toolshed. Have a look at:
http://wiki.galaxyproject.org/ToolShedToolFeature
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