Ah, thankyou, yes, I can now get results by using patterns to match the
output. I used your example but prepend 'simple' to the filename and then
searches for that with:
this solves the problem for the sample script but not generally since in
general I can't predict the filenames that will be ge
Hi,
I am encountering a problem executing the genomespace_importer tool using
the Galaxy API.
The tool works just fine to copy files in GenomeSpace into Galay a history
dataset EXCEPT when the GenomeSpace file URL includes a space (" ") of any
sort.
Below is an example problem request (the Genom
On Tue, 20 Oct 2015 14:48:08 +0200
Bjoern Gruening wrote:
> Hi Tiago,
>
> for simple tool_dependencies you can use the new planemo depbash
> command from Peter:
> https://github.com/galaxyproject/planemo/pull/310
Gosh, this is exactly what the doctor ordered. Thanks (to Peter also).
> What k
I poked around at your tool XML and the code a bit and the problem is
directory="$job_name". Galaxy expects to collect files from the job's
working directory - basically the current working directory the job runs
in. The directory= argument doesn't have variables expanded as far as I can
tell. In a
On Tue, Oct 20, 2015 at 10:01 AM, Tiago Rodrigues Antao wrote:
> Hi,
>
> I am afraid that I might be overlooking something obvious but...
>
> I am trying to add a few tools to the RAD-Seq portfolio of Galaxy. For
> that effect I am designing a few package wrappers. My problem is to
> understand th
Hi Tiago,
for simple tool_dependencies you can use the new planemo depbash command
from Peter:
https://github.com/galaxyproject/planemo/pull/310
For more complicated once I recommend to use the TTS for the time being.
You can create the initial repository install from it and change your
tool_
Hi,
If you have a line in your Apache conf like
"Listen 80"
change to
"Listen 8081"
> On 20 Oct 2015, at 21:00, Makis Ladoukakis wrote:
>
> Hello,
>
> I am sorry but I have really no experience with setting up the Apache web
> server so I am not really sure how to do that. Can you please
Hi,
I'm afraid it won't be easy to reproduce my problem with a clean galaxy
install. I think it has to do with the history of the instance, a lot of back
and forth on the tool installations and also lot's of failed installations (due
to my environment or network issues).
Investigating the issu
Hello,
I am sorry but I have really no experience with setting up the Apache web
server so I am not really sure how to do that. Can you please help me out with
it? My apache configuration file is in /etc/httpd/conf/ directory and there are
no directories such as /sites-available/ or /sites-enab
Yes, I'm sure that's where the problem lies. Writing out to the current
directory doesn't work. The files get written to
'job_working_directory/000/1/' but if I run the Upload File tool the result
is placed in 'files/000/'. I think I need to work out where to write the
files, I found some referen
Hi,
I am afraid that I might be overlooking something obvious but...
I am trying to add a few tools to the RAD-Seq portfolio of Galaxy. For
that effect I am designing a few package wrappers. My problem is to
understand the best practice to develop wrappers for dependencies of
external tools.
For
I suspect that the problem might be in the then. I'm
not an export on this, but "__name_and_ext__" turns into the
regexp r"(?P.*)\.(?P[^\.]+)?" in
lib/galaxy/tools/parameters/output_collect.py, and is used by the
DatasetCollector (line 358). This looks like it should match the filenames
you're cre
Sorry to hijack the thread, but I think the issue that Sarah has described
could be related to
https://github.com/galaxyproject/galaxy/issues/667.
(I know it's not exactly the same, but chances are we fix this, we
automatically fix Sarah's issue.)
There is also an example to reproduce
https://githu
Thanks Peter,
I did see that proviso somewhere but no, refreshing doesn't help.
That page was one of those that I referred to getting to this point.
Steve
On 20 October 2015 at 18:33, Peter van Heusden wrote:
> Just a quick check - did you refresh your history to confirm that the
> dataset *
Just a quick check - did you refresh your history to confirm that the
dataset *is* empty? We had the same thing at SANBI but it turns out that
Galaxy creates an empty output collection and then only populates it
sometime after job completion (this is a know UI bug).
See:
http://pvh.wp.sanbi.ac.za/
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