Pieter,
if the uploaded file has an ext of .Rdata and you have defined an Rdata
datatype as (eg) a subclass of gzip, then AFAIK the extension will be
matched as part of the sniff processing without the contents needing to be
examined - ie it should "just work" without a new specialised sniffer?
I
Hello all,
Because Galaxy uses the upload tool internally for the inputs for
function tests, it is possible to bundle gzipped versions of test
inputs which saves space. For example,
https://github.com/peterjc/pico_galaxy/blob/master/tools/clc_assembly_cell/clc_mapper.xml
However, what I have jus
I agree with Nicola here! :)
Am 06.11.2014 um 17:48 schrieb Nicola Soranzo:
> Hi Pieter,
> you should probably add:
>
>
>owner="pieterlukasse">
>
>
>
>
> before using the R_ROOT_DIR environment variable.
>
> Best,
> Nicola
>
> Il 2014-11-06 11:28 Lukasse, Pieter ha scritto:
>> Hi
Hi Pieter,
you should probably add:
owner="pieterlukasse">
before using the R_ROOT_DIR environment variable.
Best,
Nicola
Il 2014-11-06 11:28 Lukasse, Pieter ha scritto:
Hi Bjoern,
I tried your suggestion, but it didn't work. So now I have split up
the R part from the Bioconduct
I'v run into this same issue again (just with some other Data Library
datasets). This time, there are a few users involved with quite a few
"stuck" jobs. Does anyone have any advice on pushing these jobs
through? Maybe even a pointer to the relevant code? I'm running
latest_2014.08.11. Tha
Hi John Chilton,
Thank you very much for your help. I changed my job_conf.xml as follow,it works!
true
$defaults
/usr/bin/docker
false
/usr/bin/
Alright, I think you are right. The possible confusion is not worth the
benefits. I have switched the ordering back to the classic sorting. I will
now look into the dataset selector and see how to revise it. Thanks for
pointing these things out.
Thanks,
Sam
On Thu, Nov 6, 2014 at 8:18 AM, Peter C
Hi Sam,
I found the old approach (new repeat blocks at bottom) worked fine
when adding blocks one by one and completing them as I went
(which means once you have filled in the new block, you have
scrolled down to the button ready to add another block if needed).
If find the new approach (new bloc
Hi Peter,
Yes we changed this on purpose, however it is open to discussion. The
advantage is that the user does not have to scroll down after adding a new
repeat block. Additionally it enables users to easily add more than one
repeat block quickly, since the insert button does not relocate on the
I think you want your job_conf.xml destination to have the parameter
true
not
true
Does this help any?
-John
On Thu, Nov 6, 2014 at 1:35 AM, Weiyan Shen wrote:
> Hi,
> I integrated Docker-based tools SMALT whin my local Galaxy by the
> guid:https://github.com/apetkau/galaxy-hackathon-2014/t
Thanks Dave,
The good news is yes, the tests are running again on the
Test Tool Shed (although not the main Tool Shed yet), and
many of my tools now have successful test results from
last night.
e.g. My new basic mummer tool which now has a full set
of dependency packages thanks to Bjoern:
https:
Hi Bjoern,
I tried your suggestion, but it didn't work. So now I have split up the R part
from the Bioconductor part (blue and yellow below, respectively). But the
problem is that the part executes before the part is
finished and the $R_ROOT_DIR reference also doesn't seem to work as I get
Hi Ross,
I also found the following information:
“save works by writing a single-line header (typically RDX2\n for a binary
save: the only other current value is RDA2\n for save(files=TRUE)),”
From http://cran.r-project.org/doc/manuals/r-release/R-ints.html (section 1.8
– Serialization Formats
An alternative would be perhaps to look at the file name. If it ends in
“.RData” then I could mark it as such. Being able to access the original file
name (so not the internal one but the name that also appears in the history UI)
would allow me to do this. What would be the way to access this fr
Hi Bjoern,
Thanks for this reply. I will have to try referring to the R_ROOT_DIR from
another tool_dependency. If it doesn't work I'll come back ;)
Regards,
Pieter
-Original Message-
From: Björn Grüning [mailto:bjoern.gruen...@gmail.com]
Sent: donderdag 30 oktober 2014 11:25
To: gal
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