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:
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
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
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 install part executes before the package part is
finished and the $R_ROOT_DIR reference also doesn't seem to
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:
I think you want your job_conf.xml destination to have the parameter
param id=docker_enabledtrue/param
not
param id=smalt-galaxytrue/param
Does this help any?
-John
On Thu, Nov 6, 2014 at 1:35 AM, Weiyan Shen shenw...@gmail.com wrote:
Hi,
I integrated Docker-based tools SMALT whin my
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
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
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
Hi John Chilton,
Thank you very much for your help. I changed my job_conf.xml as follow,it works!
?xml version=1.0?
!-- A sample job config that explicitly configures job running the way it is
configured by default (if there is no explicit config). --
job_conf
plugins
plugin
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.
Hi Pieter,
you should probably add:
action type=set_environment_for_install
repository name=prims_metabolomics_r_dependencies
owner=pieterlukasse
package name=R_bioc_metams version=3.1.1 /
/repository
/action
before using the R_ROOT_DIR environment variable.
Best,
Nicola
Il
I agree with Nicola here! :)
Am 06.11.2014 um 17:48 schrieb Nicola Soranzo:
Hi Pieter,
you should probably add:
action type=set_environment_for_install
repository name=prims_metabolomics_r_dependencies
owner=pieterlukasse
package name=R_bioc_metams version=3.1.1 /
/repository
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