Hi all,
I was told that updates to packages owned by devteam should just be sent
here, since there is no public repo.
I have patches for the libxml2 and libxslt tool_dependency.xml's, that set
some more environment variables that my tool needs (specifically, the
python lxml package needs some of
Hi all,
I'm trying to create a new binary datatype in galaxy, but I'm running
into troubles. The current installer is available at
https://testtoolshed.g2.bx.psu.edu/view/geert-vandeweyer/cuffquant_datatype
When I install the repository to a local server, I get the errors below
(no module bi
Hi Geert,
please include this at the top:
from galaxy.datatypes.binary import Binary
Cheers,
Bjoern
Am 04.08.2014 um 15:02 schrieb Geert Vandeweyer:
Hi all,
I'm trying to create a new binary datatype in galaxy, but I'm running
into troubles. The current installer is available at
https://test
Hello,
How can i convert xls file to csv file on galaxy ?
Is that possible ?
Best Regards,Mert.
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Hi,
not tat I know. But you can export your xls in Excel as tab separated
file. Galaxy can handle such tab-delimited files.
Cheers,
Bjoern
Am 04.08.2014 um 14:56 schrieb Mert Mehnur KIRKALI:
Hello,
How can i convert xls file to csv file on galaxy ?
Is that possible ?
Best Regards,Mert.
Hi Mert,
Most of the Galaxy tools dealing with tables of data use "tabular"
format (tab separated variables), not csv (comma separated
variables). CVS is a horrible horrible mess of formats, see e.g.
http://tburette.github.io/blog/2014/05/25/so-you-want-to-write-your-own-CSV-code/
Also beware tha
Hi Peter,
On 08/04/2014 09:25 AM, Peter Cock wrote:
> Hi Mert,
>
> Most of the Galaxy tools dealing with tables of data use "tabular"
> format (tab separated variables), not csv (comma separated
> variables). CVS is a horrible horrible mess of formats, see e.g.
> http://tburette.github.io/blog/20
On Mon, Aug 4, 2014 at 4:28 PM, Eric Rasche wrote:
> Hi Peter,
>
> On 08/04/2014 09:25 AM, Peter Cock wrote:
>> Hi Mert,
>>
>> Most of the Galaxy tools dealing with tables of data use "tabular"
>> format (tab separated variables), not csv (comma separated
>> variables). CVS is a horrible horrible
I noticed that the instructions at
https://wiki.galaxyproject.org/Admin/DataIntegration direct admins to
update the builds.txt file when adding a new reference genome to local
Galaxy instances. Up to this point I had been actually modifying the
manual_builds.txt file and then rebuilding the bu
Solved!
After finding documentation indicating that changing the URL of the test
toolshed from http to https in the tool_sheds_config.xml file solved some
redirection issues, I tried the same thing for the URL of the main toolshed.
Message: 7
Date: Fri, 1 Aug 2014 20:30:14 +
From: "Perle
Jobs executed in the workflow appear to have a creation time, but no
execution start and end time listed. How does one determine when
something executed? I'd like to know exactly where the time is spent
computing...
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Hi Evan,
What you're looking for should be covered by the new Job Metrics plugins.
If you'd like to know more, see:
https://wiki.galaxyproject.org/Admin/Config/JobMetrics
-Dannon
On Mon, Aug 4, 2014 at 3:24 PM, Evan Bollig wrote:
> Jobs executed in the workflow appear to have a creation time
Thanks Dannon. I'll add it to the todo list. Do the metric include
time and memory info for the entire history/workflow, or does it only
report for individual tools? Max consumed storage during a workflow
execution is another data point I'd like to monitor.
-E
-Evan Bollig
Research Associate | App
These metrics would only apply to individual jobs and not for the entire
history/workflow, though there are plans (https://trello.com/c/XsQdqliU) to
expose the data via the API so that one might generate summary metrics,
among other things.
On Mon, Aug 4, 2014 at 3:40 PM, Evan Bollig wrote:
> T
Hi all,
I've updated the tool wrappers for the cufflinks tools to options
supported by cufflinks 2.2.1. I've also added the cuffquant and cuffnorm
tools, together with the cxb datatype.
As discussed with Jeremy, these updates were welcome :-)
Everything is available on the test toolshed, tes
Awesome!
Thanks Geert!
Bjoern
Am 04.08.2014 um 22:37 schrieb Geert Vandeweyer:
Hi all,
I've updated the tool wrappers for the cufflinks tools to options
supported by cufflinks 2.2.1. I've also added the cuffquant and cuffnorm
tools, together with the cxb datatype.
As discussed with Jeremy, th
Hi,
I haven't been able to find any implementation of the PHYLIP tools into
Galaxy. I know some datatype are part of the emboss datatypes but what
about the tools ? I reckon I am not the only one looking for this so I fear
I might have missed something, if this is the case could you please point
i
Hi,
I have recently upgraded Galaxy from a version I had last year. In my tool
xml file I could state:
${ __app__.model.User.get( $__user_id__ ).api_keys[0].key }
in the section to get the user's API. However, after updating to the
current version of Galaxy I get the following error when u
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