API for multi-file upload
by Neil.Burdett＠csiro.au
Hi,
I really like the multi-file upload tool in the latest version of Galaxy. Is there an API for it so we can send files via a script rather than using the user interface? If so are there any examples?
Thanks
Neil
6 years
Error with functional tests on cluster
by Sandra Derozier
Hi all,
I try to set up functional tests on different tools on my Galaxy portal.
When I run functional tests locally everything works fine. But when I run
them on the cluster it failed with this message :
/bin/sh: module: line 1: syntax error: unexpected end of file
/bin/sh: error importing function definition for `module'
The execution on the cluster is ok but the dataset state is set to ERROR.
The DIFF between the expected result and the obtained result is null.
Indeed, this two files are the same.
As I do not know what the problem is: do you have an idea?
Thanks,
Sandra DEROZIER
6 years
testing the visualization plugins
by Hans-Rudolf Hotz
Hi
As part of my upgrade/testing work, I am looking at the visualization
plugins.
In a new galaxy installation ("latest_2014.08.11"), they (ie 'Charts',
'Scatterplot', and 'Trackster') seem to work fine.
All I have done was:
- I defined the visualization_plugins_directory in the
universe_wsgi.ini file
If I comment-out this line, I only get trackster, when I click on the
icon which looks like a bar-plot
Next, I have tried it on our development server (after I have upgraded
from "release_2014.04.14" to "latest_2014.08.11"). I changed the
universe_wsgi.ini file.
I the logs I get:
galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,639
VisualizationsRegistry, loaded plugin: charts
galaxy.web.base.pluginframework WARNING 2014-08-27 09:43:45,641
VisualizationsRegistry, plugin load failed or disabled:
./config/plugins/visualizations/circster. Skipping...
galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,655
VisualizationsRegistry, loaded plugin: graphview
galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,657
VisualizationsRegistry, loaded plugin: phyloviz
galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,675
VisualizationsRegistry, loaded plugin: scatterplot
galaxy.web.base.pluginframework WARNING 2014-08-27 09:43:45,677
VisualizationsRegistry, plugin load failed or disabled:
./config/plugins/visualizations/sweepster. Skipping...
galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,679
VisualizationsRegistry, loaded plugin: trackster
wrt to 'Charts', 'Scatterplot', and 'Trackster', this looks fine to me.
However, if I hoover over the bar-plot icon, "Visualize in Trackster"
pops up (instead of just "Visualize"), and when I click on it I get
straight to the Trackster page, where, I am asked to define the Browser
name and the Reference genome. No links for 'Charts' and 'Scatterplot'.
On the other hand, the plug in infrastructure seems to work: If I change
~/config/plugins/visualizations/trackster/config/trackster.xml I see the
effects, ie if I change
result_type="datatype">data.Data<
to
result_type="datatype">interval.Interval
I can restrict the visualization to only the interval data.
Somehow, I am running a mixture of the 'old' and the 'new' visualization
set-up ?
Has anyone seen similar problems when testing the new plug in
infrastructure on an old/upgraded Galaxy installation
Thank you very much for any hints and help
Hans-Rudolf
--
Hans-Rudolf Hotz, PhD
Bioinformatics Support
Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
6 years
error with multi dataset tool run
by Robert Baertsch
I submitted 13 fastq files to tophat2 using DRMAA and got this error. Is it fatal? BTW: This is a super cool feature.
I’m running the following version of galaxy-dist.
changeset: 14212:91547729ffde
branch: stable
tag: tip
user: Nate Coraor <nate(a)bx.psu.edu>
date: Fri Aug 29 14:00:23 2014 -0400
summary: Update tag latest_2014.08.11 for changeset ea12550fbc34
-Robert
There were errors setting up 2 submitted job(s):
Error executing tool: (OperationalError) database is locked u'UPDATE history_dataset_association SET update_time=?, name=?, blurb=? WHERE history_dataset_association.id = ?' ('2014-08-30 23:14:44.683957', 'Tophat2 on data 7: insertions', 'queued', 137)
Error executing tool: (OperationalError) database is locked u'UPDATE dataset SET update_time=?, state=? WHERE dataset.id = ?' ('2014-08-30 23:15:57.204718', 'queued', 446)
6 years
