Re: [galaxy-dev] Shiny in Galaxy
by Yvan Le Bras
Dear Mohamed, Karim, galaxy-dev list,
A rapid e-mail to inform you that we plan to work on this task in the upcoming weeks with Thimothée and Valentin, copied. We have had some exchanges with Eric (Rasche) and Björn (Grüning) and it seems that using the Galaxy "interactive environment" functionality is a good way to proceed. Don't hesitate to give us more informations to collaborate on it...
Wishing you a good week end.
Cheers,
Yvan
-------- Message d'origine --------
De : "Md. Rezaul Karim" <rezaul.karim(a)insight-centre.org>
Date : 26/05/2017 15:45 (GMT+01:00)
À : Mohamed Kassam <k.mamoud(a)gmail.com>
Cc : Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org>
Objet : Re: [galaxy-dev] Shiny in Galaxy
+1
On May 26, 2017 2:44 PM, "Mohamed Kassam" <k.mamoud(a)gmail.com> wrote:
Dear all,
I have a shiny application working in my RStudio, but I would like to integrate it to Galaxy that the users can call my application via Galaxy .
Thanks in Advance,
Mohamed
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4 years, 10 months
Groovy tool for galaxy
by Anshul Tak
Hi,
I have a question regarding galaxy. Can I execute groovy scipts using
galaxy? I installed groovy in galaxy docker image and all the dependencies.
However, when I try to execute a tool which require groovy engine it
says "/export/galaxy-central/database/job_working_directory/000/2/tool_script.sh:
line 9: groovy: command not found"
So I understood the error that galaxy is not able to find groovy but
ideally it should take the groovy engine as it is installed.
Can you give me some pointers to solve this issue?
--
With Regards,
Anshul Tak
5 years, 5 months
numpy problem
by Matthias Bernt
Dear dev-list,
again some problems with software in galaxy: I can not get numpy to
install.
Here is the excerpt from the logs:
Successfully downloaded from url:
https://depot.galaxyproject.org/software/numpy/numpy_1.9p1_src_all.tar.gz
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,264 +
export
PYTHONPATH=$PYTHONPATH:/gpfs1/data/galaxy_server/galaxy/database/dependencies/numpy/1.9/iuc/package_numpy_1_9/83d12e13dbbd/lib/python
&&
export ATLAS=$ATLAS_ROOT_PATH &&
python setup.py install --install-lib
/gpfs1/data/galaxy_server/galaxy/database/dependencies/numpy/1.9/iuc/package_numpy_1_9/83d12e13dbbd/lib/python
--install-scripts
/gpfs1/data/galaxy_server/galaxy/database/dependencies/numpy/1.9/iuc/package_numpy_1_9/83d12e13dbbd/bin
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,384 Writing custom site.cfg for ATLAS in Galaxy
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,385 Traceback (most recent call last):
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,385 File "setup.py", line 264, in <module>
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,385 setup_package()
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,385 File "setup.py", line 210, in setup_package
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,385 raise RuntimeError("Writing custom
site.cfg failed! %s" % ex)
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,385 RuntimeError: Writing custom site.cfg
failed! 'ATLAS_LIB_DIR'
I need this tool for running: "Group data by a column and perform
aggregate operation on other columns." which gives me currently a numpy
error:
Traceback (most recent call last): File
"/gpfs1/data/galaxy_server/galaxy/tools/stats/grouping.py", line 15, in
<module> import numpy ImportError: No module named numpy
Thanks a lot.
Cheers,
Matthias
--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.bernt(a)ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
5 years, 5 months
Venn diagram example data
by Steven Shen
Dear Galaxy list,
I am interested in Galaxy Charts visualization.But venn diagram confuses me
when I upload my tabular data, it seems venn diagram need one column
observations
at least, actually I don't clear what should be contained in the one column
observations.
So is there any venn diagram example data or usage for this charts plugin ?
Sad to say I am not good at JavaScript :)
Thank you very much.
Regards,
Steven
5 years, 6 months
galaxy-tours : putting the box next to the preview display
by Hans-Rudolf Hotz
Dear All
I am working on a simple galaxy tour. The galaxy tour builder
(https://github.com/TailorDev/galaxy-tourbuilder) is great and helps a
lot, but unfortunately, not in this particular case:
- element: "#current-history-panel > ul.list-items >
div:nth-child(1) > div.details > div.actions.clear > div.left >
a.download-btn.icon-btn"
title: "Download your dataset"
intro: "You can download every dataset by using the floppy disc
symbol."
position: "left"
will put the box next to the floppy disc symbol.
What do I have to write as 'element' in order to get the box pointing to
the actual preview data (i.e. the white box)?
Thank you very much for your help
Regards, Hans-Rudolf
--
Hans-Rudolf Hotz, PhD
Bioinformatics Support
Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
5 years, 6 months
Accessing only to "not deleted" history datasets from a visualization plugin
by LPER
Hi everyone,
I am currently working on a visualization plugin and I would like to have access from this plugin to multiple history datasets. I managed so far to view all the history dataset in the console with the following commands :
var query = '/api/histories/'+'${trans.security.encode_id(trans.history.id)}/contents?details=all';
$.ajax({url: query, dataType : 'json', async: false, success: function(data){console.log(data);}});
Data is an array containing history dataset objects. However, it contains all the history datasets, even those that were deleted and deleted permanently from the disk. I can filter data according to the boolean purged attribute of each dataset to get only the datasets visible to the user, but I was wondering if there was a quicker and more efficient way to do this by getting only the "not deleted" history datasets with the query?
Thanks in advance for your answer(s),
Cheers and have a nice day!
Lisa
Sent with [ProtonMail](https://protonmail.com) Secure Email.
5 years, 6 months
genome upload
by Marion Cerri
To whom it concerns,
I am Marion Cerri, post doc in the Parniske’s lab, in Munich. I am working with ChIP-seq data in the moment.
I would like to use the Lotus japonicus (version 3.0) for mapping reads, but the genome is not available on galaxy. Would it be possible to upload it ? Do I have to provide the file to you, and if so in fasta format ?
Thanks in advance
Best Regards
Marion Cerri
5 years, 6 months
Uncaught Error When Installing Tools From Toolshed
by William, Van Der Pol
Hello All,
I have recently cloned and installed a clean version of Galaxy. I installed a tool from the toolshed and Galaxy says it is properly installed, however when I try to open the tool in the main page all I see is an "Uncaught Error" message. Does anyone have any ideas on what is causing this or at least how I can get a more telling error message?
Thanks
-Liam
5 years, 6 months
Galaxy @ ISMB/ECCB/BOSC 2017: Talks, posters, dinner, BoF, and tutorial
by Dave Clements
Hello all,
There are Galaxy-related events and presentations every day
<https://galaxyproject.org/events/2017-ismb-bosc/> at ISMB/ECCB 2017
<https://www.iscb.org/ismbeccb2017> and BOSC 2017
<https://www.open-bio.org/wiki/BOSC_2017>:
- A tutorial <https://www.iscb.org/ismbeccb2017-program/tutorials#p6> (
Friday <https://galaxyproject.org/events/2017-ismb-bosc/#21-july-friday>,
still space)
- 6 BOSC talks (Saturday
<https://galaxyproject.org/events/2017-ismb-bosc/#22-july-saturday>,
Sunday <https://galaxyproject.org/events/2017-ismb-bosc/#23-july-sunday>)
- 9 posters (Saturday
<https://galaxyproject.org/events/2017-ismb-bosc/#22-july-saturday>,
Sunday <https://galaxyproject.org/events/2017-ismb-bosc/#23-july-sunday>
, Monday
<https://galaxyproject.org/events/2017-ismb-bosc/#24-july-monday>,
Tuesday
<https://galaxyproject.org/events/2017-ismb-bosc/#25-july-tuesday>)
- 2 ISMB/ECCB talks (Saturday
<https://galaxyproject.org/events/2017-ismb-bosc/#22-july-saturday>,
Tuesday
<https://galaxyproject.org/events/2017-ismb-bosc/#25-july-tuesday>, both
by Galaxy PIs)
- A Galaxy BoF
<https://www.iscb.org/ismbeccb2017-program/ismbeccb2017-bof> (Monday
<https://galaxyproject.org/events/2017-ismb-bosc/#24-july-monday>)
- A Galaxy Dinner <http://bit.ly/gxyismb2017bdinner> (Monday
<https://galaxyproject.org/events/2017-ismb-bosc/#24-july-monday>, see
below)
*Galaxy Community Dinner: Monday, 24 June, 8pm*
The Galaxy Community will be gathering at ISMB/ECCB/BOSC 2017 over dinner
on Monday, 24 July at 8pm. Interested? *Then sign up now
<http://bit.ly/gxyismb2017bdinner>!* *Dinner is pay-your-own-way and space
is limited.* Once it's full, it's full, so please signup today. See the sign
up form <http://bit.ly/gxyismb2017bdinner> for more information.
See you in Prague!
--
https://galaxyproject.org/
https://getgalaxy.org/
https://usegalaxy.org/
https://gcc2017.sciencesconf.org/
5 years, 6 months