Expose local filesystem to Galaxy?
by Sandra Maksimovic
Hi there,
We are hosting an on-prem Galaxy instance in a HPC environment. Our research staff would like the ability to manipulate raw data that is located on the shared filesystem without having to manually upload it into Galaxy. Is this currently supported and would there be any related documentation?
Thanks,
Sandra
1 year, 9 months
Requesting a tool integration
by Muhammet A. Celik
To whom may it concern;
We are writing to inquire on the possibility of contributing to the Galaxy
pool of tools.
At the outset, we thank the Galaxy community for all the hard work on the
wonderful platform, which is of a big value to the scientific community.
We are participants of the Open Life Science Project-2 (OLS-2) and are
mentored by Dr. Mallory Freeberg, who is also CCed in this email. Our
project is about creating a single pipeline integrating metagenomics tools
for taxonomic classification. The pipeline would ease the work of those
interested in metagenomic studies, especially those who do not have IT
background or enough computational resources. We also want to include a
visualization tool (Krona) to illustrate the output, since the standard
output is typically a txt file. The selected tools for the taxonomic
classification are Kraken2, Centrifuge and Clark, which are widely used and
identified as the state of the art based on our literature review.
Last week, we presented our work to Dr Berenice Batut (who is also CCed
herein), who is an expert in the field. Thanks to her feedback and advice
and that of Dr Mallory, we want to explore the prospect of porting our
project onto the Galaxy platform, to benefit the wider community. We have
checked both the Galaxy servers (https://usegalaxy.eu/ and
https://usegalaxy.org), as well as the ToolShed to see if the tools that we
want to deploy are already available on Galaxy.
Kraken2 is available and is ready for use with various DB's. On the other
hand, we were not able to find Centrifuge on the tools search section,
although it appears in the ToolShed (
https://toolshed.g2.bx.psu.edu/view/jvolkening/centrifuge/be7bba8229c6),
whereas Clark (http://clark.cs.ucr.edu/) is not available on the platform.
Thus, we hope that you could import these tools on Galaxy so that we can
port our pipeline(workflow) on the Galaxy platform.
Thank you,
Muhammet
1 year, 10 months
Release of Galaxy 20.09
by Marius van den Beek
Dear Community,
The Galaxy Committers team is pleased
to announce the release of Galaxy 20.09.
The release announcement for developers and admins can be found at
https://docs.galaxyproject.org/en/master/releases/20.09_announce.html
and user facing release notes are at
https://docs.galaxyproject.org/en/master/releases/20.09_announce_user.html.
A few release highlights are:
GTN In Galaxy
--------------------
The Galaxy Training Network tutorials can now be accessed from within Galaxy
using the graduation cap icon. For updated tutorials, tools will be
highlighted as blue buttons. When clicked, these buttons will hide the GTN
and
take you directly to the correct version of the correct tool within the
Galaxy
interface.
Plugin framework for uploading datasets
------------------------------------------------------
Galaxy administrators can now configure different sources
from which users may upload files. These include global or
user-specifc webdav servers, dropbox accounts as well as
FTP and regular filesystem locations. Developers can add
new types of sources by adding PyFileSystem2
<https://docs.pyfilesystem.org/en/latest/introduction.html>
compatible plugins.
Upload directly from the Tool Form
----------------------------------------------
Datasets can now be uploaded directly from the Tool Form.
Workflow import from GA4GH TRS servers
---------------------------------------------------------
Galaxy can now search and import workflows from GA4GH TRS servers,
such as Dockstore <https://dockstore.org/> and WorkflowHub
<https://workflowhub.eu/>.
We hope that sharing workflows on these platforms will facilitate re-use
and collaboration.
Simplified workflow submission form
------------------------------------------------
Galaxy now presents a simpler and cleaner interface for submitting workflows
that focuses on the parameters to set and datasets to choose.
Accelerated batch job creation and workflow step scheduling
---------------------------------------------------------------------------------
Galaxy now batches database interactions for the creation of batch jobs.
For large batches of jobs this can speed up job creation by 100-fold or
more.
Check out the release notes for a lot more details - there are many
more enhancements, new visualizations and bug fixes as well as
instructions for upgrading your Galaxy installation.
Thanks for using Galaxy!
1 year, 10 months
Subscription
by Muhammet A. Celik
a.muhammetcelik(a)gmail.com
1 year, 10 months
November 2020 Paper Cuts Day: Nov 18
by Dave Clements
Hello all,
The second Galaxy Paper Cuts day will be held on Wednesday November 18. It
will be a day long, around-the-world event, with calls about every 3 hours,
plus Gitter chat and support all day.
https://galaxyproject.org/events/2020-11-papercuts/
"Paper cuts" are annoying, but relatively easy to fix bugs. They are also
a great way to become familiar with how to contribute code and other
updates. This paper cut event applies to the entire Galaxy ecosystem.
In addition to learning and fixing, you can also help by
1) Creating GitHub issues for anything in Galaxy that bugs you and is
likely to be easy to fix.*
2) Advertising this event in your communities. We are particularly reaching
to research software engineers and students.
We hope to see you online next week!
Cheers,
Dave C on behalf of the PaperCuts organizers
* What's easy to fix? Trust your instincts on this. We would like to hear
about glitches, even if they turn out to be harder to fix.
--
https://galaxyproject.org/
1 year, 10 months
pbs_python + python 3 issue
by Sandra Maksimovic
Hi,
Has anyone out there had any success installing the pbs_python module into a Python 3+ Galaxy installation? I run into the following issue when installing https://github.com/ehiggs/pbs-python as per the documentation.
# python setup.py install
File "setup.py", line 68
print "Version: %s is not supported" %(PBS_VERSION)
^
SyntaxError: invalid syntax
I provide the PBS/Torque version via the PBS_PYTHON_INCLUDE_DIR environment variable but it doesn't seem to detect the version properly.
Thanks,
Sandra
Disclaimer
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1 year, 10 months
November 2020 Galaxy News
by Dave Clements
Hello all,
The November newsletter is out:
https://galaxyproject.org/news/2020-11-galaxy-update/
Topics:
* JXTX: The James P. Taylor Foundation for Open Science
New name, and meet our first awardees
* Event news
Lots of them, with one starting today (if you are in Australia / East Asia)
Galaxy Admin Training will be in late January
* Galaxy platform news
GalaxyTrakr, Galaxy Africa, Australia, Europe, and UseGalaxy.*
* Blog post
Advanced Microbiology with Galaxy and TIaaS at Strathclyde
* Training material and doc updates
Metaproteomics, calling variants, and auto-generated video (!)
* Publications
Pub curation is on hiatus, but some pubs just can't be ignored :-)
* Open positions
At 8 organizations. (Yes eight!)
* New releases
The new Galaxy Language Server
Thanks for using Galaxy,
Dave C and Beatriz
--
https://galaxyproject.org/
1 year, 11 months