Dear all,
Happy new year!
For 10 years, we have been sharing news through the monthly Galactic
News. This is a milestone and we are so proud of the community that we
built together. A lot can change over 10 years and we want to know which
parts of the Galaxy newsletter are the most useful and which parts may
need to be modified to suit your needs.
Please take *2 minutes to fill out **this survey
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Thank you for reading and here's to the next 10 years,
Assunta and Bea
Dear Community,
The Galaxy Committers team is pleased to announce the release of Galaxy
21.09.
- Developer and admin release announcement
<https://docs.galaxyproject.org/en/latest/releases/21.09_announce.html>
- User release announcement
<https://docs.galaxyproject.org/en/latest/releases/21.09_announce_user.html>
.
A few release highlights are:
Tool Panel Views
We now have "Tool Panel Views"! These are different views into the same
toolbox and might help make it easier to find the tools you want. In the
future, there are plans to create user-customisable toolboxes, but until
then go explore the new EDAM Ontology-based toolboxes which organise tools
around scientific areas or processes. For example, a category like
"Filtering" might have tools like "select lines" or "filter bam by
quality", both doing the same process of filtering, despite their different
file types and formats.
Unfortunately, not all tools are fully annotated yet, and while we also
pull terms from bio.tools, this still doesn't get us full coverage and many
tools will still appear under a large section "Uncategorized". Hopefully,
this will improve as users and tool developers annotate these tools with
the appropriate terms that help everyone find them.
Collections (Beta History Updates)
Did you ever create *a collection with the wrong dbkey or datatype*? Well,
in the Beta History you can now change collections' datatypes and dbkeys!
This should save a lot of time for everyone working with large datasets (Pull
Request 11799 <https://github.com/galaxyproject/galaxy/pull/11799/>).
Additionally, did a *collection ever fail* for you? And you wondered why?
Now you can find out with the view details button for collections (Pull
Request 12261 <https://github.com/galaxyproject/galaxy/pull/12261>)!
Importing Data
Selecting datasets from the Remote Files view has gotten easier! Now, you
can select folders and files and import at once all of the datasets
recursively in those folders. Previously, you could only select files
within a folder, so this is a huge improvement in the usability of such a
key new feature of Galaxy (Pull Request 12310
<https://github.com/galaxyproject/galaxy/pull/12310>). But with great power
comes great responsibility, be careful not to import the entirety of NCBI!
Reports
Report components used to automatically arrange themselves in a smart way,
but due to some issues with the floating of components, these will now be
full width until we can figure out a good way to provide a similar
feature (Pull
Request 12085 <https://github.com/galaxyproject/galaxy/pull/12085>).
Enhancements for Working with Remote Data and Distributed Computing
Resources
Many fixes and enhancements were made to improve how Galaxy can import and
write to remote data using the configured file source plugins. In addition
to the History Export functionality, which can write to remote locations,
we have added an Export datasets Tool for exporting individual Datasets and
Dataset collections to configured remote locations. The Tool will
automatically maintain the name and structure of Datasets and Dataset
Collections. We have added the possibility to import entire folders of
remote data and made the data selection dialog more intuitive. We also
added numerous improvements and fixes to the extended metadata collection
strategy and Pulsar <https://github.com/galaxyproject/pulsar>, so that many
more tools are able to run in Pulsar
<https://github.com/galaxyproject/pulsar> and write data back to storage
without passing through Galaxy first.
Migration to FastAPI and Extended Documentation of API Routes
We have modernized and migrated many more API routes to FastAPI and have
extended the documentation and validation of these routes.
Migration to SQLAlchemy 1.4 and Declarative Mapping
Galaxy is now using SQLAlchemy <https://www.sqlalchemy.org/> version 1.4,
which is a prerequisite for asynchronously interacting with the database.
We also modernized the way our database models are defined to the more
commonly used Declarative Mapping approach, which is more concise and
better documented.
Modernization of Tool Form Interface
The tool form interface has been almost completely migrated from Backbone
<https://backbonejs.org/> to Vue <https://vuejs.org/>. This improves the
reactivity of parameter validation and enables the migration of tool
parameters to Vue, which will also allow us to add many more types of tool
parameters. We further migrated the tool form variant for the Workflow
Editor, the Workflow run form and the Show Dataset Parameter page to Vue.
New User Welcome Page
We have added a page that new users will be directed to after creating a
new Galaxy account.
Release Notes
Please see the full release notes
<https://docs.galaxyproject.org/en/latest/releases/21.09_announce.html> for
a lot more details and instructions for upgrading your Galaxy installation.
Thanks for using Galaxy!
Hello all,
The October Newsletter is out
<https://galaxyproject.org/news/2021-10-galaxy-update/>. and it covers
Galaxy involvement in Hacktoberfest, and Outreachy, plus a nice batch of
trainings, talks and a Galaxy Papercuts CoFest day too. It also brings news
of new job openings on two continents, two new platforms, blog posts (where
My Little Pony makes an appearance, really), GTN updates (few in number but
big in their coolness), publications, and releases.
In other words, another active month in the Galaxy.
Beatriz Serrano-Solano and Dave Clements, Editors
--
https://galaxyproject.org/
Hi all,
The September newsletter
<https://galaxyproject.org/news/2021-09-galaxy-update/> brings lots of
news, including
- 12 recent use cases for UseGalaxy.eu, covering a broad spectrum of
research.
- Want to help address misconceptions about Galaxy?
- The Galaxy Community Hub is now using Gridsome.
- ELIXIR community updates
- JXTX Foundation 2021 Awards
- 7 open positions in Belgium, Italy, and the US
- The Galaxy YouTube channel is growing up
- Upcoming events
- Galaxy Platforms News
- Recent Blog Posts
- Doc, Hub, and Training Updates
- Recent Publications
- and other news too.
Sit back, get comfortable, and explore the Galaxy...
Beatriz Serrano-Solano and Dave Clements, Editors
--
https://galaxyproject.org/
Dear Community,
The Galaxy Committers team is pleased to announce the release of Galaxy
21.05.
The release announcement for developers and admins can be found at
https://docs.galaxyproject.org/en/master/releases/21.05_announce.html and
user facing release notes are at
https://docs.galaxyproject.org/en/master/releases/21.05_announce_user.html.
A few release highlights are:
¡Galaxy, ahora en español!
------------------------------------
Thanks to Wendi Bacon, the Spanish language translation of Galaxy has been
finalised and merged, so if you prefer to use Galaxy in Spanish, now you
can!
This update will be part of an ongoing project from Spanish speakers within
the
Galaxy community to keep the Galaxy interface localisation up to date,
and to produce some Spanish language training materials in the GTN.
Bugfixes and Stability
-----------------------------
This release of Galaxy features fewer user-facing changes, as a huge amount
of
developer time went into making this a maintenance release with better
testing,
better stability, and more bugfixes.
But watch out, this is all in preparation for the next release of Galaxy,
21.09,
which will have some of the biggest changes in years!
New development stack
--------------------------------
Galaxy release 21.09 will ship with a new web framework (fastAPI
<https://fastapi.tiangolo.com/>),
Celery <https://docs.celeryproject.org/en/stable/index.html> task queue and
process management using Circus <https://circus.readthedocs.io/en/latest/>.
You can preview this new stack now by running *APP_WEBSERVER=dev ./run.sh*.
Celery for background tasks
--------------------------------------
Galaxy can now run certain tasks in the background. The Celery workers are
currently not required, but if activated can perform certain long-running
tasks,
such as creating history export archives. Celery tasks will bridge the gap
between
rapid requests that can be handled during a web request and jobs that
require extensive
and relatively slow setup.
More robust selection of job handlers
-------------------------------------------------
Job throughput can be increased by starting Galaxy with multiple external
job
handler processes. Jobs were traditionally assigned to a job handler process
by the web handler or workflow handler process that created the job. Since
Release 19.01 Galaxy has supported additional mechanisms that use database
serialization techniques to let job handlers assign processes to themselves.
This mechanism is more robust and doesn't require that all job handler
processes be alive and known by the web handler process. Galaxy now
determines
the best method for assigning jobs based on the database in use, if the
assignment
method is not set explicitly. Older job assignment methods will be removed
in Galaxy
release 21.09. For more details see the Job Handler Assignment Methods
section
<https://docs.galaxyproject.org/en/release_21.05/admin/scaling.html#job-hand…>
of the Galaxy documentation.
Check out the full release notes
<https://docs.galaxyproject.org/en/master/releases/21.05_announce.html> for
a lot more details, there are many more
enhancements, new visualizations and bugfixes as well as instructions for
upgrading your Galaxy installation.
Thanks for using Galaxy!
Hello all,
The early registration deadline for the 2021 Galaxy Community Conference
has been moved back to June 8. This gives you more time to take advantage
of the 50% discount off full registration prices, so make sure you sign up
now so you don't miss out! Register here
<https://www.vibconferences.be/events/gcc2021-virtual-edition#attendees>.
The draft program <https://gcc2021.sched.com/> and the speakers are now
also available online. Please bear in mind that the times are set for the
Europe/Middle East/Africa - Asia/Pacific window, and that the same schedule
will run 9 hours later for the Americas. The availability of the speakers
for the Q&A session will depend on the time zone in which they are
located. Posters
and demo sessions can still be submitted
<https://www.vibconferences.be/events/gcc2021-virtual-edition#abstracts>
until the 14th of June.
Feel free to distribute this message further in your network.
We hope to meet you online!
Dave Clements on behalf of the GCC2021 Organizing Committee
--
https://galaxyproject.org/