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Edits from Beatriz

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mvdbeek
2021-11-02 08:42:22 +01:00
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doc/source/releases/21.09_announce.rst
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and `<Pull Request 12327>`_.
(`Pull Request 12327`_, `Pull Request 12677`_, `Pull Request 12328`_, `Pull Request 12379`_).
**Enhancements for working with remote data and distributed computing resources**
**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 locations using the configured file source plugins. In addition to
@@ -44,7 +44,7 @@ Highlights
`Pull Request 12267`_, `Pull Request 11949`_, `Pull Request 12310`_,
`Pull Request 12388`_, `Pull Request 12641`_).
**Migration to FastAPI and extended Documentation of API routes**
**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.
(`Pull Request 11315`_, `Pull Request 11827`_, `Pull Request 11983`_,
@@ -53,15 +53,15 @@ Highlights
**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
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.
(`Pull Request 12042`_, `Pull Request 12045`_, `Pull Request 12064`_,
`Pull Request 12438`_, `Pull Request 12060`_, `Pull Request 12424`_,
`Pull Request 12461`_).
**Modernization of Tool Form interface**
**Modernization of Tool Form Interface**
The Tool Form interface has been almost completed migrated from
`Backbone <https://backbonejs.org/>`_ to `Vue <https://vuejs.org/>`_.
This improves the reactivity of parameter validation and enables the migration of
@@ -73,7 +73,7 @@ Highlights
12374`_, `Pull Request 12432`_, `Pull Request 12702`_, `Pull Request 12261`_).
**New User Welcome Page**
We have added a Page that new users will be directed to after creating a new Galaxy account.
We have added a page that new users will be directed to after creating a new Galaxy account.
(`Pull Request 11085`_, `Pull Request 12639`_)
doc/source/releases/21.09_announce_user.rst
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Tool Panel
----------
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 their scientific area, or based on the scientific process they do. 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 filetypes and formats.
We now have "Tool Panel Views"! These are different views into the same toolbox and might help it 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, or based on the scientific process they do. 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.
.. raw:: html
<iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/vCapB1xHjZg" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
Unfortunately not all tools are well annotated yet, and while we also pull terms from `bio.tools <https://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 their terms to help everyone find them.
Unfortunately not all tools are fully annotated yet, and while we also pull terms from `bio.tools <https://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.
More details can be found in `Pull Request 12327`_, `Pull Request 12365`_, and `Pull Request 12291`_
@@ -35,7 +35,7 @@ Additionally, did a *collection ever fail* for you? And you wondered why? Now yo
Importing Data
--------------
Selecting datasets from the Remote Files view has gotten easier! Now you can select folders and files, and it will import all of the datasets recursively in those folders. Previously you could only select files within a folder so this is a huge improvement in usability of such a key new feature of Galaxy (`Pull Request 12310`_). But with great power comes great responsibility, be careful not to import the entirety of NCBI!
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`_). But with great power comes great responsibility, be careful not to import the entirety of NCBI!
.. raw:: html
@@ -45,7 +45,7 @@ Selecting datasets from the Remote Files view has gotten easier! Now you can sel
Reports
-------
Report components used to try and arrange themselves in a smart way, but due to some issues with the floating of report components these will now be full width until we can figure out a good way to provide a similar feature allowing you to control the layout of the report (`Pull Request 12085`_).
Report components used to automatically arrange themselves in a smart way, but due to some issues with the floating of report components these will now be full width until we can figure out a good way to provide a similar feature allowing you to control the layout of the report (`Pull Request 12085`_).
.. figure:: images/21.09-reports.png
:alt: A screenshot of the reports interface is shown, there are a number of 'report components' like table previews embedded and these are full width across the report.