Galaxy Release (v 22.05)，新历史面板发布

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2022年5月2日前后，Galaxy Project 发布了 Release 22.05 版本；随后8月24日，发布该版本的 Developer/Admin/User release announcement 文档。

本文章总结了该版本一些主要的更新内容，为关注和从事 Galaxy 相关工作的中文用户提供参考。

使用用户

本部分内容主要参考 22.05 User release announcement。

重点更新

新的历史面板发布

经过开发团队和社区贡献者多年的努力，新的历史（面板）终于到来了。无论是从技术上还是从用户体验上来说，这都是对旧的历史界面的一个巨大改进，但它可能需要一些时间来适应。它有很多很棒的新功能，比如：

• 快速切换，让你在最近的历史之间快速进行切换；
• 轻松的查找输入的数据集；
• 改进的历史搜索界面；

想要体验的，快去看看！

存储仪表板(测试版)

你有没有用超过你的 Galaxy 存储配额？250GB 的存储配额一下子就用完了！现在，通过新的 Storage Dashboard，您可以快速了解清理已删除数据集和恢复一些配额分配的方法。这是这个界面的测试版本，如果您有任何问题，请让我们知道。在未来的版本中，它将被扩展以帮助您了解如何使用您的分配，以及应该首先清理哪些历史和数据集。

http://mpvideo.qpic.cn/0bc3uaaa2aaazqanzbygp5rvbigdbwqaadia.f10002.mp4?dis_k=06be533d49005c5866a28238f04bd5a2&dis_t=1672227165&play_scene=10400&vid=wxv_2546763634379751425&format_id=10002&support_redirect=0&mmversion=false

Bulk History Operations

批量化历史记录操作

新的历史记录允许执行改进后的批量化操作，选择数十或数百个数据集来自动重新标记或更改数据库密钥，这个过程在过去需要使用集合或逐个执行。 http://mpvideo.qpic.cn/0bc3feaa2aaavqan7rigmbrvakodbuuqadia.f10002.mp4?dis_k=027d9b91d4d7b0c86db995ac3cbcf193&dis_t=1672227165&play_scene=10400&vid=wxv_2546768346076315650&format_id=10002&support_redirect=0&mmversion=false

延迟数据集解析

Deferred dataset resolution enables running workflows and tools without importing data into Galaxy first. 延迟数据集解析允许在不首先将数据导入 Galaxy 的情况下运行工作流和工具。 现在可以推迟通过 URL 和“选择远程文件”对话框导入数据集的数据集解析。这意味着延迟的数据集只会在作业执行期间需要时才被下载。延迟的数据集将不计入您的存储配额，因为数据不是由 Galaxy 存储的。要启用延迟数据集解析，请单击上传对话框中的“设置”。

工作流程改进

你现在可以在跨越您的所有历史记录中看到所有调用的特定工作流程（You can now see all invocations of a specific workflow, across all of your histories.）。

如果您跨多个数据集运行单个工作流，并在多个历史记录中将它们很好地分隔开，那么这一点尤其有用。你可以在一个集中的位置看到所有的结果。

工作流程的其他改进，例如工作流程中的步骤编号。我们对工作流程的内部表示 (the internal representation) 进行了改进，从而使得保存的.ga和.gxwf.yml文件更容易在更改之间进行比较。

工作流现在也可以通过滚动放大和缩小，这个界面对任何使用过 Google 地图的人来说都应该更加熟悉：

http://mpvideo.qpic.cn/0bc3dmaa2aaaaqan5zigprrvag6dbunqadia.f10002.mp4?dis_k=e29173b17c03f477613d331605300e21&dis_t=1672227165&play_scene=10400&vid=wxv_2546770924767969281&format_id=10002&support_redirect=0&mmversion=false

保存规则

你使用基于规则的上传器 (Rule Based Uploader, RBU) 吗？(如果没有，今天就学习吧！) RBU 现在有一个非常方便的最近使用的规则列表，（这个列表）会根据它们最近使用的时间进行排序。您可以将鼠标悬停在每个条目上，以列出在 RBU 调用中执行过的步骤的预览信息：

升级版的剪贴簿

剪贴簿（scratchbook）已经更新为一个新的实现 (implementation)。现在，数据集的视图可以重叠，每个窗口的大小有了更大的自由度，并且可以最小化数据集，比如在 Windows 中最小化任务栏的窗口。 http://mpvideo.qpic.cn/0bc3omaa2aaakeanuuagmjrva46dbvzqadia.f10002.mp4?dis_k=33e4d7cf74349962f901787aafaabf18&dis_t=1672227165&play_scene=10400&vid=wxv_2546788154348044290&format_id=10002&support_redirect=0&mmversion=false

Scratchbook Upgraded

OpenAPI 文档

Galaxy API 正在升级到 FastAPI，它允许我们生成 OpenAPI 文档。如果您是一个 API 消费者，无论是通过 BioBlend 还是通过其他系统，您都可以使用它来查看 Galaxy 提供的所有 API 并进行实时测试。

新的可视化

• Add gulp target for force-rebuild of viz plugins (thanks to @dannon). Pull Request 13370
• 为新的可视化正确初始化图表设置 (thanks to @guerler). Pull Request 13561
• 指向可视化 GTN 教程的 readme (thanks to @beatrizserrano). Pull Request 13616
• 添加 3D PCA 可视化 (thanks to @xtrojak). Pull Request 13771

• 支持 phylocanvas 自动构建 (thanks to @dannon). Pull Request 14023
• 修复 PCA 工件暂存（PCA artifact staging）中阻止插件重建的错误 (thanks to @dannon). Pull Request 14148
• MSA 的可视化修复 (thanks to @dannon). Pull Request 14263

新的数据类型

• 自动化 Python 代码格式化标准 (thanks to @dannon). Pull Request 11162
• 添加新的分子数据类型 (thanks to @muon-spectroscopy-computational-project). Pull Request 12375
• 将语法升级到 Python 3.7 (thanks to @nsoranzo). Pull Request 13500
• 添加 mzqc 数据类型 (thanks to @bernt-matthias). Pull Request 13564
• 将 mypy 更新为 0.942 并修复新的 mypy 错误 (thanks to @nsoranzo). Pull Request 13650
• Create data_fetch and set_metadata celery tasks (thanks to @mvdbeek). Pull Request 13655
• 将 bigWig 添加到 Wig 转换器 (thanks to @gallardoalba). Pull Request 13708
• 替换上次使用的废弃的imp模块 (thanks to @nsoranzo). Pull Request 13817
• 添加 gfa1 和 gfa2 文件的 gz 压缩支持 (thanks to @gallardoalba). Pull Request 13927
• Tighten sniffers (thanks to @mvdbeek). Pull Request 13959
• 在运行压缩转换器时不要创建 BGZF 索引 (thanks to @nsoranzo). Pull Request 13969
• Bug 修复：set creation_date on dataset.metadata, not dataset (thanks to @jdavcs). Pull Request 14039
• Fix composite datatypes with substitute_name_with_metadata (thanks to @mvdbeek). Pull Request 14053
• 在 FastAPI 路由中为 WSGI 路由生成 URL (thanks to @mvdbeek). Pull Request 14066
• Fix collection download for BAM native files (thanks to @mvdbeek). Pull Request 14162
• 新数据类型: QIIME 2 (thanks to @ebolyen). Pull Request 14216
• Make Agp set_meta more lenient (thanks to @astrovsky01). Pull Request 14277
• Deleted, discarded and deferred file not found tweaks (thanks to @mvdbeek). Pull Request 14296
• 增加 scool 数据类型 (thanks to @bernt-matthias). Pull Request 14480
• 在parse_requirements_from_xml中修复 xml 弃用的警告 (thanks to @bernt-matthias). Pull Request 14483

内置工具更新

• 自动化 Python 代码格式化标准 (thanks to @dannon). Pull Request 11162
• 将内置转换器添加到工具面板 (thanks to @jdavcs). Pull Request 13447
• 增加 JupyTool，用户可配置的交互式 Jupyter-based 工具 (thanks to @blankenberg). Pull Request 13606
• 修复 David URL (thanks to @hexylena). Pull Request 13666
• 添加和更新各种交互式工具 (thanks to @gmauro). Pull Request 13811
• 将 ncb-data sets-cli 依赖性提升到13.14.0 (thanks to @mvdbeek). Pull Request 13853
• 新数据类型: QIIME 2 (thanks to @ebolyen). Pull Request 14216
• Fixes for JupyTool, and overlapping versions with jupyter (thanks to @blankenberg). Pull Request 14309
• 从工具搜索中删除 debug 调试语句 (thanks to @bgruening). Pull Request 14386
• Grep1 工具：修复 keep_header 参数 (thanks to @jancrichter). Pull Request 14475
• 大修和改进 Jupyter 交互工具，提供许多新的界面选项 (thanks to @blankenberg). Pull Request 13606

发布测试团队

特别感谢发布测试团队测试了许多新特性并报告了许多 bug：

• Ahmed Awan
• Catherine Bromhead
• Fabio Cumbo
• Jennifer Hillman-Jackson
• John Davis
• Simon Bray
• Tyler Collins

发行说明

面向用户的发行说明是由 Helena Rasche 编辑。

请参阅完整的发行说明（full release notes）了解更多细节。

要了解 Galaxy 的最新进展，请观看我们的视频，访问我们的社区中心，并在 Twitter 上关注 @galaxyproject 项目。

您可以随时通过 Gitter 或 IRC 与我们联系。

感谢使用 Galaxy！

开发者与管理员

本部分内容主要参考 22.05 Developer and admin release announcement。

重点更新

FastAPI 应用程序

正如在 Galaxy Release22.01 的发布说明中所宣布的，我们已经取消了对作为 WSGI 应用程序运行 Galaxy 的支持。如果您仍在使用 uwsGI，请查阅 Migrating to Gunicorn documentation 的文档。

Deferred dataset resolution

可选的延迟数据集解析允许用户选择从 URL 或远程文件源获取的数据集不应该被提取到 Galaxy 的对象存储中 (Galaxy’s objectstore)。只有在运行使用这些数据集的作业时，才会获取延迟数据集。

增强的 Celery 任务和功能

Galaxy 可以选择性将数据上传任务委托给 Celery，Galaxy 可以在 Celery 中运行元数据脚本。这会导致小作业的运行时间大大缩短。若要启用此选项，请将enable_celery_tasks设置为true，并确保至少启动一个 celery worker。如果启用了 celery 任务，还可以批量更改许多历史项的数据类型。

基于 Alembic 的新数据库迁移系统

Galaxy 有一个基于 Alembic 的新数据库迁移系统 (Galaxy has a new database migrations system based on Alembic) 。

新的迁移系统是建立在 Alembic 之上的。SQLAlchemy 迁移工具已经退役。有关使用方法，请参阅 Galaxy's migrations documentation。有关架构概述，请参见 pull request #13108。

配置变更

增加的配置

以下配置选项是新的。

config/galaxy.yml.sample:galaxy

• mapping.galaxy.mapping.celery_backend
• mapping.galaxy.mapping.celery_broker
• mapping.galaxy.mapping.display_builtin_converters
• mapping.galaxy.mapping.file_sources
• mapping.galaxy.mapping.helpsite_url
• mapping.galaxy.mapping.log_destination
• mapping.galaxy.mapping.log_rotate_count
• mapping.galaxy.mapping.log_rotate_size
• mapping.galaxy.mapping.prefer_custos_login
• mapping.galaxy.mapping.short_term_storage_cleanup_interval
• mapping.galaxy.mapping.short_term_storage_default_duration
• mapping.galaxy.mapping.short_term_storage_dir
• mapping.galaxy.mapping.short_term_storage_maximum_duration
• mapping.galaxy.mapping.tool_help_bm25f_k1
• mapping.galaxy.mapping.tool_name_exact_multiplier
• mapping.galaxy.mapping.tool_ngram_factor
• mapping.galaxy.mapping.use_legacy_history
• mapping.galaxy.mapping.workflow_monitor_sleep

变更的配置

下列配置选项已更改。

config/galaxy.yml.sample:galaxy

• mapping.galaxy.mapping.debug.desc 已经从

Debug enables access to various config options useful for development
and debugging: use_lint, use_profile, and use_printdebug.  It also
causes the files used by PBS/SGE (submission script, output, and error)
to remain on disk after the job is complete.

In addition, this will set uWSGI's `honour-stdin` option to `true`;
thus, preventing uWSGI from remapping stdin to `/dev/null` and
enabling debugging with tools like pdb. To keep uWSGI's default
setting, set `honor-stdin` to `false` in the `uwsgi` section of this
configuration file.

变更为：

Debug enables access to various config options useful for development
and debugging: use_lint, use_profile, and use_printdebug.  It also
causes the files used by PBS/SGE (submission script, output, and error)
to remain on disk after the job is complete.

• mapping.galaxy.mapping.logging.desc 已经从

Controls where and how the server logs messages. If unset, the default is to log all messages to standard
output at the level defined by the `log_level` configuration option. Configuration is described in the
documentation at:
https://docs.galaxyproject.org/en/master/admin/config_logging.html

变更为：

Controls where and how the server logs messages. If set, overrides all settings in the log_* configuration
options. Configuration is described in the documentation at:
https://docs.galaxyproject.org/en/master/admin/config_logging.html

• mapping.galaxy.mapping.metadata_strategy.desc 已经从

Determines how metadata will be set. Valid values are `directory` and `extended`.
In extended mode jobs will decide if a tool run failed, the object stores
configuration is serialized and made available to the job and is used for
writing output datasets to the object store as part of the job and dynamic
output discovery (e.g. discovered datasets <discover_datasets>, unpopulated collections,
etc) happens as part of the job.

变更为：

Determines how metadata will be set. Valid values are `directory`, `extended`,
`directory_celery` and `extended_celery`.
In extended mode jobs will decide if a tool run failed, the object stores
configuration is serialized and made available to the job and is used for
writing output datasets to the object store as part of the job and dynamic
output discovery (e.g. discovered datasets <discover_datasets>, unpopulated collections,
etc) happens as part of the job. In `directory_celery` and `extended_celery` metadata
will be set within a celery task.

• mapping.galaxy.mapping.screencasts_url.default 已经从

https://vimeo.com/galaxyproject

变更为：

https://www.youtube.com/c/galaxyproject

• mapping.galaxy.mapping.simplified_workflow_run_ui_target_history.default 已经从

current

变更为：

prefer_current

• mapping.galaxy.mapping.simplified_workflow_run_ui_target_history.desc 已经从

When the simplified workflow run form is rendered, should the invocation outputs
be sent to the 'current' history or a 'new' history.

变更为：

When the simplified workflow run form is rendered, should the invocation outputs
be sent to the 'current' history or a 'new' history. If the user should be presented
and option between these - set this to 'prefer_current' or 'prefer_new' to display
a runtime setting with the corresponding default. The default is to provide the
user this option and default it to the current history (the traditional behavior
of Galaxy for years) - this corresponds to the setting 'prefer_current'.

• mapping.galaxy.mapping.simplified_workflow_run_ui_target_history.enum 已经从

current
new

变更为：

current
new
prefer_current
prefer_new

• mapping.galaxy.mapping.tool_description_boost.default 已经从

2.0

变更为：

8.0

• mapping.galaxy.mapping.tool_description_boost.desc 已经从

Boosts are used to customize this instance's toolbox search.
The higher the boost, the more importance the scoring algorithm gives to the
given field.  Section refers to the tool group in the tool panel.  Rest of
the fields are tool's attributes.

变更为：

In tool search, a query match against a tool's description text will
receive this score multiplier.

• mapping.galaxy.mapping.tool_enable_ngram_search.desc 已经从

Enable/ disable Ngram-search for tools. It makes tool
search results tolerant for spelling mistakes in the query
by dividing the query into multiple ngrams and search for
each ngram

变更为：

Disabling this will prevent partial matches on tool names.
Enable/disable Ngram-search for tools. It makes tool
search results tolerant for spelling mistakes in the query, and will
also match query substrings e.g. "genome" will match "genomics" or
"metagenome".

• mapping.galaxy.mapping.tool_help_boost.default 已经从

0.5

变更为：

1.0

• mapping.galaxy.mapping.tool_help_boost.desc 已经从

Boosts are used to customize this instance's toolbox search.
The higher the boost, the more importance the scoring algorithm gives to the
given field.  Section refers to the tool group in the tool panel.  Rest of
the fields are tool's attributes.

变更为：

In tool search, a query match against a tool's help text will receive
this score multiplier.

• mapping.galaxy.mapping.tool_id_boost.default 已经从

9.0

变更为：

20.0

• mapping.galaxy.mapping.tool_id_boost.desc 已经从

Boosts are used to customize this instance's toolbox search.
The higher the boost, the more importance the scoring algorithm gives to the
given field.  Section refers to the tool group in the tool panel.  Rest of
the fields are tool's attributes.

变更为：

In tool search, a query match against a tool's ID text will receive
this score multiplier. The query must be an exact match against ID
in order to be counted as a match.

• mapping.galaxy.mapping.tool_label_boost.desc 已经从

Boosts are used to customize this instance's toolbox search.
The higher the boost, the more importance the scoring algorithm gives to the
given field.  Section refers to the tool group in the tool panel.  Rest of
the fields are tool's attributes.

变更为：

In tool search, a query match against a tool's label text will
receive this score multiplier.

• mapping.galaxy.mapping.tool_name_boost.default 已经从

9.0

变更为：

20.0

• mapping.galaxy.mapping.tool_name_boost.desc 已经从

Boosts are used to customize this instance's toolbox search.
The higher the boost, the more importance the scoring algorithm gives to the
given field.  Section refers to the tool group in the tool panel.  Rest of
the fields are tool's attributes.

变更为：

In tool search, a query match against a tool's name text will receive
this score multiplier.

• mapping.galaxy.mapping.tool_ngram_maxsize.desc 已经从

Set maximum size of ngrams

变更为：

Set maximum character length of ngrams

• mapping.galaxy.mapping.tool_ngram_minsize.desc 已经从

Set minimum size of ngrams

变更为：

Set minimum character length of ngrams

• mapping.galaxy.mapping.tool_search_limit.desc 已经从

Limits the number of results in toolbox search.  Can be used to tweak how many
results will appear.

变更为：

Limits the number of results in toolbox search. Use to set the
maximum number of tool search results to display.

• mapping.galaxy.mapping.tool_section_boost.desc 已经从

Boosts are used to customize this instance's toolbox search.
The higher the boost, the more importance the scoring algorithm gives to the
given field.  Section refers to the tool group in the tool panel.  Rest of
the fields are tool's attributes.

变更为：

In tool search, a query match against a tool's section text will
receive this score multiplier.

• mapping.galaxy.mapping.tool_stub_boost.default 已经从

5.0

变更为：

2.0

• mapping.galaxy.mapping.tool_stub_boost.desc 已经从

Boosts are used to customize this instance's toolbox search.
The higher the boost, the more importance the scoring algorithm gives to the
given field.  Section refers to the tool group in the tool panel.  Rest of
the fields are tool's attributes.

变更为：

A stub is parsed from the GUID as "owner/repo/tool_id".
In tool search, a query match against a tool's stub text will receive
this score multiplier.

• mapping.galaxy.mapping.wiki_url.desc 已经从

The URL linked by the "Wiki" link in the "Help" menu.

变更为：

The URL linked by the "Community Hub" link in the "Help" menu.

移除的配置

下列配置选项已被完全删除（have been completely removed）。

config/tool_shed.yml.sample

• uwsgi

config/galaxy.yml.sample

• uwsgi

config/reports.yml.sample

• uwsgi

config/galaxy.yml.sample:galaxy

• mapping.galaxy.mapping.containers_config_file
• mapping.galaxy.mapping.enable_beta_containers_interface
• mapping.galaxy.mapping.interactive_environment_plugins_directory
• mapping.galaxy.mapping.mailing_lists_url
• mapping.galaxy.mapping.qa_url
• mapping.galaxy.mapping.search_url

其他更新

更多更新信息，如 Enhancements 和 Fixes 的详细信息，请参考 Developer and admin release announcement。

参考资料

• May 2022 Galaxy Release (v 22.05) - User release announcement
• May 2022 Galaxy Release (v 22.05) - Developer and admin release announcement
• Github Issues 13960 - Publication of Galaxy Release v 22.05