diff --git a/content/admin/config/windows/index.md b/content/admin/config/windows/index.md index 66cbbe43fb..10af16ab2d 100644 --- a/content/admin/config/windows/index.md +++ b/content/admin/config/windows/index.md @@ -79,7 +79,7 @@ The effort required involves building architecture specific “eggs” (think of Please note, a simple alternative to attempting to build eggs for Windows is to simply run Linux via virtualization software (such as the free [VirtualBox](http://www.virtualbox.org/)). For best results, use a lightweight Linux such as [Xubuntu](http://www.xubuntu.org/), or disable X-Windows. -If you choose to continue, to understand Eggs and how they work in Galaxy, read the [Eggs](Admin%2FConfig%2FEggs) page. +If you choose to continue, to understand Eggs and how they work in Galaxy, read the [Eggs](/admin/config/eggs/) page. ### Building Eggs @@ -136,4 +136,4 @@ Once built, eggs need to be placed in `$GALAXY_ROOT/eggs/<platform>`, wher $ cp dist/bx_python-0.5.0_r4bf1f32e6b76-py2.4-win32.egg galaxy_dist/eggs/ ``` -Once all the required eggs have been built and copied to the proper egg directory, Galaxy can now be run as normal, see [Admin/GetGalaxy](Admin%2FGetGalaxy) to continue. +Once all the required eggs have been built and copied to the proper egg directory, Galaxy can now be run as normal, see [/admin/get-galaxy/](/admin/get-galaxy/) to continue. diff --git a/content/admin/data-preparation/index.md b/content/admin/data-preparation/index.md index 82fd62c98d..f125f8ae07 100644 --- a/content/admin/data-preparation/index.md +++ b/content/admin/data-preparation/index.md @@ -1,4 +1,6 @@ -# Data Preparation +--- +title: Data Preparation +--- **Please note that "built-in" or "cached" data can now be managed directly from within the Galaxy admin interface. For details, see [Data Managers Overview](/admin/tools/data-managers/)** and our **[Data Managers Tutorial](https://github.com/galaxyproject/dagobah-training/blob/2017-montpellier/sessions/05-reference-genomes/ex1-reference-genomes.md)**. @@ -6,7 +8,7 @@ # Builds list changes -If you still choose to do this manually, follow the instructions at [Data Integration](/admin/data-integration/) to start, (**impact**: more than just a builds.txt file is needed to establish a new reference genome), making certain that your server has the necessary changes/additions to the [Data Tables](/admin/tools/Data%20Tables.md) model or use the alternate configuration file, then follow the guide here for the organization and execution of **data preparation** tasks in a local or cloud instance. +If you still choose to do this manually, follow the instructions at [Data Integration](/admin/data-integration/) to start, (**impact**: more than just a builds.txt file is needed to establish a new reference genome), making certain that your server has the necessary changes/additions to the [Data Tables](/admin/tools/data-tables/) model or use the alternate configuration file, then follow the guide here for the organization and execution of **data preparation** tasks in a local or cloud instance. # Data and indexes hosted at http://usegalaxy.org @@ -67,7 +69,7 @@ The Extract tool is downloaded from [http://genome.ucsc.edu](http://genome.ucsc. #### Megablast installation -Megablast in Galaxy was updated to use [NCBI BLAST+](http://blast.ncbi.nlm.nih.gov) (`BLASTN`) in April 2012 (changeset [0b5cb60e4810](https://bitbucket.org/galaxy/galaxy-central/changeset/0b5cb60e4810#chg-tools/metag_tools/megablast_wrapper.xml)). See [dependencies wiki](admin/config/tool-dependencies/) for current version then [download blast+](http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download). Many data indexes are available directly at NCBI from [ftp://ftp.ncbi.nlm.nih.gov/blast/db/](ftp://ftp.ncbi.nlm.nih.gov/blast/db/) +Megablast in Galaxy was updated to use [NCBI BLAST+](http://blast.ncbi.nlm.nih.gov) (`BLASTN`) in April 2012 (changeset [0b5cb60e4810](https://bitbucket.org/galaxy/galaxy-central/changeset/0b5cb60e4810#chg-tools/metag_tools/megablast_wrapper.xml)). See [dependencies wiki](/admin/config/tool-dependencies/) for current version then [download blast+](http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download). Many data indexes are available directly at NCBI from [ftp://ftp.ncbi.nlm.nih.gov/blast/db/](ftp://ftp.ncbi.nlm.nih.gov/blast/db/) #### Picard/SRMA installation diff --git a/content/admin/faq/index.md b/content/admin/faq/index.md index a63b2ce320..1408d43b98 100644 --- a/content/admin/faq/index.md +++ b/content/admin/faq/index.md @@ -1,6 +1,7 @@ --- title: Frequently Asked Questions for Galaxy Administration --- + @@ -8,7 +9,6 @@ title: Frequently Asked Questions for Galaxy Administration See [Learn/FAQ](/learn/faq/) for questions about using any Galaxy instance, and [Main/FAQ](/main/faq/) for questions specifically about using Galaxy's free public server [Main](/main/). - ---- ## Galaxy license @@ -121,7 +121,7 @@ The following alignment tools available in Galaxy enable this: **I've read about GALAXY_SLOTS but I don't understand what it is and how it works?** -[Follow this link for a detailed description](/admin/config/galaxy_slots/) +[Follow this link for a detailed description](/admin/config/galaxy-slots/) ---- diff --git a/content/blog/2019-07-galaxy-resources/index.md b/content/blog/2019-07-galaxy-resources/index.md index cd8e0ee6ba..dc90244266 100644 --- a/content/blog/2019-07-galaxy-resources/index.md +++ b/content/blog/2019-07-galaxy-resources/index.md @@ -13,7 +13,7 @@ This blog post does not keep track of it all either, but it does highlight some # Learning -## Galaxy Training Network training materials +## [Galaxy Training Network](https://training.galaxyproject.org/) training materials This library of training materials has something for everyone. You can learn how to use Galaxy, how to deploy Galaxy, and even how to create new training materials. The library features slides and hands on tutorials that often include complete workflows. If you want to learn about Galaxy then start here @@ -90,7 +90,7 @@ It's all about community. There are many Galaxy communities and one (or more) o Running your own single-user Galaxy instance on your laptop is easy to do. Administering a multi-user, production-grade Galaxy instance is harder and requires significantly more compute knowledge. In either case, there is training available to help you along the way. -* [Go at your own pace admin training](https://training.galaxyproject.org/training-material/topics/admin/) is available from the [Galaxy Training Network](index,md#galaxy-training-network) +* [Go at your own pace admin training](https://training.galaxyproject.org/training-material/topics/admin/) is available from the [Galaxy Training Network](#galaxy-training-network-training-materials) * In person multi-day admin training is also available, at least twice a year. * The annual [Galaxy Community Conferences](#galaxy-community-conferences-gcc) offer a dedicated admin training day, followed by a selection of other admin training topics on a second training day. * Week-long Galaxy Admin training workshops have been offered every year since 2016. The most recent one was in [January 2019](/events/2019-admin-training/). The next one will likely be between October 2019 and March 2020 - probably in Europe. diff --git a/content/blog/2020-06-gvl5-beta3/index.md b/content/blog/2020-06-gvl5-beta3/index.md index 70f0962d99..9cf2ce5df0 100644 --- a/content/blog/2020-06-gvl5-beta3/index.md +++ b/content/blog/2020-06-gvl5-beta3/index.md @@ -45,10 +45,10 @@ level. This provides isolation and flexibility where different Galaxy instances can run differentiated toolsets, be supported by different cloud allocations, or be made available to targeted users. -
- - - +
+ +[![](./gvl-projects.png)](/blog/2020-06-gvl5-beta3/gvl-projects.png) +
While a managed deployment of the GVL that anyone can access and request their @@ -76,10 +76,10 @@ tools with extensive sharing capabilities. As a user, you have unrestricted access to those applications and can install any additional packages within those applications that are needed for the analysis. -
- - - +
+ +[![](./gvl-apps.png)](/blog/2020-06-gvl5-beta3/gvl-apps.png) +
Having access to multiple applications on the same platform needs to be diff --git a/content/galaxy-updates/2015-11/index.md b/content/galaxy-updates/2015-11/index.md index d1c1f4b2a7..977f1be27f 100644 --- a/content/galaxy-updates/2015-11/index.md +++ b/content/galaxy-updates/2015-11/index.md @@ -247,7 +247,7 @@ There are [upcoming events](/events/) on 3 continents in 4 countries, *and a ver November 30 - December 1 IUC Contribution Fest - Metagenomics Tools and Workflows Around the World Online - /iuc/, John Chilton + IUC, John Chilton diff --git a/content/galaxy-updates/2015-12/index.md b/content/galaxy-updates/2015-12/index.md index fe32e71872..7fe0ed2d0b 100644 --- a/content/galaxy-updates/2015-12/index.md +++ b/content/galaxy-updates/2015-12/index.md @@ -139,7 +139,7 @@ There are [many upcoming events](/events/) in the next few months. See the [Gal November 30 - December 1 IUC Contribution Fest - Metagenomics Tools and Workflows Around the World Online - /iuc/, John Chilton + IUC, John Chilton diff --git a/content/galaxy-updates/2017-03/index.md b/content/galaxy-updates/2017-03/index.md index 8c72c576b3..285b323a70 100644 --- a/content/galaxy-updates/2017-03/index.md +++ b/content/galaxy-updates/2017-03/index.md @@ -260,7 +260,7 @@ Some highlights from the past two months: Connor Wytko, Brian Soto, Stephen P. Ficklin. *Database*, Vol. 2017 (10 January 2017), baw154, doi:10.1093/database/baw154 * [A guide and best practices for R/Bioconductor tool integration in Galaxy](https://doi.org/10.12688/f1000research.9821.1) - [Nitesh Turaga](/people/nitesh-turaga/), Mallory A. Freeberg, [Dannon Baker](/people/dannon-baker/), [John Chilton](/people/john-chilton/), [Anton Nekrutenko](/people/anton/), [James Taylor](/james=taylor/). *F1000Research*, Vol. 5 (24 November 2016), 2757, doi:10.12688/f1000research.9821.1 + [Nitesh Turaga](/people/nitesh-turaga/), Mallory A. Freeberg, [Dannon Baker](/people/dannon-baker/), [John Chilton](/people/john-chilton/), [Anton Nekrutenko](/people/anton/), [James Taylor](/people/james-taylor/). *F1000Research*, Vol. 5 (24 November 2016), 2757, doi:10.12688/f1000research.9821.1 * [MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets](https://doi.org/10.1007/s41048-016-0033-4) Xilin Xu, Aiping Wu, Xinlei Zhang, Mingming Su, Taijiao Jiang, Zhe-Ming Yuan. *Biophysics Reports* (2017), pp. 1-10, doi:10.1007/s41048-016-0033-4 diff --git a/content/galaxy-updates/2017-11/index.md b/content/galaxy-updates/2017-11/index.md index 01921d7f5b..56abc5de9c 100644 --- a/content/galaxy-updates/2017-11/index.md +++ b/content/galaxy-updates/2017-11/index.md @@ -18,7 +18,7 @@ The blog is off to a running start with these posts in October: * [ELIXIR Galaxy Community](/blog/2017-10-05-elixir-galaxy-community/), by Frederik Coppens, Gildas Le Corguillé, and [Björn Grüning](/people/bjoern-gruening/) * [Public Galaxy Server Dashboard](/blog/2017-10-public-galaxy-dashboard/), by [Helena Rasche](/people/helena-rasche/) * [SciPy and scikit-learn integration into Galaxy](/blog/2017-10-10-scipy-galaxy/), by [Björn Grüning](/people/bjoern-gruening/) -* [Small genome assembly in Galaxy](/blog/2017-10-16-UnicyclerTutorial/), by [Anton Nekrutenko](/people/anton/) +* [Small genome assembly in Galaxy](/blog/2017-10-16-unicycler-tutorial/), by [Anton Nekrutenko](/people/anton/) * [Galaxy: the first 5,000 pubs](/blog/2017-10-5000-pubs/), by [Dave Clements](/people/dave-clements/) ## The Galactic Blog needs you! diff --git a/content/learn/privacy-features/index.md b/content/learn/privacy-features/index.md index 9448aab7d5..4f278d2687 100644 --- a/content/learn/privacy-features/index.md +++ b/content/learn/privacy-features/index.md @@ -33,7 +33,7 @@ For datasets you have created (or were given permissions) you can control what r You can make all datasets in a given history private to you by choosing the 'Make Data Private' option in the dropdown menu available under the 'cog - History options' icon in the top of the history. Also sets the default settings for all new datasets in this history to private. [Watch animation](/learn/privacy-features/this-hist-priv-perm.gif). * ### Set the default privacy settings for current history -Under the 'cog - History options' menu you can choose 'Dataset Security' and set the default permissions for all new datasets created in this history. [Watch animation](/learn/privacy-features/current-hist-perm.gif). +Under the 'cog - History options' menu you can choose 'Dataset Security' and set the default permissions for all new datasets created in this history. * ### Set the default privacy settings for new histories Under 'User - Preferences' you can find the 'Set dataset permissions for new histories' item which will allow you to set default privacy settings for contents of _newly_ created histories. [Watch animation](/learn/privacy-features/new-hist-perm.gif). diff --git a/content/news/2012-11-14-distribution-news-brief/index.md b/content/news/2012-11-14-distribution-news-brief/index.md index ccb168e8c9..acc9f915dd 100644 --- a/content/news/2012-11-14-distribution-news-brief/index.md +++ b/content/news/2012-11-14-distribution-news-brief/index.md @@ -3,7 +3,13 @@ title: "Nov 14, 2012 Distribution & News Brief" date: "2012-11-14" --- **Complete [News Brief](/archive/dev-news-briefs/2012-11-14/)** -
dist-readthedocs
Read the DocsSphinx Python Documentation Generator
+ +
+ + dist-readthedocs
Read the DocsSphinx Python Documentation Generator + +
+ **Highlights:** * **NGS: Picard (beta)** tools have moved from the **[Galaxy distribution](https://bitbucket.org/galaxy/galaxy-dist)** to the **[Galaxy Main Tool Shed](http://toolshed.g2.bx.psu.edu/)**. * The **Galaxy Project** is now using *[Sphinx](http://sphinx-doc.org/) Python* hosted at [Read the Docs](http://readthedocs.org) to document the **[galaxy-central](http://galaxy-central.readthedocs.org)** and **[galaxy-dist](http://galaxy-dist.readthedocs.org)** code base. That's a peek on the right → diff --git a/content/news/2021-01-galaxy-update/index.md b/content/news/2021-01-galaxy-update/index.md index ee61c2c474..91f37532e7 100644 --- a/content/news/2021-01-galaxy-update/index.md +++ b/content/news/2021-01-galaxy-update/index.md @@ -152,8 +152,16 @@ The application deadline for the [January 2021 Galaxy Admin Training](/events/20
-Structural Variant Detection using ONT Data -
[Structural Variant Detection using ONT Data](/events/2021-01-sv-wtih-ont/sv-with-ont.pdf)
+
+ +![Structural Variant Detection using ONT Data](/events/2021-01-sv-with-ont/sv-with-ont-workshop.png) + +
+
+ +[Structural Variant Detection using ONT Data](/events/2021-01-sv-with-ont/sv-with-ont.pdf) + +
**January 26, Online** diff --git a/content/news/2021-03-galaxy-update/index.md b/content/news/2021-03-galaxy-update/index.md index 205dc23141..ca7b3ffeba 100644 --- a/content/news/2021-03-galaxy-update/index.md +++ b/content/news/2021-03-galaxy-update/index.md @@ -597,7 +597,7 @@ We are pleased to [announce the 21.01 Galaxy release](/news/2021-03-galaxy-relea This include support for a workflow best practices checker, workflow reports, and tracking your workflow invocations. -The new [Remote Files interface](news/2021-03-galaxy-release-21-01/#remote-files) is an absolutely fantastic new way to browse your data. Browse files on many remote file services, from your Dropbox to TCGA. +The new [Remote Files interface](/news/2021-03-galaxy-release-21-01/#remote-files) is an absolutely fantastic new way to browse your data. Browse files on many remote file services, from your Dropbox to TCGA. **And there is a *lot* more in the full [user](https://docs.galaxyproject.org/en/master/releases/21.01_announce_user.html) and the [developer and admin](https://docs.galaxyproject.org/en/master/releases/21.01_announce.html) release announcements.**
diff --git a/content/news/gcc2012-scheduled/index.md b/content/news/gcc2012-scheduled/index.md index 3182025de3..599cfe8a87 100644 --- a/content/news/gcc2012-scheduled/index.md +++ b/content/news/gcc2012-scheduled/index.md @@ -12,4 +12,4 @@ Some things will be the same as in previous years, but we are also using feedbac Please reserve July 25-27 on your calendars! -[Dave Clements](/people/dave-clements/) and [Neil Bahroos](/NeilBahroos/) +[Dave Clements](/people/dave-clements/) and Neil Bahroos diff --git a/content/news/ismb2011-slides-now-available/index.md b/content/news/ismb2011-slides-now-available/index.md index 1a994680bf..fd804365b2 100644 --- a/content/news/ismb2011-slides-now-available/index.md +++ b/content/news/ismb2011-slides-now-available/index.md @@ -2,9 +2,18 @@ title: "ISMB2011 Slides" date: "2011-07-29" --- -
[[BOSC 2011   ISMB/ECCB 2011
-Slides for for 10 of the Galaxy-related presentations at [ISMB/ECCB/BOSC 2011](/events/ISMB-ECCB-BOSC 2011/) are [now available online](/events/ISMB-ECCB-BOSC 2011/). Presentations include: +
+ + BOSC 2011 + +     + + ISMB/ECCB 2011 + +
+ +Slides for for 10 of the Galaxy-related presentations at [ISMB/ECCB/BOSC 2011](/events/ismb-eccb-bosc2011/) are [now available online](/events/ismb-eccb-bosc2011/). Presentations include: * [Enacting Taverna Workflows through Galaxy](https://depot.galaxyproject.org/hub/attachments/documents/presentations/ISMB2011_TavernaInGalaxy.pdf) * [Enabling NGS Analysis with(out) the Infrastructure](https://depot.galaxyproject.org/hub/attachments/documents/presentations/BOSC2011_Cloud.pdf) diff --git a/content/support/diff-expression/index.md b/content/support/diff-expression/index.md index f60b6b7df2..a3f920660e 100644 --- a/content/support/diff-expression/index.md +++ b/content/support/diff-expression/index.md @@ -6,7 +6,7 @@ title: Help for Differential Expression Analysis FAQs and Galaxy Help Q`&`A. Most tool errors have been discussed or have existing help: * [My job ended with an error. What can I do?](/support/tool-error/) -* [Support FAQs](/support/inde.md) +* [Support FAQs](/support/) * [Galaxy Help](https://help.galaxyproject.org/) Related topics diff --git a/content/support/loading-data/index.md b/content/support/loading-data/index.md index ca0b94fb0f..839e1993ec 100644 --- a/content/support/loading-data/index.md +++ b/content/support/loading-data/index.md @@ -52,8 +52,8 @@ Data is loaded using the tools in the _**Get Data**_ tool group. Some access spe * Search for your data directly in the tool and use the Galaxy links * There are a few links, so [which data do I load?](/support/ebi-sra-data-load/) * Be sure to check your sequence data for correct quality score formats and the metadata "datatype" assignment. - * [How to format fastq data for tools that require .fastqsanger format?](/learn/fastqsanger/) - * [Understanding compressed fastq data (fastq.gz)](/learn/compressed-fastq/) + * [How to format fastq data for tools that require .fastqsanger format?](/support/fastqsanger/) + * [Understanding compressed fastq data (fastq.gz)](/support/compressed-fastq/) ### Get Data: Upload tool used with FTP diff --git a/content/support/metadata/index.md b/content/support/metadata/index.md index 8979a1d97f..89d989be05 100644 --- a/content/support/metadata/index.md +++ b/content/support/metadata/index.md @@ -1,6 +1,7 @@ --- - title: Metadata +title: Metadata --- + [Back to Support Hub](/support/) # When and how are metadata assigned? @@ -41,4 +42,4 @@ The dataset will turn yellow in the history while the job is processing. Once co ### **If problems persist** -Your error may not really be related to metadata, or changing metadat may not be enough to resolve the input/tool usage problems. Review the other **[FAQ solutions](/support/#troubleshooting)** for more data input help. Review the **[Galaxy Tutorials](/support/learn/)** for tool usage help. +Your error may not really be related to metadata, or changing metadat may not be enough to resolve the input/tool usage problems. Review the other **[FAQ solutions](/support/#troubleshooting)** for more data input help. Review the **[Galaxy Tutorials](/learn/)** for tool usage help. diff --git a/content/support/sort-your-inputs/index.md b/content/support/sort-your-inputs/index.md index 82b5809458..48cc5fe2d7 100644 --- a/content/support/sort-your-inputs/index.md +++ b/content/support/sort-your-inputs/index.md @@ -1,6 +1,7 @@ --- title: Sorting your inputs --- + [Back to Support Hub](/support/) ~~Many tools require inputs to be sorted in a specific way prior to use.~~ @@ -97,5 +98,5 @@ Please click the bug icon to report this problem if you need help. Different errors can be reported and some may seem unrelated to sort order. Try sorting as a first pass troubleshooting solution. If sorting does not work, it could be that your FASTQ data is not actually in *.fastqsanger* format. This occurs quite often in reported issues. For the quickest resolution, instead of reporting the bug and being sent back this link, first double check your data format directly. -* [How to format fastq data for tools that require .fastqsanger format?](/learn/fastqsanger/) -* [Understanding compressed fastq data (fastq.gz)](/learn/compressed-fastq/) +* [How to format fastq data for tools that require .fastqsanger format?](/support/fastqsanger/) +* [Understanding compressed fastq data (fastq.gz)](/support/compressed-fastq/)