Merge pull request #960 from NickSto/internal-link-repair2

Another bunch of internal links fixed.

content/cloud/storage/index.md

@@ -67,7 +67,7 @@ A sample payload:
 }
 ```
 
-[Read this page](/cloud/storage/get_step_by_step/) for step-by-step description on how to use this API.
+[Read this page](/cloud/storage/get-step-by-step/) for step-by-step description on how to use this API.
 
 
 ## `Send` Data to Cloud
@@ -110,5 +110,5 @@ Or:
 }
 ```
 
-[Read this page](/cloud/storage/send_step_by_step/) for step-by-step description on how to use this API.
+[Read this page](/cloud/storage/send-step-by-step/) for step-by-step description on how to use this API.
 

content/events/admin-training2016/logistics/index.md

@@ -105,9 +105,9 @@ See the [event map for details](https://drive.google.com/open?id=1vC6J8BdrMDQo_c
 
 # Training Venues
 
-The **[Basics Session](/events/admin-training2016/logistics/BasicsSession/)** will be held at the **[Salt Lake City Main Public Library](http://www.slcpl.lib.ut.us/branches/view/Main+Library).**  This [stunning venue](https://www.google.com/search?tbm=isch&q=salt+lake+city+library) is located in downtown Salt Lake City at [210 East 400 South](https://drive.google.com/open?id=1vC6J8BdrMDQo_cIJvTr9pjUGGcA&usp=sharing), and is a stop on the [UTA TRAX Red Line](https://www.rideuta.com/Rider-Tools/Schedules-and-Maps/703-Red-Line) and just [5 stops from conference housing](https://drive.google.com/open?id=1vC6J8BdrMDQo_cIJvTr9pjUGGcA&usp=sharing).  We'll be meeting in [Conference Room 4](http://www.slcpl.lib.ut.us/rooms/) 
+The **[Basics Session](/events/admin-training2016/basics-session/)** will be held at the **[Salt Lake City Main Public Library](http://www.slcpl.lib.ut.us/branches/view/Main+Library).**  This [stunning venue](https://www.google.com/search?tbm=isch&q=salt+lake+city+library) is located in downtown Salt Lake City at [210 East 400 South](https://drive.google.com/open?id=1vC6J8BdrMDQo_cIJvTr9pjUGGcA&usp=sharing), and is a stop on the [UTA TRAX Red Line](https://www.rideuta.com/Rider-Tools/Schedules-and-Maps/703-Red-Line) and just [5 stops from conference housing](https://drive.google.com/open?id=1vC6J8BdrMDQo_cIJvTr9pjUGGcA&usp=sharing).  We'll be meeting in [Conference Room 4](http://www.slcpl.lib.ut.us/rooms/) 
 
-The **[Advanced Session](/events/admin-training2016/logistics/AdvancedSession/)** will be held at the **[Commanders House](http://www.universityguesthouse.com/Commanders-House) on the [University of Utah](http://utah.edu/) campus**.  This is a short walk from the [University Guest House](/events/admin-training2016/logistics/#lodging), where participants are staying.
+The **[Advanced Session](/events/admin-training2016/advanced-session/)** will be held at the **[Commanders House](http://www.universityguesthouse.com/Commanders-House) on the [University of Utah](http://utah.edu/) campus**.  This is a short walk from the [University Guest House](/events/admin-training2016/logistics/#lodging), where participants are staying.
 
 <div class='left'>
 <a href='http://ucgd.genetics.utah.edu/'><img src="/images/logos/USTAR-UCGD-Logo.jpg" alt="USTAR Center for Genetic Discovery (UCGD)" width="280" /></a></div>

content/events/bio-it-world2014/w14/index.md

@@ -466,10 +466,10 @@ Explanations of these options:
 Honorable mentions for features we won't use today but that are common in big setups:
 
 * `ftp_upload_dir` and `ftp_upload_site` - Allow users to upload data to the server using FTP
-* `use_remote_user` and `remote_user_maildomain` - Use your institution's existing authentication system to log in to Galaxy. [Apache documentation](/admin/config/ExternalUserDatbases/) or [nginx documentation](https://galaxyproject.org/admin/config/nginx-external-user-auth/#nginx-external-authentication)
+* `use_remote_user` and `remote_user_maildomain` - Use your institution's existing authentication system to log in to Galaxy. [Apache documentation](/admin/config/apache-external-user-auth/) or [nginx documentation](/admin/config/nginx-external-user-auth/#nginx-external-authentication)
 * `allow_user_impersonation` - Users configured as administrators (with `admin_users`) can "become" other users to view Galaxy exactly as the impersonated user does. Useful for providing support.
-* `library_import_dir` - Administrators can directly import datasets from this directory on the server to Data Libraries.  This includes an option that allows an effective "symlink" to the data, rather than copying it in to Galaxy's `file_path` directory. [documentation](/data-libraries/uploading-library-files/)
-* `user_library_import_dir` - Non-administrators can directly import datasets from this directory on this server to Data Libraries from which they have been given write permission. [documentation](/data-libraries/uploading-library-files/)
+* `library_import_dir` - Administrators can directly import datasets from this directory on the server to Data Libraries.  This includes an option that allows an effective "symlink" to the data, rather than copying it in to Galaxy's `file_path` directory. [documentation](/archive/data-libraries/uploading-library-files/)
+* `user_library_import_dir` - Non-administrators can directly import datasets from this directory on this server to Data Libraries from which they have been given write permission. [documentation](/archive/data-libraries/uploading-library-files/)
 * `allow_library_path_paste` - Administrators can import datasets from anywhere on the server's filesystem(s) by entering their paths in to a text box
 * `object_store_config_file` - Configure Galaxy's "object storage" layer to store data in multiple filesystems, Amazon S3, iRODS, etc.
 * `error_email_to` (with `smtp_server`) - Allow users to send bug reports directly to you

content/events/gcc2012/lightning-talks/index.md

@@ -16,7 +16,7 @@
 |  | <div class="float-right"> *[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Joshi.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=414d642ce0a44ad) (starts @ xx:yy)*</div> *Differential Expression with Diagnostic Plots using sam2counts and DESeq* <div class='indent'> Nikhil Joshi, UC Davis </div> |
 |  |<div class='float-right'> *[PDF](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Jagtap.pdf), [PPT](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Jagtap.ppt), Video*</div> *Galaxy-P* <div class='indent'> Pratik Jagtap, University of Minnesota  </div> |
 |  |<div class='float-right'> *[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Sandve.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=ea7962cd5bbf421)*</div> *The Genomic Hyperbrowser: Prove Your Point* <div class='indent'> Geir Kjetil Sandve, University of Oslo </div> |
-|  |<div class='float-right'> *[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Gruning.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=ea7962cd5bbf421) (starts @ 6:10)*</div> *[ChemicalToolBox](/chemical-tool-box/)* <div class='indent'> Björn Grüning, Albert-Ludwigs-University Freiburg </div> |
+|  |<div class='float-right'> *[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Gruning.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=ea7962cd5bbf421) (starts @ 6:10)*</div> *[ChemicalToolBox](/use/chemicaltoolbox/)* <div class='indent'> Björn Grüning, Albert-Ludwigs-University Freiburg </div> |
 
 
 ## Goals

content/events/gcc2012/promotion/index.md

@@ -51,4 +51,4 @@ The conference logo is available in 2 formats in several widths.
 
 # Sponsorships
 
-Interested in sponsoring the meeting?  See [Sponsorships](/events/gcc2012/promotion/Sponsorships/).
+Interested in sponsoring the meeting?  See [Sponsorships](/events/gcc2012/sponsorships/).

content/events/gcc2012/training-day/ws5/index.md

@@ -82,7 +82,7 @@ I changed the following settings:
 * `tool_dependency_dir = /home/galaxy/tool-deps` - The directory that will house tool dependencies.  [Admin/Config/Tool Dependencies](/admin/config/tool-dependencies/) explains how these dependencies can be configured.  Tools installed from the tool shed that manage their own dependencies (e.g. freebayes) will also use this directory.
 * `debug = False` - Disables debugging middleware that loads server responses in to memory (can crash the server when handling large files).
 * `use_interactive = False` - Disables live client browser debugging (insecure).
-* `library_import_dir = /home/galaxy/import` - Administrators can directly import datasets from this directory on the server to Data Libraries.  This includes an option that allows an effective "symlink" to the data, rather than copying it in to Galaxy's `file_path` directory.  Documented at [Admin/DataLibraries/UploadingLibraryFiles](/data-libraries/uploading-library-files/).
+* `library_import_dir = /home/galaxy/import` - Administrators can directly import datasets from this directory on the server to Data Libraries.  This includes an option that allows an effective "symlink" to the data, rather than copying it in to Galaxy's `file_path` directory.  Documented at [Admin/DataLibraries/UploadingLibraryFiles](/archive/data-libraries/uploading-library-files/).
 * `user_library_import_dir = /home/galaxy/user-import` - Non-administrators can directly import datasets from this directory on this server to Data Libraries from which they have been given write permission.  Documented at the same link as above.
 * `allow_library_path_paste = True` - Administrators can import datasets from anywhere on the server's filesystem(s) by entering their paths in to a textarea.
 * `id_secret = <random text>` - Ensures that the encoded IDs used by Galaxy (especially session IDs) are unique.  One simple way to generate a value for this is with a shell command like `% date | md5sum`

content/events/gcc2014/training-day/admin-walkthrough/index.md

@@ -360,7 +360,7 @@ Explanations of these options:
 Honorable mentions for features we won't use today but that are common in big setups:
 
 * `ftp_upload_dir` and `ftp_upload_site` - Allow users to upload data to the server using FTP
-* `use_remote_user` and `remote_user_maildomain` - Use your institution's existing authentication system to log in to Galaxy. [Apache documentation](/admin/config/external-user-databases/) or [nginx documentation](https://galaxyproject.org/admin/config/nginx-external-user-auth/)
+* `use_remote_user` and `remote_user_maildomain` - Use your institution's existing authentication system to log in to Galaxy. [Apache documentation](/admin/config/apache-external-user-auth/) or [nginx documentation](https://galaxyproject.org/admin/config/nginx-external-user-auth/)
 * `allow_user_impersonation` - Users configured as administrators (with `admin_users`) can "become" other users to view Galaxy exactly as the impersonated user does. Useful for providing support.
 * `user_library_import_dir` - Non-administrators can directly import datasets from this directory on this server to Data Libraries from which they have been given write permission. [documentation](/data-libraries/#user-folder)
 * `object_store_config_file` - Configure Galaxy's "object storage" layer to store data in multiple filesystems, Amazon S3, iRODS, etc.

content/installing-repositories/index.md

@@ -13,7 +13,7 @@ title: Installing Repositories
 
 [Installing repositories that contain tools migrated from the Galaxy code distribution to the main Galaxy Tool Shed](/toolshed/migrating-tools-from-galaxy-distribution/)
 
-[Installing tool dependency packages along with Galaxy tools](/installing-tool-dependency-packages/)
+[Installing tool dependency packages along with Galaxy tools](/installingtooldependencypackages/)
 
 [The Tool Shed provides tool version lineage information to Galaxy](/galaxy-tool-version-lineage/)