Skip to content

Commit

Permalink
Merge pull request galaxyproject#899 from dannon/src-index-link-refac…
Browse files Browse the repository at this point in the history 
…toring

Address trimming remaining src and index.md from links
  • Loading branch information
@dannon
dannon authored Oct 4, 2021
2 parents 8e38fc0 + d63d4d7 commit 17c23cc
Show file tree
Hide file tree
Showing 936 changed files with 5,033 additions and 5,033 deletions.
2 changes: 1 addition & 1 deletion content/admin/config/performance/cluster/legacy/index.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ This documentation applies to old Galaxy releases. For the April 1, 2013 (tag `

## Cluster Resources Managers

<div class='left'><a href='http://www.drmaa.org'><img src="/src/images/logos/DRMAALogo200.png" alt="DRMAA" /></a></div>Galaxy is known to work with [TORQUE PBS](http://www.clusterresources.com/pages/products/torque-resource-manager.php), [Sun Grid Engine](http://gridengine.sunsource.net/), [Platform LSF](http://www.platform.com/workload-management/high-performance-computing), [PBS Pro](http://www.pbsworks.com/Product.aspx?id=1) and there's work in progress for [SLURM](https://computing.llnl.gov/linux/slurm/) (see this [blog post](http://mdahlo.blogspot.com/2011/06/galaxy-on-uppmax.html)). However, since Galaxy uses the [Distributed Resource Management Application API](http://www.drmaa.org), it should work with [any distributed resource manager (DRM) which implements the DRMAA](http://www.drmaa.org/implementations.php). Galaxy interfaces with these systems via [drmaa-python](http://code.google.com/p/drmaa-python/), although for legacy reasons, [pbs_python](https://subtrac.sara.nl/oss/pbs_python) can be used for TORQUE. If you successfully run Galaxy with another DRM, please let us know via an email to the [galaxy-dev mailing list](/mailing-lists/).
<div class='left'><a href='http://www.drmaa.org'><img src="/images/logos/DRMAALogo200.png" alt="DRMAA" /></a></div>Galaxy is known to work with [TORQUE PBS](http://www.clusterresources.com/pages/products/torque-resource-manager.php), [Sun Grid Engine](http://gridengine.sunsource.net/), [Platform LSF](http://www.platform.com/workload-management/high-performance-computing), [PBS Pro](http://www.pbsworks.com/Product.aspx?id=1) and there's work in progress for [SLURM](https://computing.llnl.gov/linux/slurm/) (see this [blog post](http://mdahlo.blogspot.com/2011/06/galaxy-on-uppmax.html)). However, since Galaxy uses the [Distributed Resource Management Application API](http://www.drmaa.org), it should work with [any distributed resource manager (DRM) which implements the DRMAA](http://www.drmaa.org/implementations.php). Galaxy interfaces with these systems via [drmaa-python](http://code.google.com/p/drmaa-python/), although for legacy reasons, [pbs_python](https://subtrac.sara.nl/oss/pbs_python) can be used for TORQUE. If you successfully run Galaxy with another DRM, please let us know via an email to the [galaxy-dev mailing list](/mailing-lists/).



Expand Down
14 changes: 7 additions & 7 deletions content/admin/config/user-information/index.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,30 +8,30 @@ A recent addition to Galaxy introduced the ability to collect specific informati

### Details for using this feature

This feature uses a Galaxy form, which must be created by a Galaxy [admin](/src/admin/interface) user.
This feature uses a Galaxy form, which must be created by a Galaxy [admin](/admin/interface) user.

On the admin page, click on "Manage Forms" link on the left go to the "Create a new form" page.

Provide a name and description of the form, select "User Information" for the "Type" and click the "Add fields" button. You can add any number of fields of any supported type ( TextField, NumberField, TextArea, etc ). These fields will be displayed on the user registration page. When you are finished, click the "Save" button to save the form.

`![](/src/admin/config/user-information/create_form.png)`
`![](/admin/config/user-information/create_form.png)`

After a form of type "User Information" has been created, the fields defined in the form will be displayed on the User Registration page.

`![](/src/admin/config/user-information/user_registration.png)`
`![](/admin/config/user-information/user_registration.png)`

Users can maintain this information by clicking the "Manage your information" link on the User Preferences page.

`![](/src/admin/config/user-information/user_preferences.png)`
`![](/admin/config/user-information/user_preferences.png)`

Here is a sample of the Manage User Information page. Notice the "Add a new address" button. Users can add any number of addresses to their information.

`![](/src/admin/config/user-information/user_information.png)`
`![](/admin/config/user-information/user_information.png)`

Clicking the "Add a new address" button displays the following page.

`![](/src/admin/config/user-information/user_address.png)`
`![](/admin/config/user-information/user_address.png)`

When the address is saved, it is included on the Manage User Information page.

`![](/src/admin/config/user-information/user_information_with_address.png`)
`![](/admin/config/user-information/user_information_with_address.png`)
2 changes: 1 addition & 1 deletion content/admin/data-integration/index.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ Built-in data files are critical for many Galaxy tools. This page will describe

There are several steps needed for adding a genome to Galaxy. The first is to get the actual data needed and to put it into an appropriate directory accessible to the Galaxy instance. Then you need to establish the particular `.loc` ("location") file. Finally, make sure that the genome is referenced in the `$GALAXYROOT/tool-data/shared/ucsc/builds.txt` file.

**Note that as of early 2014, more than a builds.txt file change is needed to establish a new reference genome. If not using** [Data Managers](/admin/tools/data-managers/) **, you must make the necessary changes/additions to the new [Data Tables](/src/admin/tools/data-tables) or use the alternative configuration file.**
**Note that as of early 2014, more than a builds.txt file change is needed to establish a new reference genome. If not using** [Data Managers](/admin/tools/data-managers/) **, you must make the necessary changes/additions to the new [Data Tables](/admin/tools/data-tables) or use the alternative configuration file.**

### Get the data

Expand Down
2 changes: 1 addition & 1 deletion content/admin/data-preparation/index.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@

# 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](/src/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%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.

# Data and indexes hosted at http://usegalaxy.org

Expand Down
2 changes: 1 addition & 1 deletion content/admin/faq/index.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -127,5 +127,5 @@ The following alignment tools available in Galaxy enable this:

## Any other question

<div class='left'><a href='/search/'><img src="/src/images/galaxy-logos/galaxy-web-search.png" alt="Galaxy Search" width="150" /></a></div>
<div class='left'><a href='/search/'><img src="/images/galaxy-logos/galaxy-web-search.png" alt="Galaxy Search" width="150" /></a></div>
[Galaxy Search](/search/) searches all online Galaxy resources. This includes this hub, the [Mailing Lists](/mailing-lists/), [Main](/main/), the [Tool Shed](/toolshed/), and the [Galaxy source code](https://github.com/galaxyproject/galaxy).
4 changes: 2 additions & 2 deletions content/admin/internals/data-model/index.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ TODO: Describe data model. For now, have a picture!
Marten: I use DB Visualizer for the Galaxy's database and it works pretty well. (http://www.dbvis.com/)

<div class='center'>
<a href='/src/admin/internals/data-model/galaxy_schema.png'><img src="/src/admin/internals/data-model/galaxy_schema.png" alt="Galaxy Data Model; click to enlarge" width="600" /></a>
<a href='/src/admin/internals/data-model/galaxy_schema.png'><img src="/admin/internals/data-model/galaxy_schema.png" alt="Galaxy Data Model; click to enlarge" width="600" /></a>

[Galaxy Data Model; click to enlarge](/src/admin/internals/data-model/galaxy_schema.png).
[Galaxy Data Model; click to enlarge](/admin/internals/data-model/galaxy_schema.png).
</div>
4 changes: 2 additions & 2 deletions content/admin/license/index.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ Copyright (c) 2005-2015 Pennsylvania State University

## Source Code License

<div class='right'><a href='http://opensource.org/licenses/AFL-3.0'><img src="/src/images/logos/OSIApprovedLicenseLogo.png" alt="An Open Source Initiative (OSI) approved license" /></a></div>
<div class='right'><a href='http://opensource.org/licenses/AFL-3.0'><img src="/images/logos/OSIApprovedLicenseLogo.png" alt="An Open Source Initiative (OSI) approved license" /></a></div>

Galaxy source code is licensed under the [Academic Free License version 3.0](http://opensource.org/licenses/AFL-3.0).

Expand Down Expand Up @@ -58,6 +58,6 @@ e) to display the Original Work publicly.

## Images and Documentation License

<div class='right'><a href='http://creativecommons.org/licenses/by/3.0/'><img src="/src/images/logos/CCBY3.0Logo.png" alt="Creative Commons License" /></a></div>
<div class='right'><a href='http://creativecommons.org/licenses/by/3.0/'><img src="/images/logos/CCBY3.0Logo.png" alt="Creative Commons License" /></a></div>

Images and documentation are licensed under the [Creative Commons Attribution 3.0 (CC BY 3.0) License](http://creativecommons.org/licenses/by/3.0/).
20 changes: 10 additions & 10 deletions content/admin/objectstore/gce/index.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -22,16 +22,16 @@ In order to do so, you may take the following steps:
with your Google credentials. You will then be redirected to your dashboard
on Google Cloud Platform:

![image](/src/admin/objectstore/gce/01.png)
![image](/admin/objectstore/gce/01.png)

2. Go to _[service accounts](https://cloud.google.com/compute/docs/access/service-accounts)_
page as shown in the following figure:

![image](/src/admin/objectstore/gce/02.png)
![image](/admin/objectstore/gce/02.png)

3. Create a _service account_ by clicking on the `CREATE SERVICE ACCOUNT` button:

![image](/src/admin/objectstore/gce/03.png)
![image](/admin/objectstore/gce/03.png)

This will create a service account under currently selected project (e.g.,
the `first Test` project as shown in our example figures). You can select a
Expand All @@ -41,15 +41,15 @@ page as shown in the following figure:
4. Fill in the required fields for the service account details, then
click on the `CREATE` button.

![image](/src/admin/objectstore/gce/04.png)
![image](/admin/objectstore/gce/04.png)

5. Grant the _service account_ with permission to read/write
objects in a bucket under your account (e.g., by assigning the
[`Storage Admin`](https://cloud.google.com/iam/docs/understanding-roles#storage-roles)
role to the _service account_), then click on the `CONTINUE` button.
See the following figure:

![image](/src/admin/objectstore/gce/05.png)
![image](/admin/objectstore/gce/05.png)

You may refer to the [roles documentation page](https://cloud.google.com/iam/docs/understanding-roles)
for a complete list of roles and their permissions.
Expand All @@ -58,7 +58,7 @@ See the following figure:
then choose `JSON`, and then click on the `CREATE` button, and then
click on the `DONE` button.

![image](/src/admin/objectstore/gce/06.png)
![image](/admin/objectstore/gce/06.png)

This will create a private key and downloads a json file containing all the
required information to access your Google cloud storage under your account.
Expand All @@ -67,20 +67,20 @@ click on the `DONE` button.
1. On the [_console page_](https://console.cloud.google.com/), click on the _navigation menu_
button (`☰`), and go to `Storage > Browse`. See the following figure:

![image](/src/admin/objectstore/gce/07.png)
![image](/admin/objectstore/gce/07.png)

2. On the _Storage_ page, click on the `CREATE BUCKET` button, see the following
figure:

![image](/src/admin/objectstore/gce/08.png)
![image](/admin/objectstore/gce/08.png)

> Note: in order to create a bucket, you would need to have an active subscription
and have set-up payment options.

3. On the _create bucket_ page, enter the required fields, and note the **bucket name**,
and then click on the `Create` button.

![image](/src/admin/objectstore/gce/09.png)
![image](/admin/objectstore/gce/09.png)

## Step 2/2: Configure Galaxy ObjectStore

Expand Down Expand Up @@ -114,4 +114,4 @@ on the `config/galaxy.yml` file (not `config/galaxy.yml.sample`):
uploaded to Galaxy, or generated by Galaxy (as a result of tool/workflow execution)
will be uploaded to the specified bucket. See the following figure:

![image](/src/admin/objectstore/gce/10.png)
![image](/admin/objectstore/gce/10.png)
Loading

0 comments on commit 17c23cc

Please sign in to comment.