Merge pull request #863 from dannon/link-fixes

Many broken internal link fixes.

content/admin/capacity-planning/index.md

@@ -5,21 +5,21 @@ title: Galaxy Capacity Planning
 
 
 
-One of the recurring questions on the [Mailing Lists](/src/mailing-lists/index.md) is
+One of the recurring questions on the [Mailing Lists](/mailing-lists/) is
 
- . *How much computing power / disk space / network bandwidth / ... do I need to [set up my own Galaxy server](/src/admin/get-galaxy/index.md)?*
+ . *How much computing power / disk space / network bandwidth / ... do I need to [set up my own Galaxy server](/admin/get-galaxy/)?*
 
-There is no one set answer to this question.  It depends upon how many users you have, what your dataset sizes are, and what type of analyses your users will be doing.  The [GalaxyAdmins survey results](/src/community/galaxy-admins/surveys/index.md) are the best source of information.
+There is no one set answer to this question.  It depends upon how many users you have, what your dataset sizes are, and what type of analyses your users will be doing.  The [GalaxyAdmins survey results](/community/galaxy-admins/surveys/) are the best source of information.
 
 Note that Galaxy itself, and many of the basic tools, can run on an average or even older laptop.  However, to run computationally intensive tools such as mappers and assemblers, you will need some computational power behind it.
 
 ## Can we use the Cloud?
 
-Absolutely.  In fact, if your needs tend to be characterized by long periods of no use (days / weeks / months) interspersed by short periods of intense use, then you should consider the [Cloud](/src/cloud/index.md).  Setting up a compute cluster / server farm (if you need something that big) can take months, as you may be delayed repeatedly by details like air conditioning upgrades, electrical capacity, and finding a sys admin.
+Absolutely.  In fact, if your needs tend to be characterized by long periods of no use (days / weeks / months) interspersed by short periods of intense use, then you should consider the [Cloud](/cloud/).  Setting up a compute cluster / server farm (if you need something that big) can take months, as you may be delayed repeatedly by details like air conditioning upgrades, electrical capacity, and finding a sys admin.
 
-See the [Cloud page](/src/cloud/index.md) for information on getting started with the cloud.
+See the [Cloud page](/cloud/) for information on getting started with the cloud.
 
 ## See Also
 
-* [Cloud](/src/cloud/index.md) - Galaxy on the cloud options
-* [Public Galaxy Servers](/src/use/index.md) - a list of known, publicly accessible, Galaxy servers.
+* [Cloud](/cloud/) - Galaxy on the cloud options
+* [Public Galaxy Servers](/use/) - a list of known, publicly accessible, Galaxy servers.

content/admin/config/access-control/index.md

@@ -133,7 +133,7 @@ def admin( context, section ):
 ```
 
 
-To rewrite the important points from [UserDefinedToolboxFilters](/src/user-defined-toolbox-filters/index.md) page, 
+To rewrite the important points from [UserDefinedToolboxFilters](/user-defined-toolbox-filters/) page, 
 
 * Every filter is a small python function under lib/galaxy/tools/toolbox/filters/. 
 

content/admin/config/apache-proxy/index.md

@@ -1,6 +1,6 @@
----
-redirect: "https://docs.galaxyproject.org/en/latest/admin/special_topics/apache.html"
----
-
-This page has been migrated to the [Galaxy docs](https://docs.galaxyproject.org/en/latest/admin/special_topics/apache.html), please check there for up-to-date information.
-
+---
+redirect: "https://docs.galaxyproject.org/en/latest/admin/special_topics/apache.html"
+---
+
+This page has been migrated to the [Galaxy docs](https://docs.galaxyproject.org/en/latest/admin/special_topics/apache.html), please check there for up-to-date information.
+

content/admin/config/external-user-auth/index.md

@@ -4,7 +4,7 @@ title: External User Authentication
 
 By default, Galaxy will manage its own users, allowing standard username/password login. However, it may be more useful at your site to tie into an external authentication system like CAS, LDAP, AD, PAM, etc.
 
-Galaxy supports LDAP and AD authentication natively, but you must still use upstream [Nginx](/src/admin/config/nginx-external-user-auth/index.md) or [Apache](/src/admin/config/apache-external-user-auth/index.md) for other authentication schemes like CAS.
+Galaxy supports LDAP and AD authentication natively, but you must still use upstream [Nginx](/admin/config/nginx-external-user-auth/) or [Apache](/admin/config/apache-external-user-auth/) for other authentication schemes like CAS.
 
 # Activate authentication through LDAP
 

content/admin/config/galaxy_slots/index.md

@@ -4,7 +4,7 @@ See the Planemo [documentation](http://planemo.readthedocs.org/en/latest/writing
 
 # GALAXY_SLOTS (for server admins)
 
-How you configure GALAXY_SLOTS depends on the cluster system being used. More about the subject on the [supported cluster systems page](/src/admin/config/performance/cluster/index.md).
+How you configure GALAXY_SLOTS depends on the cluster system being used. More about the subject on the [supported cluster systems page](/admin/config/performance/cluster/).
 
 In all cases you need to include a parameter on your job_conf.xml that specifies the number of processes to be used for a given destination. If correctly defined your should see your GALAXY_SLOTS variable contain the specified value.
 

content/admin/config/index.md

@@ -9,26 +9,26 @@ title: Galaxy Configuration for Admins
 * [Running Galaxy in a production environment](https://docs.galaxyproject.org/en/latest/admin/production.html)
 * [Running Galaxy Tools on a Cluster](https://docs.galaxyproject.org/en/latest/admin/cluster.html)
 * [Galaxy Job Configuration](https://docs.galaxyproject.org/en/latest/admin/jobs.html)
-* [Authentication with LDAP/AD](/src/admin/config/external-user-auth/index.md)
+* [Authentication with LDAP/AD](/admin/config/external-user-auth/)
 * [Apache Proxy](https://docs.galaxyproject.org/en/latest/admin/special_topics/apache.html)
-  * [Apache External User Auth](/src/admin/config/apache-external-user-auth/index.md)
+  * [Apache External User Auth](/admin/config/apache-external-user-auth/)
 * [Nginx Proxy](https://docs.galaxyproject.org/en/latest/admin/special_topics/nginx.html)
-  * [Nginx External User Auth](/src/admin/config/nginx-external-user-auth/index.md)
+  * [Nginx External User Auth](/admin/config/nginx-external-user-auth/)
 
 ## Tools
 
-* [Tool Dependencies](/src/admin/config/tool-dependencies/index.md)
-* [Set up Visualizations](/src/visualization-setup/index.md)
+* [Tool Dependencies](/admin/config/tool-dependencies/)
+* [Set up Visualizations](/visualization-setup/)
 * [Collecting Job Metrics](https://docs.galaxyproject.org/en/latest/admin/special_topics/job_metrics.html)
 
 
 ## FTP
 
 * [Upload via FTP](https://docs.galaxyproject.org/en/latest/admin/special_topics/ftp.html)
-* [Setup ProFTPd with AD/LDAP auth](/src/admin/config/proftpd-with-ad/index.md)
+* [Setup ProFTPd with AD/LDAP auth](/admin/config/proftpd-with-ad/)
 
 ## Other
 
-* [User Information (Collecting information during registration)](/src/admin/config/user-information/index.md)
-* [Running on Windows](/src/admin/config/windows/index.md)
-* [Access Control (ACLs)](/src/admin/config/access-control/index.md)
+* [User Information (Collecting information during registration)](/admin/config/user-information/)
+* [Running on Windows](/admin/config/windows/)
+* [Access Control (ACLs)](/admin/config/access-control/)

content/admin/config/nginx-proxy/index.md

@@ -1,5 +1,5 @@
----
-redirect: "https://docs.galaxyproject.org/en/latest/admin/nginx.html"
----
-
-This page has been migrated to the [Galaxy docs](https://docs.galaxyproject.org/en/latest/admin/nginx.html), please check there for up-to-date information.
+---
+redirect: "https://docs.galaxyproject.org/en/latest/admin/nginx.html"
+---
+
+This page has been migrated to the [Galaxy docs](https://docs.galaxyproject.org/en/latest/admin/nginx.html), please check there for up-to-date information.

content/admin/config/performance/cluster/legacy/index.md

@@ -9,7 +9,7 @@ Galaxy is designed to run jobs on your local system by default, but it can be co
 
 
 ```wiki red/solid/light
-This documentation applies to old Galaxy releases.  For the April 1, 2013 (tag `release_2013.04.01`) Galaxy release and newer, use the [current](/src/admin/config/performance/cluster/index.md) documentation.
+This documentation applies to old Galaxy releases.  For the April 1, 2013 (tag `release_2013.04.01`) Galaxy release and newer, use the [current](/admin/config/performance/cluster/) documentation.
 ```
 
 
@@ -23,12 +23,12 @@ 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](/src/mailing-lists/index.md).
+<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/).
 
 
 
 
-Galaxy contributor John Chilton has also written [Pulsar](/src/admin/config/pulsar/index.md) which does not require an existing cluster or a shared filesystem and can also run jobs on Windows hosts. Please see the README included with Pulsar for instructions on how to set it up.
+Galaxy contributor John Chilton has also written [Pulsar](/admin/config/pulsar/) which does not require an existing cluster or a shared filesystem and can also run jobs on Windows hosts. Please see the README included with Pulsar for instructions on how to set it up.
 
 
 
@@ -61,7 +61,7 @@ The drmaa egg is provided by Galaxy, but you must tell it where your resource ma
 
 ### pbs_python egg
 
-pbs_python is dependent upon TORQUE and is not provided by Galaxy. You must "scramble" it yourself (for more information on Galaxy's Python Egg dependencies, see the [Eggs](/src/admin/config/Eggs/index.md) page). Fortunately, this process should be simple:
+pbs_python is dependent upon TORQUE and is not provided by Galaxy. You must "scramble" it yourself (for more information on Galaxy's Python Egg dependencies, see the [Eggs](/admin/config/Eggs/) page). Fortunately, this process should be simple:
 
 
 
@@ -122,7 +122,7 @@ node1%
 
 
 
-One should also check that the job manager can accept jobs from the `galaxy` user.  This is typically not an issue unless the `galaxy` user lacks a shell login (not uncommon with secure server configurations); this may be an assigned shell of `/bin/false` (Debian/Ubuntu) or `/bin/nologin` (Fedora[/RedHat](/src/admin/config/performance/cluster/legacy/RedHat/index.md)).  A default shell login is typically required for job submission with [TORQUE/PBS](http://www.clusterresources.com/pages/products/torque-resource-manager.php); this can be set using `usermod`:
+One should also check that the job manager can accept jobs from the `galaxy` user.  This is typically not an issue unless the `galaxy` user lacks a shell login (not uncommon with secure server configurations); this may be an assigned shell of `/bin/false` (Debian/Ubuntu) or `/bin/nologin` (Fedora[/RedHat](/admin/config/performance/cluster/legacy/RedHat/)).  A default shell login is typically required for job submission with [TORQUE/PBS](http://www.clusterresources.com/pages/products/torque-resource-manager.php); this can be set using `usermod`:
 
 
 
@@ -385,7 +385,7 @@ Or, if you want a tool to use a different DRM server or queue than the default s
 
 ### Tool Handler Configuration
 
-You can also control which job handler will be used via the similarly named [galaxy:tool_handlers] configuration section.  The synax on the left hand of the assignment (tool_id[params]) syntax is identical to the tool_runners options.  On the right hand of the assignment, you can specify which handler should be used to handle jobs for the specified tool/params.  More details about how to configure multiple job handlers can be found on the [Admin/Config/Performance/Scaling](/src/admin/config/performance/scaling/index.md) page.
+You can also control which job handler will be used via the similarly named [galaxy:tool_handlers] configuration section.  The synax on the left hand of the assignment (tool_id[params]) syntax is identical to the tool_runners options.  On the right hand of the assignment, you can specify which handler should be used to handle jobs for the specified tool/params.  More details about how to configure multiple job handlers can be found on the [Admin/Config/Performance/Scaling](/admin/config/performance/scaling/) page.
 
 
 
@@ -445,4 +445,4 @@ If your sudo config contains `Defaults    requiretty`, this option must be disab
 
 
 
-Some maintenance and support of this code will be provided via the usual [Support](/src/support/index.md) channels, but improvements and fixes would be greatly welcomed, as this is a complex feature which is not used by the Galaxy Development Team.
+Some maintenance and support of this code will be provided via the usual [Support](/support/) channels, but improvements and fixes would be greatly welcomed, as this is a complex feature which is not used by the Galaxy Development Team.

content/admin/config/performance/linkbox.md

@@ -1,8 +1,8 @@
 <div class='linkbox'>
-**[Performance](/src/admin/config/performance/production-server/index.md)**<br />
-[Cluster](/src/admin/config/performance/cluster/index.md)<br />
-[Apache](/src/admin/config/apache-proxy/index.md)<br />
-[Nginx](/src/admin/config/nginx-proxy/index.md)<br />
-[Purge H&D](/src/admin/config/performance/purge-histories-and-datasets/index.md)<br />
-[Scaling](/src/admin/config/performance/scaling/index.md)<br />
+**[Performance](/admin/config/performance/production-server/)**<br />
+[Cluster](/admin/config/performance/cluster/)<br />
+[Apache](/admin/config/apache-proxy/)<br />
+[Nginx](/admin/config/nginx-proxy/)<br />
+[Purge H&D](/admin/config/performance/purge-histories-and-datasets/)<br />
+[Scaling](/admin/config/performance/scaling/)<br />
 </div>

content/admin/config/tool-dependencies/index.md

@@ -1,10 +1,10 @@
 ## Tool Dependencies
 
-Galaxy provides a method for managing the dependencies of Galaxy tools installed from the [Tool Shed](/src/toolshed/index.md).  In this case, it is simply necessary to set the `tool_dependency_dir` option of `config/galaxy.ini` to a path writable by the Galaxy server.
+Galaxy provides a method for managing the dependencies of Galaxy tools installed from the [Tool Shed](/toolshed/).  In this case, it is simply necessary to set the `tool_dependency_dir` option of `config/galaxy.ini` to a path writable by the Galaxy server.
 
 However, some tools which have not been migrated to the Tool Shed still require manual installation of dependent binaries. In addition, administrators may choose to utilize existing versions of dependencies already installed on the system, rather than rely on versions installed from the Tool Shed. The documentation below covers these cases.
 
-A list of dependencies for unmigrated tools can be found on the [Admin/Tools/Tool-Dependencies-List](/src/admin/config/tool-dependencies-list/index.md) page.
+A list of dependencies for unmigrated tools can be found on the [Admin/Tools/Tool-Dependencies-List](/admin/config/tool-dependencies-list/) page.
 
 ### $PATH
 
@@ -33,7 +33,7 @@ Changes to `$PATH` can be persisted by setting them in your shell's startup file
 
 ### Cluster Jobs
 
-Setting `$PATH` in your shell startup files may work depending on your DRM - this is how we set up the environment for the [Public Galaxy Site](http://usegalaxy.org/) which runs TORQUE PBS.  However, this may not work for other DRMs such as Sun Grid Engine (SGE).  For SGE, please see the `-v` and `-V` options to [qsub](http://gridscheduler.sourceforge.net/htmlman/htmlman1/qsub.html) and how to set these in [sge_request](http://gridscheduler.sourceforge.net/htmlman/htmlman5/sge_request.html) or [the job runner URL](/src/admin/config/performance/cluster/index.md).
+Setting `$PATH` in your shell startup files may work depending on your DRM - this is how we set up the environment for the [Public Galaxy Site](http://usegalaxy.org/) which runs TORQUE PBS.  However, this may not work for other DRMs such as Sun Grid Engine (SGE).  For SGE, please see the `-v` and `-V` options to [qsub](http://gridscheduler.sourceforge.net/htmlman/htmlman1/qsub.html) and how to set these in [sge_request](http://gridscheduler.sourceforge.net/htmlman/htmlman5/sge_request.html) or [the job runner URL](/admin/config/performance/cluster/).
 
 ### Managed Tool Dependencies