Merge pull request #961 from NickSto/internal-link-repair3

Another batch of internal links fixed.

content/events/gcc2012/abstracts/index.md

@@ -6,12 +6,11 @@ title: Abstract submission is now closed
 <slot name="/events/gcc2012/linkbox" />
 
 
-
-Abstracts for talks that were presented at the [GCC2012 main sessions](/events/gcc2012/abstracts/Program/).  See [Training Day](/events/gcc2012/training-day/) for training abstracts.
-
+Abstracts for talks that were presented at the [GCC2012 main sessions](/events/gcc2012/program/).  See [Training Day](/events/gcc2012/training-day/) for training abstracts.
 
 
 <br /><br />
+
 # Session 1
 
 ## State of the Galaxy

content/events/gcc2012/program/index.md

@@ -6,7 +6,7 @@ title: Program
 
 <slot name="/events/gcc2012/linkbox" />
 
-The [2012 Galaxy Community Conference](/events/gcc2012/program//) included two full days of accepted talks, [lightning talks](/events/gcc2012/program/LightningTalks/), breakout sessions, and networking time.  The conference was preceded by a full day of training sessions that cover 10 topics over four 90 minute sessions.
+The [2012 Galaxy Community Conference](/events/gcc2012/program/) included two full days of accepted talks, [lightning talks](/events/gcc2012/lightning-talks/), breakout sessions, and networking time.  The conference was preceded by a full day of training sessions that cover 10 topics over four 90 minute sessions.
 
 ### Summaries
 
@@ -108,7 +108,7 @@ The main meeting started on Thursday, July 26, and featured submitted talks from
 | 4:20  | <div class="float-right"> *[PDF](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Reddy.pdf), [PPTX](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Reddy.pptx), [Video part 1](https://uic.sharestream.net/ssdcms/i.do?u=a6208a4628164b7) (starts @ 35:30), [part 2](https://uic.sharestream.net/ssdcms/i.do?u=6b93204632704bd)* </div> *[NGS analysis for Biologists: experiences from the cloud](/events/gcc2012/abstracts/#ngs-analysis-for-biologists-experiences-from-the-cloud)* <div class='indent'> Karen Reddy, Johns Hopkins University </div>  |
 | 4:40  | <div class="float-right"> *[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Goecks.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=6b93204632704bd) (starts @ 8:40)* </div> *[The Galaxy Visualization Framework](/events/gcc2012/abstracts/#the-galaxy-visualization-framework)* <div class='indent'> [Jeremy Goecks](/people/jeremy-goecks/), Emory University </div>  |
 | **5:00-5:15** | **Break** |
-| **5:15-6:15** | ***[Ion Torrent](http://www.lifetechnologies.com/): [Open, Accessible, Enabling](Events/GCC2012/Abstracts#Ion Torrent: Open, Accessible, Enabling)*** <br /> <div class="indent"> Mike Lelivelt, Ion Torrent, Director of Bioinformatics and Software Products<br />[Ion Torrent](http://www.lifetechnologies.com/) Sponsor Presentation<br /> *[PDF](/attachment:Documents/Presentations/GCC2012/Lelivelt.pdf), [PPT](/attachment:Documents/Presentations/GCC2012/Lelivelt.ppt), [Video](https://uic.sharestream.net/ssdcms/i.do?u=66878bd05a11401)* </div> |
+| **5:15-6:15** | ***[Ion Torrent](http://www.lifetechnologies.com/): [Open, Accessible, Enabling](Events/GCC2012/Abstracts#Ion Torrent: Open, Accessible, Enabling)*** <br /> <div class="indent"> Mike Lelivelt, Ion Torrent, Director of Bioinformatics and Software Products<br />[Ion Torrent](http://www.lifetechnologies.com/) Sponsor Presentation<br /> *[PDF](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lelivelt.pdf), [PPT](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lelivelt.ppt), [Video](https://uic.sharestream.net/ssdcms/i.do?u=66878bd05a11401)* </div> |
 | **7pm** | ***Conference Dinner @ [Haymarket Pub & Brwery](http://www.haymarketbrewing.com/)<br />Sponsored by [Ion Torrent](http://www.lifetechnologies.com/)*** |
 
 ### Day 2: July 27, Friday
@@ -141,10 +141,10 @@ The main meeting started on Thursday, July 26, and featured submitted talks from
 |  | <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> |
 | **2:45**| <div class="float-right"> *[Video](https://uic.sharestream.net/ssdcms/i.do?u=ea7962cd5bbf421) (starts @ 12:35)* </div>  **Closing Remarks**<div class="indent"> [Anton Nekrutenko](/people/anton/), Penn State University, [James Taylor](/people/james-taylor/), Emory University</div> |
 | **2:55-3:15** | **Break** |
-| **3:15-5:00** | **Session 8: Breakouts**<br />Moderator: Dave Clements, [Emory University](http://www.emory.edu/) <br /> [Breakouts](/eents/gcc2012/program/breakouts/) |
+| **3:15-5:00** | **Session 8: Breakouts**<br />Moderator: Dave Clements, [Emory University](http://www.emory.edu/) <br /> [Breakouts](/events/gcc2012/program/breakouts/) |
 | **5:00** | **[2012 Galaxy Community Conference](/events/gcc2012/) ends** |
 
 <slot name="/events/gcc2012/ask-the-organizers" />

content/events/gcc2012/sponsorships/index.md

@@ -90,7 +90,7 @@ If your organization is interested in participating in [GCC 2012](/events/gcc201
 
 ## About GCC 2012
 
-The *Galaxy Community Conference* is the [Galaxy Project's](http://galaxyproject.org/) annual community gathering.  GCC 2012 will be the third annual meeting.  Attendance doubled between the first meeting in [2010 (Cold Spring Harbor Laboratories)](/events/gcc2012/GDC2010/) and [2011 (Lunteren, the Netherlands)](https://galaxyproject.org/gcc2011/), and we expect attendance to double again this year to nearly 300 participants.  Participants mainly come from these groups:
+The *Galaxy Community Conference* is the [Galaxy Project's](http://galaxyproject.org/) annual community gathering.  GCC 2012 will be the third annual meeting.  Attendance doubled between the first meeting in [2010 (Cold Spring Harbor Laboratories)](/events/gdc2010/) and [2011 (Lunteren, the Netherlands)](/events/gcc2011/), and we expect attendance to double again this year to nearly 300 participants.  Participants mainly come from these groups:
 * Sequencing core facility staff
 * Bioinformatics core staff
 * Bioinformatics tool and workflow developers

content/galaxy-updates/2012-02/index.md

@@ -4,8 +4,6 @@ title: February 2012 Galaxy Update
 <div class='center'>**Looking for the [March 2012 Galaxy Update](/galaxy-updates/2012-03/)?  Click [here](/galaxy-updates/2012-03/).**<br />Sorry about the bad link in the email announcement!  [Dave C](/people/dave-clements/)</div>
 
 
-
-
 <div class='left'><a href='/galaxy-updates/'><img src="/images/logos/GalaxyUpdate200.png" alt="Galaxy Updates" width=150 /></a></div>
 
 Welcome to the inaugural edition of *[Galaxy Update](/galaxy-updates/)*, a (mostly) monthly summary of what is going on in the Galaxy community.  Galaxy Updates will complement the *[Galaxy Development News Briefs](/docs/)* which accompany new Galaxy releases and focus on Galaxy code updates.
@@ -36,7 +34,7 @@ Plus [27 other papers](http://www.citeulike.org/group/16008/library) that use, r
 Got a Galaxy-related opening?  Send it to [email protected] and we'll include it in next month's update.
 
 <div class='right'>
-<a href='/gmod:April 2012 GMOD Meeting/'><img src="/images/logos/GMODApril2012Logo.png" alt="April 2012 GMOD Meeting" height=100 /></a>&nbsp;&nbsp; <a href='http://www.iscb.org/ismb2012'><img src="/images/logos/ISMB2012.jpg" alt="ISMB 2012" height=105 /></a>&nbsp;&nbsp; <a href='/events/gcc2012/'><img src="/images/galaxy-logos/GCC2012Logo200.png" alt="2012 Galaxy Community Conference" height="100" /></a>
+<a href='http://gmod.org/wiki/April_2012_GMOD_Meeting'><img src="/images/logos/GMODApril2012Logo.png" alt="April 2012 GMOD Meeting" height=100 /></a>&nbsp;&nbsp; <a href='http://www.iscb.org/ismb2012'><img src="/images/logos/ISMB2012.jpg" alt="ISMB 2012" height=105 /></a>&nbsp;&nbsp; <a href='/events/gcc2012/'><img src="/images/galaxy-logos/GCC2012Logo200.png" alt="2012 Galaxy Community Conference" height="100" /></a>
 </div>
 
 ## Upcoming Events and Deadlines

content/galaxy-updates/2012-03/index.md

@@ -49,7 +49,7 @@ Got a Galaxy-related opening?  Send it to [email protected] and we'll p
 ## Upcoming Events and Deadlines
 
 <div class='center'>
-<a href='/gmod:April 2012 GMOD Meeting/'><img src="/images/logos/GMODApril2012Logo.png" alt="April 2012 GMOD Meeting" height=100 /></a>&nbsp;&nbsp; <a href='http://bioinformatics.ca/workshops/high_throughput'><img src="/images/logos/CanadianBioinfWorkshopsLog.png" alt="Informatics on High Throughput Sequencing Data Workshop" height=100 /></a>  <a href='https://www.nescent.org/sites/academy/Next-gen_sequencing'><img src="/images/logos/NESCentAcademyLogo.png" alt="Next-gen Sequencing in Evolutionary Biology Course" height="100" /></a> <a href='http://www.iscb.org/ismb2012'><img src="/images/logos/ISMB2012.jpg" alt="ISMB 2012" height=100 /></a>
+<a href='http://gmod.org/wiki/April_2012_GMOD_Meeting'><img src="/images/logos/GMODApril2012Logo.png" alt="April 2012 GMOD Meeting" height=100 /></a>&nbsp;&nbsp; <a href='http://bioinformatics.ca/workshops/high_throughput'><img src="/images/logos/CanadianBioinfWorkshopsLog.png" alt="Informatics on High Throughput Sequencing Data Workshop" height=100 /></a>  <a href='https://www.nescent.org/sites/academy/Next-gen_sequencing'><img src="/images/logos/NESCentAcademyLogo.png" alt="Next-gen Sequencing in Evolutionary Biology Course" height="100" /></a> <a href='http://www.iscb.org/ismb2012'><img src="/images/logos/ISMB2012.jpg" alt="ISMB 2012" height=100 /></a>
 </div>
 
 ### Deadlines

content/galaxy-updates/2012-04/index.md

@@ -56,7 +56,7 @@ Got a Galaxy-related opening?  Send it to [email protected] and we'll p
 ## Upcoming Events and Deadlines
 
 <div class='center'>
-<a href='/gmod:April 2012 GMOD Meeting/'><img src="/images/logos/GMODApril2012Logo.png" alt="April 2012 GMOD Meeting" height=100 /></a>&nbsp;&nbsp; <a href='http://bioinformatics.ca/workshops/high_throughput'><img src="/images/logos/CanadianBioinfWorkshopsLog.png" alt="Informatics on High Throughput Sequencing Data Workshop" height=100 /></a>  <a href='https://www.nescent.org/sites/academy/Next-gen_sequencing'><img src="/images/logos/NESCentAcademyLogo.png" alt="Next-gen Sequencing in Evolutionary Biology Course" height="100" /></a> <a href='http://www.iscb.org/ismb2012'><img src="/images/logos/ISMB2012.jpg" alt="ISMB 2012" height=100 /></a>
+<a href="http://gmod.org/wiki/April_2012_GMOD_Meeting"><img src="/images/logos/GMODApril2012Logo.png" alt="April 2012 GMOD Meeting" height=100 /></a>&nbsp;&nbsp; <a href='http://bioinformatics.ca/workshops/high_throughput'><img src="/images/logos/CanadianBioinfWorkshopsLog.png" alt="Informatics on High Throughput Sequencing Data Workshop" height=100 /></a>  <a href='https://www.nescent.org/sites/academy/Next-gen_sequencing'><img src="/images/logos/NESCentAcademyLogo.png" alt="Next-gen Sequencing in Evolutionary Biology Course" height="100" /></a> <a href='http://www.iscb.org/ismb2012'><img src="/images/logos/ISMB2012.jpg" alt="ISMB 2012" height=100 /></a>
 </div>
 
 ### Deadlines

content/galaxy-updates/2013-02/index.md

@@ -141,7 +141,7 @@ The next [GalaxyAdmins meetup](/community/galaxy-admins/) will be Wednesday, Mar
 <div class='center'>
 <a href='http://bit.ly/UFefFx'><img src="/images/logos/UCDavisGenomeCenterLogo.jpg" alt="Introduction to Galaxy Boot Camp @ UC Davis Bioinformatics Core" height="80" /></a>
 <a href='http://conf.abrf.org/'><img src="/images/logos/ABRF2013LogoSquare300.png" alt="ABRF 2013" height="80" /></a>
-<a href='/gmod:April_2013_GMOD_Meeting/'><img src="/images/logos/GMOD2013Logo240.png" alt="GMOD 2013" height="80" /></a>
+<a href='http://gmod.org/wiki/April_2013_GMOD_Meeting'><img src="/images/logos/GMOD2013Logo240.png" alt="GMOD 2013" height="80" /></a>
 <a href='/events/gcc2013/'><img src="/images/logos/GCC2013Logo200.png" alt="2013 Galaxy Community Conference (GCC2013)" width="135px" /></a>
 </div>
 
@@ -178,7 +178,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the
   </tr>
   <tr>
     <th> April 5-6 </th>
-    <td> <em><a href='http://gmod.org/wiki/April 2013 GMOD Meeting'>2013 GMOD Meeting</a></em> </td>
+    <td> <em><a href='http://gmod.org/wiki/April_2013_GMOD_Meeting'>2013 GMOD Meeting</a></em> </td>
     <td> Cambridge, United Kingdom, immediately prior to <a href='http://www.ebi.ac.uk/biocuration2013/'>Biocuration 2013</a> </td>
     <td> <a href='/people/dave-clements/'>Dave Clements</a> </td>
   </tr>

content/galaxy-updates/2013-03/index.md

@@ -114,10 +114,10 @@ See the [meetup page](/community/galaxy-admins/meetups/2013-03-20/) for details.
 
 ## Galaxy at GMOD 2013 and Biocuration 2013
 
-<div class='right'> <a href='/gmod:April_2013_GMOD_Meeting/'><img src="/images/logos/GMOD2013Logo240.png" alt="GMOD 2013" height="80" /></a>
+<div class='right'> <a href='http://gmod.org/wiki/April_2013_GMOD_Meeting'><img src="/images/logos/GMOD2013Logo240.png" alt="GMOD 2013" height="80" /></a>
 <a href='http://www.ebi.ac.uk/biocuration2013/content/workshop-descriptions'><img src="/images/logos/ISBLogoWAcronym223.png" alt="Biocuration 2013" height="70" /></a></div>
 
-Galaxy will [have a presence](/news/galaxy-gmod-biocuration2013/) at both the [GMOD 2013](http://gmod.org/wiki/April 2013 GMOD Meeting) and [Biocuration 2013](http://www.ebi.ac.uk/biocuration2013/home).  Both are being held in Cambridge, UK in early April.  If you are interested in either community, then it would be great to see you there.
+Galaxy will [have a presence](/news/galaxy-gmod-biocuration2013/) at both the [GMOD 2013](http://gmod.org/wiki/April_2013_GMOD_Meeting) and [Biocuration 2013](http://www.ebi.ac.uk/biocuration2013/home).  Both are being held in Cambridge, UK in early April.  If you are interested in either community, then it would be great to see you there.
 
 GMOD is also running a [community-wide survey](http://gmod.org/survey.html) through March 1. The survey "aims to find out how you are using GMOD, what you find useful (or otherwise), what support you need, and some information on the GMOD components you use." The survey results will be published and past surveys have been extremely useful to the project.  If that's not enough motivation, you can enter to win a free genome profile from 23andMe.
 
@@ -174,7 +174,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the
   </tr>
   <tr>
     <th> April 5-6 </th>
-    <td> <em><a href='http://gmod.org/wiki/April 2013 GMOD Meeting'>2013 GMOD Meeting</a></em> </td>
+    <td> <em><a href='http://gmod.org/wiki/April_2013_GMOD_Meeting'>2013 GMOD Meeting</a></em> </td>
     <td> Cambridge, United Kingdom, immediately prior to <a href='http://www.ebi.ac.uk/biocuration2013/'>Biocuration 2013</a> </td>
     <td> <a href='/people/dave-clements/'>Dave Clements</a> </td>
   </tr>

content/galaxy-updates/2014-05/index.md

@@ -202,7 +202,7 @@ And don't worry if you are not near Norwich or Edinburgh in May.  There are [at
 
 <div class='center'> 
 <a href='/events/uk-may2014/'><img src="/images/logos/UKMay2014Tour.png" alt="" height="80" /></a>&nbsp;
-<a href='/gmod:GMOD_Online_Training_2014/'><img src="/images/logos/GMODOnlineTraining2014.png" alt="GMOD Online Training" height="80" /></a> &nbsp;
+<a href='http://gmod.org/wiki/GMOD_Online_Training_2014'><img src="/images/logos/GMODOnlineTraining2014.png" alt="GMOD Online Training" height="80" /></a> &nbsp;
 <a href='/events/gcc2014/'><img src="/images/logos/GCC2014LogoWide200.png" alt="GCC2014 early registration and abstract submission are now open" height="75" /></a>&nbsp;
 
 </div>

content/galaxy-updates/2016-03/index.md

@@ -196,10 +196,10 @@ We will do our best to coordinate and make this hackathon a nice and productive
 ## GMOD Meeting, June 30 - July 1
 
 <div class='right'>
-<a href='/gmod:Jun_2016_GMOD_Meeting/'><img src="/images/logos/GMODLogo.png" alt="2016 GMOD meeting" width="160" /></a>
+<a href='http://gmod.org/wiki/Jun_2016_GMOD_Meeting'><img src="/images/logos/GMODLogo.png" alt="2016 GMOD meeting" width="160" /></a>
 </div>
 
-The [2016 GMOD meeting](http://gmod.org/wiki/Jun_2016_GMOD_Meeting) will be held **immediately following GCC2016 and in the same venue as GCC2016**.  [http://gmod.org/wiki/|GMOD](http://gmod.org/wiki/|GMOD) is a consortium of open-source software project, including Galaxy, that address common challenges with biological data.  Other projects in the GMOD consortium include 
+The [2016 GMOD meeting](http://gmod.org/wiki/Jun_2016_GMOD_Meeting) will be held **immediately following GCC2016 and in the same venue as GCC2016**.  [GMOD](http://gmod.org/wiki/GMOD) is a consortium of open-source software project, including Galaxy, that address common challenges with biological data.  Other projects in the GMOD consortium include 
 * [Tripal](http://gmod.org/wiki/Tripal): A web front end for [Chado](http://gmod.org/wiki/Chado) databases.  Galaxy is working with the Tripal project to make Galaxy be Tripal's analysis engine.
 * [JBrowse](http://gmod.org/wiki/JBrowse): A client-side genome browser and successor to the venerable [http://gmod.org/wiki/GBrowse](http://gmod.org/wiki/GBrowse).  [JBrowse as a Galaxy Tool](http://gcc2015.tsl.ac.uk/Lightning/#JBrowse_as_a_Galaxy_Tool) was presented by Helena Rasche at [GCC2015](http://gcc2015.tsl.ac.uk/). Ian Holmes, the JBrowse PI, has put JBrowse-Galaxy integration  at "top of the list" for JBrowse's infrastructure upcoming infrastructure work.
 * [MAKER](http://gmod.org/wiki/MAKER): A genome annotation pipeline that integrates several gene annotation engines, and combines them to produce annotation that is better than any individual tool produces.  A [MAKER-Galaxy](https://depot.galaxyproject.org/hub/attachments/documents/posters/ISMB2014_Kandalaft_GenomeAnnotation.pdf) by Agriculture and Agri-Food Canada was presented at ISMB 2014.

content/installingtooldependencypackages/index.md

@@ -2,7 +2,7 @@
 
 [Installing and compiling tool dependency packages](/toolshed/installing-and-compiling-packages/)
 
-[Installing tool dependencies with initial repository installation](/tool-dependencies-with-initial-install/)
+[Installing tool dependencies with initial repository installation](/toolshed/tool-dependencies-with-initial-install/)
 
 [Updating an installed repository to a revision with defined tool dependencies](/updating-to-revision-with-new-tool-dependencies/)