From feab6e585f1e11be7cc0c770fae0e2c4a27e21b7 Mon Sep 17 00:00:00 2001 From: Nick Date: Thu, 21 Oct 2021 18:21:09 -0400 Subject: [PATCH] Another batch of internal links fixed. --- content/events/gcc2012/abstracts/index.md | 5 ++--- content/events/gcc2012/program/index.md | 8 ++++---- content/events/gcc2012/sponsorships/index.md | 2 +- content/galaxy-updates/2012-02/index.md | 4 +--- content/galaxy-updates/2012-03/index.md | 2 +- content/galaxy-updates/2012-04/index.md | 2 +- content/galaxy-updates/2013-02/index.md | 4 ++-- content/galaxy-updates/2013-03/index.md | 6 +++--- content/galaxy-updates/2014-05/index.md | 2 +- content/galaxy-updates/2016-03/index.md | 4 ++-- content/installingtooldependencypackages/index.md | 2 +- 11 files changed, 19 insertions(+), 22 deletions(-) diff --git a/content/events/gcc2012/abstracts/index.md b/content/events/gcc2012/abstracts/index.md index dc413c3b8b..0d114a2058 100644 --- a/content/events/gcc2012/abstracts/index.md +++ b/content/events/gcc2012/abstracts/index.md @@ -6,12 +6,11 @@ title: Abstract submission is now closed - -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.

+ # Session 1 ## State of the Galaxy diff --git a/content/events/gcc2012/program/index.md b/content/events/gcc2012/program/index.md index f529cb3031..94695ffa13 100644 --- a/content/events/gcc2012/program/index.md +++ b/content/events/gcc2012/program/index.md @@ -6,7 +6,7 @@ title: Program -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 |
*[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)*
*[NGS analysis for Biologists: experiences from the cloud](/events/gcc2012/abstracts/#ngs-analysis-for-biologists-experiences-from-the-cloud)*
Karen Reddy, Johns Hopkins University
| | 4:40 |
*[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)*
*[The Galaxy Visualization Framework](/events/gcc2012/abstracts/#the-galaxy-visualization-framework)*
[Jeremy Goecks](/people/jeremy-goecks/), Emory University
| | **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)***
Mike Lelivelt, Ion Torrent, Director of Bioinformatics and Software Products
[Ion Torrent](http://www.lifetechnologies.com/) Sponsor Presentation
*[PDF](/attachment:Documents/Presentations/GCC2012/Lelivelt.pdf), [PPT](/attachment:Documents/Presentations/GCC2012/Lelivelt.ppt), [Video](https://uic.sharestream.net/ssdcms/i.do?u=66878bd05a11401)*
| +| **5:15-6:15** | ***[Ion Torrent](http://www.lifetechnologies.com/): [Open, Accessible, Enabling](Events/GCC2012/Abstracts#Ion Torrent: Open, Accessible, Enabling)***
Mike Lelivelt, Ion Torrent, Director of Bioinformatics and Software Products
[Ion Torrent](http://www.lifetechnologies.com/) Sponsor Presentation
*[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)*
| | **7pm** | ***Conference Dinner @ [Haymarket Pub & Brwery](http://www.haymarketbrewing.com/)
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 | |
*[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)*
*Differential Expression with Diagnostic Plots using sam2counts and DESeq*
Nikhil Joshi, UC Davis
| | |
*[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*
*Galaxy-P*
Pratik Jagtap, University of Minnesota
| | |
*[Slides](https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2012/Lightning_Sandve.pdf), [Video](https://uic.sharestream.net/ssdcms/i.do?u=ea7962cd5bbf421)*
*The Genomic Hyperbrowser: Prove Your Point*
Geir Kjetil Sandve, University of Oslo
| -| |
*[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)*
*[ChemicalToolBox](/chemical-tool-box/)*
Björn Grüning, Albert-Ludwigs-University Freiburg
| +| |
*[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)*
*[ChemicalToolBox](/use/chemicaltoolbox/)*
Björn Grüning, Albert-Ludwigs-University Freiburg
| | **2:45**|
*[Video](https://uic.sharestream.net/ssdcms/i.do?u=ea7962cd5bbf421) (starts @ 12:35)*
**Closing Remarks**
[Anton Nekrutenko](/people/anton/), Penn State University, [James Taylor](/people/james-taylor/), Emory University
| | **2:55-3:15** | **Break** | -| **3:15-5:00** | **Session 8: Breakouts**
Moderator: Dave Clements, [Emory University](http://www.emory.edu/)
[Breakouts](/eents/gcc2012/program/breakouts/) | +| **3:15-5:00** | **Session 8: Breakouts**
Moderator: Dave Clements, [Emory University](http://www.emory.edu/)
[Breakouts](/events/gcc2012/program/breakouts/) | | **5:00** | **[2012 Galaxy Community Conference](/events/gcc2012/) ends** | diff --git a/content/events/gcc2012/sponsorships/index.md b/content/events/gcc2012/sponsorships/index.md index 227dbce94b..6d7d981347 100644 --- a/content/events/gcc2012/sponsorships/index.md +++ b/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 diff --git a/content/galaxy-updates/2012-02/index.md b/content/galaxy-updates/2012-02/index.md index c589529758..3cc4a68de7 100644 --- a/content/galaxy-updates/2012-02/index.md +++ b/content/galaxy-updates/2012-02/index.md @@ -4,8 +4,6 @@ title: February 2012 Galaxy Update
**Looking for the [March 2012 Galaxy Update](/galaxy-updates/2012-03/)? Click [here](/galaxy-updates/2012-03/).**
Sorry about the bad link in the email announcement! [Dave C](/people/dave-clements/)
- -
Galaxy Updates
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 outreach@galaxyproject.org and we'll include it in next month's update.
-April 2012 GMOD Meeting   ISMB 2012   2012 Galaxy Community Conference +April 2012 GMOD Meeting   ISMB 2012   2012 Galaxy Community Conference
## Upcoming Events and Deadlines diff --git a/content/galaxy-updates/2012-03/index.md b/content/galaxy-updates/2012-03/index.md index 5013a837b8..285f1db2da 100644 --- a/content/galaxy-updates/2012-03/index.md +++ b/content/galaxy-updates/2012-03/index.md @@ -49,7 +49,7 @@ Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll p ## Upcoming Events and Deadlines
-April 2012 GMOD Meeting   Informatics on High Throughput Sequencing Data Workshop Next-gen Sequencing in Evolutionary Biology Course ISMB 2012 +April 2012 GMOD Meeting   Informatics on High Throughput Sequencing Data Workshop Next-gen Sequencing in Evolutionary Biology Course ISMB 2012
### Deadlines diff --git a/content/galaxy-updates/2012-04/index.md b/content/galaxy-updates/2012-04/index.md index 689fa47e5f..1106f5d664 100644 --- a/content/galaxy-updates/2012-04/index.md +++ b/content/galaxy-updates/2012-04/index.md @@ -56,7 +56,7 @@ Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll p ## Upcoming Events and Deadlines
-April 2012 GMOD Meeting   Informatics on High Throughput Sequencing Data Workshop Next-gen Sequencing in Evolutionary Biology Course ISMB 2012 +April 2012 GMOD Meeting   Informatics on High Throughput Sequencing Data Workshop Next-gen Sequencing in Evolutionary Biology Course ISMB 2012
### Deadlines diff --git a/content/galaxy-updates/2013-02/index.md b/content/galaxy-updates/2013-02/index.md index 94942e69bd..e75dbb3206 100644 --- a/content/galaxy-updates/2013-02/index.md +++ b/content/galaxy-updates/2013-02/index.md @@ -141,7 +141,7 @@ The next [GalaxyAdmins meetup](/community/galaxy-admins/) will be Wednesday, Mar
Introduction to Galaxy Boot Camp @ UC Davis Bioinformatics Core ABRF 2013 -GMOD 2013 +GMOD 2013 2013 Galaxy Community Conference (GCC2013)
@@ -178,7 +178,7 @@ See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on the April 5-6 - 2013 GMOD Meeting + 2013 GMOD Meeting Cambridge, United Kingdom, immediately prior to Biocuration 2013 Dave Clements diff --git a/content/galaxy-updates/2013-03/index.md b/content/galaxy-updates/2013-03/index.md index c743bfb034..79d7ca3e53 100644 --- a/content/galaxy-updates/2013-03/index.md +++ b/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 -
GMOD 2013 +
GMOD 2013 Biocuration 2013
-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 April 5-6 - 2013 GMOD Meeting + 2013 GMOD Meeting Cambridge, United Kingdom, immediately prior to Biocuration 2013 Dave Clements diff --git a/content/galaxy-updates/2014-05/index.md b/content/galaxy-updates/2014-05/index.md index b98a596ddf..327e4f4efa 100644 --- a/content/galaxy-updates/2014-05/index.md +++ b/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
  -GMOD Online Training   +GMOD Online Training   GCC2014 early registration and abstract submission are now open 
diff --git a/content/galaxy-updates/2016-03/index.md b/content/galaxy-updates/2016-03/index.md index b38bfc0a18..20f278831b 100644 --- a/content/galaxy-updates/2016-03/index.md +++ b/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
-2016 GMOD meeting +2016 GMOD meeting
-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. diff --git a/content/installingtooldependencypackages/index.md b/content/installingtooldependencypackages/index.md index b189edb069..b1272061a4 100644 --- a/content/installingtooldependencypackages/index.md +++ b/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/)