use https where possible

CONTRIBUTING.md

@@ -49,7 +49,7 @@ Once you are feeling more comfortable, you can propose changes to this training
 
 In [issues](https://github.com/galaxyproject/training-material/issues) and [project management system](https://github.com/galaxyproject/training-material/projects), you will find lists of issues to fix and features to change (with the "newcomer-friendly" label for example). Feel free to solve them.
 
-We strongly recommend you read and follow Software Carpentry's recommendations on [lesson design](https://swcarpentry.github.io/lesson-example/01-design/) and [lesson writing](http://swcarpentry.github.io/instructor-training/19-lessons/) if you plan to add or change some training materials, and also to check the [structure of the training material](#how-the-training-material-is-structured).
+We strongly recommend you read and follow Software Carpentry's recommendations on [lesson design](https://swcarpentry.github.io/lesson-example/01-design/) and [lesson writing](https://swcarpentry.github.io/instructor-training/19-lessons/) if you plan to add or change some training materials, and also to check the [structure of the training material](#how-the-training-material-is-structured).
 
 ## Pull Requests
 
@@ -98,7 +98,7 @@ The `images` directory collects all images/pictures needed for the training mate
 
 Images shared between several topics are in the `shared/images` directory at the root.
 
-All images for the slides must be in `images` directory. The images must be in good quality. The sources (`svg` or other) of the images must also be added to the `images` directory. We encourage you to use [yEd](http://www.yworks.com/products/yed) to easily generate diagrams and [Inkscape](https://inkscape.org/en/) for any other images.
+All images for the slides must be in `images` directory. The images must be in good quality. The sources (`svg` or other) of the images must also be added to the `images` directory. We encourage you to use [yEd](https://www.yworks.com/products/yed) to easily generate diagrams and [Inkscape](https://inkscape.org/en/) for any other images.
 
 ## `slides` directory
 
@@ -112,7 +112,7 @@ This directory collects the tutorials related to the topic, one per subdirectory
 
 The templates for the tutorials are different from the other pages to help users to focus on the content of the tutorial. To improve the output of the tutorial, several metadata are mandatory for every tutorials, such as the requirements or the objectives of the tutorials. Boxes are also used to highlight some key points as the hands-on or the tips.
 
-The content of each tutorial is generated with [Jekyll](http://jekyllrb.com/) from a Markdown file and some metadata (e.g. the requirements, the Zenodo link, the questions) defined inside the metadata of the related topic.
+The content of each tutorial is generated with [Jekyll](https://jekyllrb.com/) from a Markdown file and some metadata (e.g. the requirements, the Zenodo link, the questions) defined inside the metadata of the related topic.
 
 > Want to contribute to a tutorial?
 > - [Check out how to add a new tutorial?](#how-do-i-add-a-new-tutorial)
@@ -130,7 +130,7 @@ The `docker` image must also integrate a Galaxy tour from the [`galaxy-tours` re
 
 # How do I add new content?
 
-Most of the content is written in Markdown with some metadata (or variables) stored in YAML. To generate the website, we are using [Jekyll](http://jekyllrb.com/) and its templating system.
+Most of the content is written in Markdown with some metadata (or variables) stored in YAML. To generate the website, we are using [Jekyll](https://jekyllrb.com/) and its templating system.
 
 So if you want to visualise locally how the website will look like, you need to run a local Jekyll server. So, Jekyll must be installed using [RubyGems](https://rubygems.org/pages/download):
 
@@ -172,7 +172,7 @@ You can then visualize locally ([http://localhost:4000/](http://localhost:4000/)
     - `maintainers`: the two maintainers of the topic with their `name`, `github_username`, `email`
     - `contributors`: list of people who contributed to the topic with `name`, `github_username`, `email`
 
-    This information is used with [Jekyll](http://jekyllrb.com/) to generate the webpage related to the topic
+    This information is used with [Jekyll](https://jekyllrb.com/) to generate the webpage related to the topic
 
 3. Fill the introduction slides
 
@@ -200,7 +200,7 @@ You can then visualize locally ([http://localhost:4000/](http://localhost:4000/)
     - `time_estimation`: estimation of the time needed to complete the hands-on
     - `key_points`: take home messages
 
-    This information will appear in the top and bottom of the online hands-on generated using [Jekyll](http://jekyllrb.com/)
+    This information will appear in the top and bottom of the online hands-on generated using [Jekyll](https://jekyllrb.com/)
 
     ![](shared/images/tutorial_header.png)
 
@@ -223,7 +223,7 @@ You can then visualize locally ([http://localhost:4000/](http://localhost:4000/)
 
 2. Fill the `tutorial.md` with the tutorial
 
-The content of a tutorial hands-on is written in Markdown. They are rendered by [Jekyll](http://jekyllrb.com/) into the webpage for the tutorial.
+The content of a tutorial hands-on is written in Markdown. They are rendered by [Jekyll](https://jekyllrb.com/) into the webpage for the tutorial.
 
     The header of the file must be something like:
 

LICENSE.md

@@ -1 +1 @@
-This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.
+This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.

README.md

@@ -28,15 +28,15 @@ The Galaxy community offers many different ways of training. The table above lis
 
 # License
 
-This work is licensed under the [Creative Commons Attribution 4.0 International License](http://creativecommons.org/licenses/by/4.0/).
+This work is licensed under the [Creative Commons Attribution 4.0 International License](https://creativecommons.org/licenses/by/4.0/).
 
 # Acknowledgment and Funding
 
 We would like to thank all contributors to our Galaxy courses, especially those mentioned in the [Contributors list](CONTRIBUTORS.md), the Galaxy community for their constant support and our funding partners.
 
-<a href="http://www.denbi.de/"><img src="https://raw.githubusercontent.com/bgruening/rbc_docs/master/logo/deNBI_Logo_rgb.png" width="15%"></a> 	&emsp;<a href="http://www.sfb992.uni-freiburg.de/"><img src="https://raw.githubusercontent.com/bgruening/presentations/bce348bb606c312d531c479e63a66efc2bc38d44/shared/resources/img/MEDEP.jpg" width="15%"></a> 	&emsp;<a href="http://www.ie-freiburg.mpg.de"><img src="https://raw.githubusercontent.com/bgruening/presentations/master/shared/resources/img/14_MPI_IE_logo_mit_180.gif" width="15%"></a> 	&emsp;<a href="https://www.uni-freiburg.de/"><img src="https://raw.githubusercontent.com/bgruening/presentations/a2e38e4b007994af798320db3a0131c4bb891c0e/shared/resources/img/logo_freiburg.jpg" width="15%"></a>
+<a href="https://www.denbi.de/"><img src="https://raw.githubusercontent.com/bgruening/rbc_docs/master/logo/deNBI_Logo_rgb.png" width="15%"></a> 	&emsp;<a href="http://www.sfb992.uni-freiburg.de/"><img src="https://raw.githubusercontent.com/bgruening/presentations/bce348bb606c312d531c479e63a66efc2bc38d44/shared/resources/img/MEDEP.jpg" width="15%"></a> 	&emsp;<a href="http://www.ie-freiburg.mpg.de"><img src="https://raw.githubusercontent.com/bgruening/presentations/master/shared/resources/img/14_MPI_IE_logo_mit_180.gif" width="15%"></a> 	&emsp;<a href="https://www.uni-freiburg.de/"><img src="https://raw.githubusercontent.com/bgruening/presentations/a2e38e4b007994af798320db3a0131c4bb891c0e/shared/resources/img/logo_freiburg.jpg" width="15%"></a>
 <a href="https://wiki.galaxyproject.org/Teach/GTN"><img src="./shared/images/GTNLogo1000.png" width="15%"></a>
-<a href="http://www.france-bioinformatique.fr/"><img src="http://www.france-bioinformatique.fr/sites/default/files/ifb-logo_1.png" width="15%"></a> &emsp;
+<a href="https://www.france-bioinformatique.fr/"><img src="http://www.france-bioinformatique.fr/sites/default/files/ifb-logo_1.png" width="15%"></a> &emsp;
 ---
 
 You want to help us on this project? Please, see the [`CONTRIBUTING`](CONTRIBUTING.md) file.

_layouts/home.html

@@ -77,7 +77,7 @@ <h1>Acknowledgment and Funding</h1>
 
     <p>
       <a href="https://www.denbi.de/"><img src="https://raw.githubusercontent.com/bgruening/rbc_docs/master/logo/deNBI_Logo_rgb.png" width="15%" style="max-width:100%;"></a>
-      <a href="http://www.sfb992.uni-freiburg.de/"><img src="https://raw.githubusercontent.com/bgruening/presentations/bce348bb606c312d531c479e63a66efc2bc38d44/shared/resources/img/MEDEP.jpg" width="15%" style="max-width:100%;"></a>
+      <a href="https://www.sfb992.uni-freiburg.de/"><img src="https://raw.githubusercontent.com/bgruening/presentations/bce348bb606c312d531c479e63a66efc2bc38d44/shared/resources/img/MEDEP.jpg" width="15%" style="max-width:100%;"></a>
       <a href="https://www.ie-freiburg.mpg.de"><img src="https://raw.githubusercontent.com/bgruening/presentations/master/shared/resources/img/14_MPI_IE_logo_mit_180.gif" width="15%" style="max-width:100%;"></a>
       <a href="https://www.uni-freiburg.de/"><img src="https://raw.githubusercontent.com/bgruening/presentations/a2e38e4b007994af798320db3a0131c4bb891c0e/shared/resources/img/logo_freiburg.jpg" width="15%" style="max-width:100%;"></a>
       <br>

shared/literature.md

@@ -2,36 +2,36 @@
 
 ##Deep sequencing
 
-**Zentner and Henikoff (2012):** [Surveying the epigenomic landscape, one base at a time](http://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-10-250), (doi:10.1186/gb-2012-13-10-250) - Overview of popular *-seq techniques; very nice description of DNase-seq, MNase-seq, FAIRE-seq etc.
+**Zentner and Henikoff (2012):** [Surveying the epigenomic landscape, one base at a time](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-10-250), (doi:10.1186/gb-2012-13-10-250) - Overview of popular *-seq techniques; very nice description of DNase-seq, MNase-seq, FAIRE-seq etc.
 
 **Son and Taylor (2011):** [Preparing DNA Libraries for Multiplexed Paired-End Deep Sequencing for Illumina GA Sequencers](https://www.ncbi.nlm.nih.gov/pubmed/21400673), (doi:10.1002/9780471729259.mc01e04s20) - Paper on multiplexing; describes the individual steps of the Illumina deep sequencing protocols quite in detail
 
-**Illumina's technical report** - focuses on [Illumina's sequencing technology](http://www.illumina.com/technology.html); nice educative figures
+**Illumina's technical report** - focuses on [Illumina's sequencing technology](https://www.illumina.com/technology.html); nice educative figures
 
 ##NGS data formats
 
 - UCSC has a very good overview with brief descriptions of BED, bedGraph, bigWig etc.: https://genome.ucsc.edu/FAQ/FAQformat.html
 
-- [VCF format](http://gatkforums.broadinstitute.org/gatk/discussion/1268/how-should-i-interpret-vcf-files-produced-by-the-gatk) (encoding SNPs, indels etc.): Very readable, albeit not exhausting description
+- [VCF format](https://gatkforums.broadinstitute.org/gatk/discussion/1268/how-should-i-interpret-vcf-files-produced-by-the-gatk) (encoding SNPs, indels etc.): Very readable, albeit not exhausting description
 
 - Transcriptomes are often saved in [GFF3 format](https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md) (this is what TopHat needs, for example), but just to make things more complicated, GTF is another format used for transcriptome information, too
 
 
 ##Bioinformatic Tools (Linux, R, BEDTools etc.) - Manuals, courses, original papers
 
-- Why and how is bioinformatics software special? **Altschul et a. (2013)** [The anatomy of successful computational biology software](http://www.ncbi.nlm.nih.gov/pubmed/24104757), (doi:10.1038/nbt.2721) **(Highly recommended to read!)**
-- **Bild et al. (2014)** [A Field Guide to Genomics Research](http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001744), (doi:10.1371/journal.pbio.1001744) - Very readable introduction about the different caveats of genomics research (with cute cartoons!)
+- Why and how is bioinformatics software special? **Altschul et a. (2013)** [The anatomy of successful computational biology software](https://www.ncbi.nlm.nih.gov/pubmed/24104757), (doi:10.1038/nbt.2721) **(Highly recommended to read!)**
+- **Bild et al. (2014)** [A Field Guide to Genomics Research](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001744), (doi:10.1371/journal.pbio.1001744) - Very readable introduction about the different caveats of genomics research (with cute cartoons!)
 
 **Linux Command Line**
 
-- [Linux & Perl Primer for Biologists](http://korflab.ucdavis.edu/Unix_and_Perl/unix_and_perl_v3.1.1.html) - Very entertaining introduction to command line commands and perl scripts with a focus on bioinformatic application, i.e. handling of DNA sequences
+- [Linux & Perl Primer for Biologists](https://korflab.ucdavis.edu/Unix_and_Perl/unix_and_perl_v3.1.1.html) - Very entertaining introduction to command line commands and perl scripts with a focus on bioinformatic application, i.e. handling of DNA sequences
 - [Linux Tutorial for Beginners](http://www.ee.surrey.ac.uk/Teaching/Unix/) - Thorough, but concise online tutorial introducing the very basics of handling the Linux command line
-- [Writing Linux shell scripts](http://www.freeos.com/guides/lsst/index.html) - Useful for slightly more advanced Linux command line users
+- [Writing Linux shell scripts](https://www.freeos.com/guides/lsst/index.html) - Useful for slightly more advanced Linux command line users
 
 **R**
 
-- [Hands on R course](http://www.uwyo.edu/mdillon/hor.html) - For beginners - R is probably the most widely used open-source statistical software; through our epicenter website you can also access RStudio which provides are very nice interface to working and plotting with R. In fact, most of the plots generated within Galaxy are generated through R scripts, so if you're not happy with the default formats of the Galaxy graphs, definitely have a look at R yourself. The learning curve is steep, but it is worth it.
+- [Hands on R course](https://www.uwyo.edu/mdillon/hor.html) - For beginners - R is probably the most widely used open-source statistical software; through our epicenter website you can also access RStudio which provides are very nice interface to working and plotting with R. In fact, most of the plots generated within Galaxy are generated through R scripts, so if you're not happy with the default formats of the Galaxy graphs, definitely have a look at R yourself. The learning curve is steep, but it is worth it.
 
 **BEDTools**
 
-- [BEDTools Manual](http://bedtools.readthedocs.org) - When working with genomic intervals (e.g. genes, peaks, enriched regions...), BEDTools are invaluable! The manual is a very good read and we refer to it almost daily.
+- [BEDTools Manual](https://bedtools.readthedocs.org) - When working with genomic intervals (e.g. genes, peaks, enriched regions...), BEDTools are invaluable! The manual is a very good read and we refer to it almost daily.

topics/admin/slides/index.html

@@ -11,7 +11,7 @@
 
 ###  Several different ways
 
-- [Main](http://usegalaxy.org/) and [others](https://galaxyproject.org/public-galaxy-servers/) free public servers
+- [Main](https://usegalaxy.org/) and [others](https://galaxyproject.org/public-galaxy-servers/) free public servers
 - Run your [local instance](https://galaxyproject.org/admin/get-galaxy/) or a [docker](https://github.com/bgruening/docker-galaxy-stable) image
 - Use Galaxy on the [Cloud](https://galaxyproject.org/cloud/)
 - Get the SlipStream [Galaxy Appliance](https://bioteam.net/products/galaxy-appliance/)

topics/admin/tutorials/database-schema/tutorial.md

@@ -31,7 +31,7 @@ The session description is database centric and we’ll be focusing on the relat
 database that backs Galaxy servers.  But that’s only half the picture of the this data.
 The other is the object model which is the object-oriented view of this same data.
 The object model is used by the code to manipulate and access the database.
-The translation between the two worlds is handled by an object-relational mapping implemented with SQLAlchemy (http://www.sqlalchemy.org).
+The translation between the two worlds is handled by an object-relational mapping implemented with SQLAlchemy (https://www.sqlalchemy.org).
 
 Today we are covering the database and how to access it with SQL.  We aren’t going to cover the corresponding object model or object relational mapping.
 
@@ -55,7 +55,7 @@ What’s not in the database is the data. Datasets are stored outside the databa
 
 #### ER diagrams and SchemaSpy
 
-Entity-relationship diagrams are a way to understand tables and the relationships between them inside a relational database.  SchemaSpy (http://schemaspy.sourceforge.net/) is a free (and remarkable tool) for generating ER diagrams.  We’be used it generate a description of the database backing the server in this container.  See
+Entity-relationship diagrams are a way to understand tables and the relationships between them inside a relational database.  SchemaSpy (https://schemaspy.sourceforge.net/) is a free (and remarkable tool) for generating ER diagrams.  We’be used it generate a description of the database backing the server in this container.  See
 
     <!-- TODO: following link is broken, update with new link once fixed on Hub -->
     https://galaxyproject.org/schema/SchemaSpy/index.html
@@ -327,7 +327,7 @@ https://docs.google.com/presentation/d/1l4DD0IaJjuvk1zAT1Sjv26bLyrSOg3VUm7rD-TQl
 To run SchemaSpy in your container you’ll need to get it, and also install some required software packages.
 
 >   ```sh
->   wget http://downloads.sourceforge.net/project/schemaspy/schemaspy/SchemaSpy%205.0.0/schemaSpy_5.0.0.jar
+>   wget https://downloads.sourceforge.net/project/schemaspy/schemaspy/SchemaSpy%205.0.0/schemaSpy_5.0.0.jar
 >   apt-get update
 >   apt-get install libpostgresql-jdbc-java
 >   apt-get install graphviz

topics/admin/tutorials/dev-to-production/tutorial.md

@@ -63,7 +63,7 @@ To bind Galaxy to any avalaible network interface edit the config/galaxy.ini fil
 ## What did you just installed ?
 The galaxy you have just installed is configured with the following:
 
-- [SQLite](http://www.sqlite.org/): a servless database.
+- [SQLite](https://www.sqlite.org/): a servless database.
 - A built-in HTTP server, written in Python.
 
 The tools are run locally and the galaxy server itself run in a single process.

topics/admin/tutorials/galaxy-docker/slides.html

@@ -682,7 +682,7 @@
 docker run -i -t -p 8080:80 quay.io/bgruening
 ```
 
-http://bgruening.github.io/docker-galaxy-stable/
+https://bgruening.github.io/docker-galaxy-stable/
 
 ---
 

topics/assembly/tutorials/debruijn-graph-assembly/tutorial.md

@@ -7,7 +7,7 @@ tutorial_name: debruijn-graph-assembly
 # Optimised de Bruijn Graph assemblies using the Velvet Optimiser and SPAdes
 In this activity, we will perform *de novo* assemblies of a short read set using the Velvet Optimiser and the SPAdes assemblers. We are using the Velvet Optimiser for illustrative purposes. For real assembly work, a more suitable assembler should be chosen - such as SPAdes.
 
-The Velvet Optimiser is a script written by Simon Gladman to optimise the k-mer size and coverage cutoff parameters for Velvet. More information can be found [here](http://github.com/slugger70/VelvetOptimiser)
+The Velvet Optimiser is a script written by Simon Gladman to optimise the k-mer size and coverage cutoff parameters for Velvet. More information can be found [here](https://github.com/slugger70/VelvetOptimiser)
 
 SPAdes is a de novo genome assembler written by Pavel Pevzner's group in St. Petersburg. More details on it can be found [here](http://cab.spbu.ru/software/spades/)