Merge pull request #25 from sanger-pathogens/update-data-url

Convert FTP links to HTTP downloads

F1/introduction.md

@@ -5,7 +5,7 @@ Phylogenetic tree based on whole genome data tell us about the relationships of
 
 
 **Data files**
-<br/>We have provided data files required for this module, available for download [here](ftp://ftp.sanger.ac.uk/pub/pathogens/bactGen_training/f1/).
+<br/>We have provided data files required for this module, available for download [here](https://github.com/sanger-pathogens/bactgen-training-app/releases/download/v0.1.20-data/F1_Training_Data.zip).
 
 **Slack channel**
 <br/>Throughout the module, there will be questions referring you to answer or comment on the slack channel. Please note that this is a private slack channel and access is only for Juno and GPS2 project partners. If you are not part of these projects, you are more than welcome to undertake the modules, however there will be no support.

F1/microreact.md

@@ -7,7 +7,7 @@
 ### File formats
 Microreact allows users to upload and visualise their own data, with the user needing only to provide a phylogenetic tree (in .nwk format) and a metadata file (in .csv format). The newick (nwk) file format is a computer readable file produced by most tree-building programs. This text-based file details how to graphically display the relatedness of samples in a phylogenetic tree. To view what the text looks like you can open the file in TextEdit or BBEdit for macOS and notepad for Windows systems.
 
-From the files we have provided from the [repository](ftp://ftp.sanger.ac.uk/pub/pathogens/bactGen_training/f1/), open the **F1_tree.nwk** file provided. You will see a series of numbers and/or names in brackets/parentheses separated by a comma or colon. The first name (stm8 in this instance), is the name of a node relating to a sample. The colon (:) separates the name from the branch length (with or without a decimal point). Following that is a comma (,) which separates the node and the tree ends with a semicolon (;). More information on the newick file format can be found [here](https://en.wikipedia.org/wiki/Newick_format).
+From the files we have provided [here](https://github.com/sanger-pathogens/bactgen-training-app/releases/download/v0.1.20-data/F1_Training_Data.zip), open the **F1_tree.nwk** file provided. You will see a series of numbers and/or names in brackets/parentheses separated by a comma or colon. The first name (stm8 in this instance), is the name of a node relating to a sample. The colon (:) separates the name from the branch length (with or without a decimal point). Following that is a comma (,) which separates the node and the tree ends with a semicolon (;). More information on the newick file format can be found [here](https://en.wikipedia.org/wiki/Newick_format).
 
 The second file you will need as an input for microreact is the metadata file in csv format. You can create and edit the file in Microsoft Excel if you wish then ‘save as’ a CSV (UTF-8 comma delimited) file. Open the **F1_metadata.xls** file. You will notice, it only contains some very basic information including, ID, year, Month and address. Sometimes this is the only information provided. Before we can use it in microreact, we have to add a few things to display useful information and make it compatible with the software.
 

F1/phandango.md

@@ -36,7 +36,7 @@ When you are ready to save the image you can either take a screenshot or press _
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 ### Visualising grouped data
-The advantage of using phandango to visualise metadata, is that you can quickly look at genetic attributes of your samples. In this next section we are going to visualise predicted antimicrobial resistance (AMR) gene data. You will need the **F1_resistance_data.xls** file which you can download from [here](ftp://ftp.sanger.ac.uk/pub/pathogens/bactGen_training/f1/). Included are the resistance profiles for three acquired genes, _aadA2_, _cmlA_ and _sul_, normally found on plasmids and are subject to [horizontal gene transfer](https://en.wikipedia.org/wiki/Horizontal_gene_transfer) (HGT). This means these plasmid located genes can be transferred between other bacterial cells nearby by a process known as conjugation. The remaining gene, _gyrA_, is located on the chromosome of the bacteria. 
+The advantage of using phandango to visualise metadata, is that you can quickly look at genetic attributes of your samples. In this next section we are going to visualise predicted antimicrobial resistance (AMR) gene data. You will need the **F1_resistance_data.xls** file which you can download from [here](https://github.com/sanger-pathogens/bactgen-training-app/releases/download/v0.1.20-data/F1_Training_Data.zip). Included are the resistance profiles for three acquired genes, _aadA2_, _cmlA_ and _sul_, normally found on plasmids and are subject to [horizontal gene transfer](https://en.wikipedia.org/wiki/Horizontal_gene_transfer) (HGT). This means these plasmid located genes can be transferred between other bacterial cells nearby by a process known as conjugation. The remaining gene, _gyrA_, is located on the chromosome of the bacteria. 
 We are going to format the table to visualise the AMR data. The resistance profile is denoted by two letters, _R_ and _S_, which stand for resistant, meaning the sample possesses the gene conferring resistance, and sensitive, meaning it lacks the gene. For some information it would be a good idea to group the data to look for similarities in the samples. We will group them by colour. Phandango accepts multiple ways to group samples by colour. More information can be found [here](https://github.com/jameshadfield/phandango/wiki/Input%20data%20formats). However to customise the data we will add HEX values in a separate column as in the example below. You may find this method more useful if you need to transfer the data across to other platforms such as microreact with minimal editing. As with the microreact metadata sheet, the column header must start with the same name and add ‘<span style="font-family:papyrus">:colour</span>’ to the name. Use [colorpicker](https://www.webfx.com/web-design/color-picker/) to select suitable colours to group _R_ and _S_.
 
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