1. When you boot your VM and go to the designated IP address, you will see the initial page for the site.
2. You can sign into the browser as an administrator (required for set up) by clicking the Log In button at the top of the page.
3. Once you log in, you will see the page changes a bit. You will now see a set of tabs at the top of the page, which we will discuss later. The default username is: Browser_user and the default password is: Browsers4All!
4. If you click "Log In" again, it will take you to your profile page.
5. If you click Edit, you will see the information below - this allows you to reset your password, and set you email! You should do this, as all browsers are seeded with the same password, meaning anyone could sign in if you do not change it.
6. You are now ready to set up your Browser. Click Genome Browsers, then Add A Reference.
7. There are two options for loading a reference. You can upload the file through the web (only works for small files), or preload the file to the server. We will show you both. Either way, NOTE THE NAME YOU GIVE THE BROWSER - you will need it to add tracks.
If you prefer to preload the file (recommended for large files!!), use the terminal on your computer to send files to the server. You can do this with rsync. The format for the command is "rsync -a --rsync-path="sudo -u www-data rsync" LOCAL/FILE/LOCATION www/html/jbrowse/uploads".
Then, simply tell the webform what you called your file (THIS MUST BE EXACT), and indicate that it has been preloaded.
You will get a message saying that the file was found or that the file was uploaded. You can then follow the link the new browser or add tracks to the new browser. You may want to copy the link to your browser and save it to your notes - you will need it to link from the website later.
Your browser will look rather blank at this point!
8. To add tracks, click back, and follow the link given to add tracks. You can also get here by clicking Genome Browsers, then Add a Track. Again, you can upload files via the web, or preload them the same way you did for the reference.
You will see a success or error page next. If you have success, you can follow the link to your browser to see the new track. This is recommended, as it guarentees the track loaded. If you don't see the track, you may have to clear your browser cache - JBrowse does a LOT of caching to go faster.
You can click back and use the same file name to load another track. While this makes little sense in this example, it is helpful if you have multiple versions of a browser - say a locked down version for unpublished data and a public version. Here we use the same file to demonstrate the presupload function.
9. To remove a track, you have to go to Genome Browser, then Delete a Track.
1. After you have a browser, you can set up a blast server and link it to the JBrowse you just built - allowing your blast hits to be visualized on the browser! Go to Either Genome Browser or Tools, then Add a BLAST DB. You can use upload the file (as shown below) or you can use a reference fasta that you used to create the browser (it is preloaded!).
2. This will return to you a location of the browser file, which you will need to add to the site. This is done through "Add content" in the top left corner, then Add a Blast Database. Add the information you just received.
3. To use blast, either go to YOURIP/blast or click Tools, then Blast Server.
Select the blast type you wish to use. Blastn is the only preloaded option, you will have to make appropriate databased for your data if you wish to use other types.
4. Each blast type has a page for loading data, for using input data, and specifying options. All blast databases loaded with the correct type (( i.e. nucleotide for blast n), will automatically be listed in the drop box at the bottom. More options for fine tuning your blast job are listed under advanced options.
5. Once you hit submit, you job will go to the queue. You can ignore the information in the pink box, it is a result of the admin user not having a defined location at initial set up.
Your page will refresh regularly, and you will see messages telling you the status of your job.
6. You will get results that look like this. You can download any number of formats for the output from the top. You can also expand the results to see the alignment on the page. You can also pull up previous recent jobs.
You can also visualize your results on jbrowse if you loaded the browser through the above tool. This link will only show up if the blast database was linked to a jbrowse instance. Follow the link, click on the Blast Results Track, and you can see your results!
1. You will want to control who has access to your browsers, who can add tracks, and certainly who can remove tracks. To do that, there are a couple ways that permissions are controlled. For "basic" pages - ones you create through the "Add Content" form, or menu pages that are premade - you can click the "Grant button above any page.
This will bring up a form that allows you to decide who can see what. Administrators are defined when accounts are set up (more later), authenticated users are users that can sign in, and anonymous users are anyone showing up at the page (basically "public"). These functions are managed through Node Access - more information can be found here.
You can add people or change their role through the "People" tab on the Admin menu.
You can also change the permissions for any module using the "permissions" tab in the top right hand side of this form.
If you scroll all the way to the bottom, you will see the permission controls for the browser and blast tools.
1. You can edit any "Basic" page by clicking "Edit" at the top of the page (by View and Grant).
You can edit pages as full HTML, PHP, plain text, etc. The pages here are done in HTML and PHP to allow features like buttons. There is an example of how to make new buttons at the bottomw of the Tools page, or you can copy and paste the ones you already have. Google is a wonderful source for developing new functions or adding new content to these pages (images, etc).