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University of Hawaii System

STACKs Web Interface

Stacks Virtualbox Appliance Setup Instructions for Using the STACKs Web Interface

INSTALL VIRTUALBOX APPLIANCE

  1. Download virutalbox for MAC here https://www.virtualbox.org/wiki/Downloads
  2. Install virtualbox
  3. Download the stacks virtual image from the hawaii#UH-HPC1 or hawaii#UH-HPC2 globus endpoint at /lus/scratch/stacks-image/ubuntu-stacks.ova.zip
  4. Open virtualbox
  5. Got the “File” and select “Import Appliance”
    1. then select the downloaded ubuntu-stacks-disk1.vmdk file on your machine
  6. In the virtualbox “Oracle VM VirtualBox Manager” select the “ubuntu-stacks” from the left column
    1. Right click it and choose “Setting”
    2. Click the “Network” icon at the top of the dialog
      1. Make sure that “Adapter 1” has the “Attached to:” dropdown set to “Bridged Adapter”
      2. Make sure the “Name” is set to whatever internet input your machine is using – if you are using Wi-FI it should look like “en0:Wi-Fi (AirPort)”
    3. Click the “Shared Folders” icon at the top of the dialog
      1. click the small folder with a plus to the far right of the “Folder list” content pane
      2. Select a Folder page by clicking the dropdown and selecting “other”
        • Now either select a folder you want to share with the virtualbox appliance – this will allow you to share files between your MAC and the virtualbox appliance which will be necessary for your load data into the Stacks MySQL database
      3. Check the “Auto-mount” box and click “OK”
    4. Click the “OK” button on the Settings Dialog and it will save your settings and close
  7. Right click the “ubuntu-stacks” virtualbox appliance in the far left column again and select “start” and select “Normal Start”.  This will start the virtualbox appliance in a new window – let it boot up and it should get to a screen with a “guest” login page.
  8. To test that the appliance is passing it’s webserver back to your MAC open a browser.
    1. Go to http://168.105.95.173/stacks/
    2. The stacks web interface should load if it doesn’t log into the virtualbox appliance by clicking on the “ubuntu-stacks” window and logging in as the guest user with the password: guest.  If it did you can skip the three steps below.
      1. Click the “Activities” text in the upper left corner
      2. type “terminal” in the search box and then click the icon of the terminal

at the terminal prompt type “ifconfig”  the result will show all the network interfaces the virtualbox appliance has.  You only care about the “eth0” one.  Next to the “eth0” text there will be two lines the second line has “inet addr:” and next to it is the ip address that it has been assigned if it is not 168.105.95.173 then use that ip address in place of the ip address listed above in step 8a in the browser on your MAC instead of the 168.105.95.173 – hopefully the stack web interface will now be present.  If it is not contact uh-hpc-help@list.hawaii.edu to further troubleshoot the issue.

LOAD STACKS DATA FOR WEB INTERFACE VISUALIZATION

At this point you should have a working stacks web interface to display results from your stacks run you did on the HPC.

  1. Now you need to import the data from the stacks runs performed on the HPC or elsewhere.  NOTE that when running denovo_mapping.pl on the clusetr you do not use the “-B” flag to indicate a database instead your use the “-S” flag to indicate you are not using a database.
    1. First copy the files generated to your MAC into the folder you shared with the virtualbox appliance
    2. now click on the “ubuntu-stacks” virtualbox appliance window
      1. click the “Activities” text in the upper left and type “terminal” in the search box and click the terminal icon to launch the terminal application.
      2. In the terminal type “df -h” this will display all the mounted storage volumes the system has.  The shared folder show be listed on the left hand side and a root path starting with “/media/” should be present.
      3. Navigate to the “/media/somesharedfolder” and check that your data is there.
      4. Assuming it is you can then load the data into the stacks mysql database doing the following
        • First you must create an empty database with the correct structure for the data to go into
          • mysql -e “create database somename_radtags”
        • You must have each database name end with “_radtags” or else stacks will not see it in the web interface
        • Second you can load the data using load_radtags.pl
          • load_radtags.pl -D someoname_radtags -b 1 -p . -e “Some comment about the data I’m loading” -c
          • The above will load the data into the database.  The “-p” flag is followed by the path to the data if you used “cd” to be inside the same directory as you data you can use “.” otherwise use the path to your data
        • Lastly you need to index the data using the index_radtags.pl command
          • index_radtags.pl -D somename_radtags -c
        • Here is a tutorial for cleaning up data that shows how to load the files into the database as well http://catchenlab.life.illinois.edu/stacks/manual/#prun
  2. You can now go to the browser interface on you MAC and refresh your view of the stacks web application and the database should appear and you can drill down into your data.

MANAGING DATABASES WITH PHPMYADMIN

Also of Note: PhpMyAdmin is installed on the virtualbox appliance and can be accessed at the same ip address as the stacks application but instead of /stacks use /phpmyadmin. The phpmyadmin application will give you access to the MySQL database instance on the virtualbox appliance in a GUI manner. The username is: stacks_user and the password is: stackspassword. If at some point you get to many radtags databases loaded and you want to remove some you can use the phpmyadmin interface to easily delete them by clicking on a database after logging in and going to the “Operations” tab and find the “Delete database” link and clicking it – be aware that once you do this you can’t get it back.