Skip to 0 minutes and 2 seconds Hello. I’m Martin Aslett, IT Manager for Wellcome Genome Campus Advanced Courses and Scientific Conferences. In this video, we will learn how to install the genome browser Artemis on both a Windows PC and a Mac. We’ll start with the Windows PC. First thing to do is to download the software. To do this, I’ll go to my web browser and search for Artemis Sanger.
Skip to 0 minutes and 31 seconds This leads to the top hit, which is the page at the [Wellcome] Sanger Institute. This gives brief details of the software, and also about more advanced details of how to use Artemis. What we need to do is click on the GitHub link to download the software. GitHub is a repository for scientific software. This page contains more details of Artemis and other associated software. We need to scroll down to the Software Availability section of the page. Here, we can download the software. As I’m on a Windows PC, I will click the Windows link and save the file.
Skip to 1 minute and 9 seconds This may take a few seconds to download. Once this is done, I’ll minimise my browser and go to the software on the computer. I’ll now browse to my download folder on my PC, click on the Artemis Windows compressed file. You’ll notice there are four JAR files here, Act, Artemis, Bamview and DNAPlotter. We’re only interested in Artemis. For convenience, I will drag the Artemis file to my desktop. I can now just run this by clicking on the icon.
Skip to 1 minute and 47 seconds First thing we need to do is set up our working directory. I’ll leave this as the desktop. We now have the initial Artemis window. Having installed this on a Windows PC, we will now instal the software on a Mac. I’ll again, start by browsing to Sanger Artemis and click the link.
Skip to 2 minutes and 19 seconds Again, go to the GitHub page and scroll down to the software availability. This time, I’ll click on the Mac OS link. This is downloading and may take a while. With the download complete, I will now click on the DMG file which we have downloaded for the Mac and install this.
Skip to 2 minutes and 57 seconds We can either just click on the Artemis icon here, drag it to the Apps folder, or just drag it to the desktop to run it. I’ll copy it to the desktop.
Skip to 3 minutes and 11 seconds And then, I will just double click the Artemis icon to run the software.
Skip to 3 minutes and 23 seconds Macs often have a security issue with Artemis in that it comes from an unidentified developer. To fix this, simply go to your System Preferences, click on Security and Privacy, and click on the Open Anyway button.
Skip to 3 minutes and 49 seconds Artemis should now open.
Skip to 3 minutes and 54 seconds Again, we need to set our working directory. On a Mac, this defaults to the Java folder under the Artemis app directory. I want to change this to the desktop. To do this, I’ll simply browse, go to my home directory, and select the desktop.
Skip to 4 minutes and 17 seconds Now click on OK. Again, the Artemis window comes up. I’m Martin Aslett. In this video, we have shown you how to install Artemis on both a Windows PC and a Mac. Thank you for viewing. Please leave your suggestions and questions in the comments area.
Installing Artemis, the bacterial genome browser
In this Video Step, a Screencast Demonstration, you will learn how to download and install Artemis.
Artemis, named after the ancient Greek goddess of hunting, is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data, and the results of analyses within the context of the sequence, and its six-frame conceptual translation intro proteins.
Artemis is written in Java, and is available for UNIX, Macintosh (MAC) and Windows systems. It can read a number of different file formats including the most popular FASTA, GENBANK, GFF and EMBL.
Click here to visit the Artemis webpage on the Wellcome Sanger Institute website for more information about this software. If you wish, do join the email discussion list to keep updated with the newest additional functionalities of Artemis.
Click here to visit the Artemis download pages to download the latest version of Artemis.
Look for the ‘Software Availability’ section where you will find a version of Artemis for your operating system.
Note: To run the Artemis software effectively, you will require a computer (Windows, Mac or Linux) with 2GB RAM. The current version of Artemis requires version 11 of Java to run successfully. Java can be downloaded from this link. The previous version of Artemis will run with version 8 of Java and is available from the Wellcome Sanger Institute ftp site:
You may need to copy and paste the link in your internet browser.
Java 8 can be downloaded from this link.
Please also note that, in some academic organisations, you may be behind a firewall, restricting the software you can download, and also that, if using a work computer, you may not have administration rights for it, meaning you are unable to install Java. If either of these situations is true, please see your systems administrator.
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