Installing SeqMonk ------------------- Windows ------- Download the seqmonk zip file, and unzip it on your machine. Windows has a virtual filesystem view of zip files which allows you to look at the contents in windows explorer without actually unzipping the file - this isn't enough to run seqmonk, you need to right click on the zip file and extract the contents to a conventional folder. Once you've done that just double click seqmonk.exe to run the program. You may find that the first time you run the app you get a Windows Smart Screen dialog saying that the app has been blocked. You may be able to click on the button which says "Run anyway", or you might have to click on a link to "more information" and then click on the button which says "Run anyway". You only need to do this once and the app will be allowed to run after that. MacOS ----- SeqMonk is distributed as a dmg file which is a virtual filesystem on a mac. Just download the dmg file and double click on it. You will see the seqmonk app appear in a finder window. Simply drag it from there to your Applications folder to install it. If you don't have administrator rights on your Mac then you can drag SeqMonk to any other folder to run it, but you will then only be able to read and save data to your home directory. Since seqmonk is not a signed application, the first time you want to launch it right click (or control click) on the app and select Open (rather than double clicking). You should then be prompted as to whether you trust this application. If you say yes then you will be able to open it by double clicking in future. If the app doesn't open then go to your OS preferences and look in the security section. There will be a message saying that the app was blocked, and giving you an option to unblock it. Once you've done that then it will work as normal. When first installed, the security settings on OSX will restrict which parts of your filesystem seqmonk can read from (only your home directory by default). If seqmonk detects that it has only limited ability to read the filesystem it will put a notification on the welcome screen with a pointer to instructions to grant it more permissions if you want this. Linux ----- On linux seqmonk is distributed as a tar.gz file which contains a launch script and an embedded java runtime. You will need to extract the program from the tar file using something like: tar -xzf seqmonk_v1.45.0_linux64.tar.gz ..but using whatever the file you downloaded is called. You can then run the program by using the launcher. cd SeqMonk ./seqmonk You can link (NOT COPY) the seqmonk launcher into somewhere like /usr/local/bin/ to allow you to run seqmonk from anywhere on your filesystem. Configuring SeqMonk -------------------- When you first run seqmonk you will be prompted to set up two file locations: 1. A cache file which will store temporary data used when seqmonk is running. This folder needs to be on a local disk (rather than a network drive) since lots of data will be written to and read from it. It will default to a folder called seqmonk_cache in your home directory, but you can change this. 2. A genomes folder which will hold a cache of the genome annotations for genomes you use in your projects. This folder will retain information between seqmonk sessions, but it can be re-downloaded at any point if lost so it doesn't need to be backed up. This will default to a folder called seqmonk_genomes in your home directory, but you can change this if you like. Once these are set up you can run seqmonk. You can now optionally install and configure R. Configuring R ------------- For some of the advanced statistical filters SeqMonk talks to a locally installed instance of R to do the statistical analysis. Configuring R is optional, and SeqMonk will run without it, but the R based filters and some of the graphical plots will not be available. To configure SeqMonk and R you first need to install R on your system. R can be downloaded from http://www.r-project.org/ and you should follow the instructions there to load it. For OSX and Linux users the installation of some R packages will require that you have suitable development tools installed. For OSX the easiest way to get these is to install the OSX R Tools Package which can be found at: https://github.com/rmacoslib/r-macos-rtools For Linux users you should install the normal build environment on your system. Many systems will have this already, but you can explicitly install them with: Ubuntu: sudo apt install build-essential CentOS: sudo yum groupinstall "Development tools" In addition you may need to install some additional development libraries. The exact set can change over time, but the one which often crops up is the xml2-dev library Ubuntu: sudo apt install libxml2-dev CentOS: sudo yum install libxml2-devel SeqMonk should prompt you to identify the location of your R installation (if it's not found automatically), and will attempt to install any packages it requires for you during initial setup.