#Due to the license restrictions the only download mechanism is via your web browser. If you are using it for non-commercial research purposes you can use the free version. Since the Broad Institute has commercialized the toolset with Appistry you will need to first register/login to accept the usage agreement. To download, search google for "GATK tools" and follow the download links. It also has a large number of additional applications that you will use frequently. Clearly this will only work with updated pipelines.į) GATK - This JAVA application contains a number of "best-practices" applications for post-processing alignment files. jar files for each application seen in previous versions. NOTE: This example version is dramatically different than previous versions as it adopts a GATK like command format as all the applications are embeded in a single. Test the install by opening a new terminal window and typing the followingĬd ~/local wget unzip cd picard-tools-1.125 cp picard.jar ~/local/bin/ To install, click on the download (MacPorts-2.3.) To download, google "MacPorts" and follow the "Installing MacPorts" instructions for your OS version (Make sure Xcode is available). To install these and many other tools MacPorts is an excellent resource. There are many unix commands that do not come pre-loaded on Macs like dos2unix, wget or md5sum. Select Python 3 version from the "Python Interpreter" drop-down list P圜harm>Preferences>Build, Execution, Deployment>Console>Python Console To install, google Pycharm, and follow the prompts to download the program and click on the install package (pycharm-professional-2016.3.2.dmg). The professional version requires a license that is generally free academic use. There are two versions a community version and professional version. This is a python IDE with good plugins for bash and other programs. (version 1.5.3) pip3 install sympy (version 1.0) pip3 install pandas (version 0.19.2) pip3 install jupyter (version 1.0.0) # samtools in python pip3 install pysam. (version 5.1.0) pip3 install scipy (version 0.18.1) pip3 install matplotlib. Pip3 install numpy (version 1.11.3) pip3 install ipython. Open the python interpreter in the terminal NOTE/WARNING: Several essential Mac applications use python 2.7, so you need to leave it as default but you can easily use the 3.4 environment To install, click on the install package (python-3.6.0-macosx10.6.pkg). To download the newer version google "python" and follow the links to download the "Mac OS X 64-bit/32-bit installer". Macs ship with python 2.7 but if you are starting out it is not a bad idea to update to python 3.x. To install, click on the download (RStudio-1.0.136.dmg) and drag the RStudio application to your applications folder. To download search google for "R studio" and follow the links to download the Open Source version of RStudio Desktop. It made it much less scary to use R for making graphs as you get instantaneous feed back. Rstudio is a nice graphical interface for using R. VennDiagram, also (bvenn, colorfulVennPlot, eVenn, venn, venneuler) NOTE: It is good habit to select the "Install Dependencies" radio button Then install the following using the Package Installer (Packages & Data > Package Installer). Once installed open the application (Applications>R) To install open the install package (R-3.2.2.pkg) and follow the prompts. (current version is R-3.3.2, Sincere Pumpkin Patch, ). To download, search google for "R" and follow the links to a CRAN download page of your choosing.ĭownload by clicking the " Download R for (Mac) OS X" link to the pre-compiled binary. R is free software that supports a multitude of statistical and graphic applications. Java -version #Output should now indicate the updated or installed version of JAVA java version "1.8.0_111" Java(TM) SE Runtime Environment (build 1.8.0_111-b14) Java HotSpot(TM) 64-Bit Server VM (build 25.111-b14, mixed mode) # In the terminal type make ( This will bring up a dialog box to facilitate the install It is an excellent code editor but more importantly it contains the application "make" that you will need to install most ngs applications. This is software provided by Apple that is used for building applications for Mac computers or iOS devices. # Define PATH locations # export PATH=$HOME/local/bin:$PATH # Configure Window Naming Function #Window Naming Function function winname # Alias # This alias allows you to type "ll" in the terminal to execute "ls -lh" alias ll='ls -lh' # Remote connections # These alias's are examples that open connections to a computation resource (standard or ftp connections shown) alias computer='ssh alias cftp='sftp # save updated profile (press "esc" then ":w" then ":q")
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