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. Open the python interpreter in the terminalĬd ~/local wget unzip cd picard-tools-1.125 cp picard.jar ~/local/bin/ 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
XCODE MAC OS 10.9.5 INSTALL
To install, click on the install package (python-3.4.2-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".
XCODE MAC OS 10.9.5 UPDATE
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-.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, 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-3.1.2-mavericks.pkg) and follow the prompts. (current version is R-3.1.2, Pumpkin Helmet, ). 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 # The output should now indicate the updated 1.7 version is available as default java version "1.7.0_71" Java(TM) SE Runtime Environment (build 1.7.0_71-b14) Java HotSpot(TM) 64-Bit Server VM (build 24.71-b01, mixed mode) This will open a dialogue window that will ask if you want to install the command line tools, select "Install" # Open a new terminal window and enter the following command Search for Xcode ( current version is v6.1, that is compatible with OS X 10.9.4+)ĭownload Xcode (it can take a long time since its 2.4 Gb)Ĭlick on "Launchpad" and open the Xcode applicationįlow the prompts to complete the primary install Open the APP STORE application on your mac It is an excellent code editor but more importantly it contains the application "make" that you will need to install most ngs applications.
XCODE MAC OS 10.9.5 FOR MAC
This is software provided by Apple that is used for building applications for Mac computers or iOS devices. # save updated profile (press "esc" then ":w" then ":q") # This adds the local/bin directory to the path export PATH=$HOME/local/bin:$PATH # This alias allows you to type "ll" in the terminal to execute "ls -l" alias ll='ls -l' # These alias's are examples that open connections to a computation resource (standard or ftp connections shown)
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