The last element of the command, fastqc, specifies the software package to install. The -name (or -n) flag specifies the environment's name. The -y flag tells conda not to ask you for confirmation about downloading software. This takes a few minutes (you'll see the message "Solving environment"). Now, let's create a conda environment with fastqc installed in it, as demonstrated below:Ĭreate conda environment and install FastQC. Setup the conda installer and initialize the settings: As illustrated below, you can then create additional environments with their own software installations, including other versions of the same software (i.e., python 3 in base environment and python 2.7 in a separate environment). The base environment contains a version of python (specified during installation) and some basic packages. of your results is to have an independent conda environment in the directory. The conda installer sets up two things: Conda and the base environment (also called "root"). Conda provides a great way to install packages that are already compiled. Either click Run or type Cmd + Enter on Macs and Ctrl + Enter on Windows computers. To follow along, copy/paste commands into the terminal OR run the commands from the "workshop_commands.sh" file in the binder (in File Rstudio panel). youre now in your conda virtual environment. ![]() We'll talk more about setting conda up on your local system later in the lesson! Initialize conda ¶ Once the installation is complete, run conda list to make sure you have conda installed. Type a descriptive name for the new environment, or use the existing name. ![]() Select the corresponding folder icon to choose the environment you want to import. In the Import Environment dialog, choose whether to import from your Local drive or from Anaconda Nucleus. The binder or internet connection may have timed out.Ĭonda is already installed in the binder so the next step is to set it up. At the bottom of the environments list, select Import. ![]() Try clicking on the launch button again to re-launch. What happens if I get a 502, 503, or 504 error from the binder? Method 3: specify software to install with a YAML file Method 2: install both software during environment creation Method 1: install software in existing environment Incorporating GTEx Data in Kids First Analyses Using the CFDE Search Portal to Find FilesĬavatica - View, Filter, Tag and Download
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