Getting strange mixtures of defaults and conda-forge?.conda config -set safety_checks disabled.
Feeling frustrated with “verifying transaction” and also feeling lucky?.Instead of specifying only “r-essentials”, specify “r-base=3.5 r-essentials” If you are using R, specifying a particular implementation makes the problem much simpler.Instead of “numpy”, think “numpy=1.15” or even better, “numpy=1.15.4” Letting conda filter more candidates makes it faster. Use conda-metachannel to reduce conda’s problem size.We’re working on it and we wanted to explain a few of the facets that we’re looking at to solve the problem. The last element of the command, fastqc, specifies the software package to install.Lately, we have been responding to issues about Conda’s speed. 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. The conda installer sets up two things: Conda and the base environment (also called "root"). 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). We'll talk more about setting conda up on your local system later in the lesson! Initialize conda ¶ 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. 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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