Please note that you do need to add the prefix flag -p ~/work/shared/uenv when Conda installing packages on a multinode cluster so they will be installed in the correct environment. For example: conda create -p ~/work/shared/uenv -clone uenvconda activate ~/work/shared/uenvconda install -p ~/work/shared/uenv -y python myscript_with_package-name_calls.py rm -rf ~/work/shared/uenv Then if you run a conda install -p ~/work/shared/uenv -y afterwards that package will be available to all compute nodes. NOTE: This is only necessary if a more than one node is used for the cluster. To do this you can add the following commands to the job: conda create -p ~/work/shared/uenv -clone uenvconda activate ~/work/shared/uenv. . Run workflow .rm -rf ~/work/shared/uenv Rather than installing all requisite packages on each node individual it is recommended to clone the Conda env to the NFS mounted ~/work/shared directory. Regardless of which environment you select the Conda commands will behave the same, so commands listed here should work for both Miniconda and Anaconda.īefore beginning the set up of a Python parallel environment there are some details with regards to how a multi-node cluster is set up on Rescale that should be discussed. If you know your analysis requires many of the pre-installed packages in the Anaconda environment, the additional cluster start up time is likely worth it, as you would need to install all the packages once the cluster is up and running otherwise. If you are using a custom Python post-processing script in addition to a CFD simulation for example, then a Miniconda environment should be sufficient. This makes it an ideal choice if only one or two different Python packages are required for the analysis. The Miniconda environment is a much smaller snapshot to load onto the cluster, so start up times will be shorter.
There are different advantages to using either based on the needs of the user. There are two “types” of a Conda environment available on Rescale, one that contains a number of pre-installed packages (Anaconda), and one that is an empty environment (Miniconda). Please contact us if you’re having trouble.
This tutorial will go over how to set up Conda environments for various applications on Rescale. There are a number of different ways to leverage the capabilities of Conda package management for custom data and post-processing analysis using Python.
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. 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
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