👋 Introduction
In January 2023, we introduced new functionality which allows TRE users to install packages available within conda-forge, without needing to make a request to HIC Support to add packages for you. This works in the same way as our CRAN proxy, which performs live scanning of packages as they are downloaded. If your workspace was created prior to January, some manual changes will be required to your workspace. As of August 2024, we also allow package installation from the bioconda repository, enabling installation of packages like plink.
Conda is an open source management system that is used to managing packages in various programming languages. This may be more applicable to Python TRE Users.
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If your workspace was created <Feb 2023 you will need to complete the following steps |
🤔 Configuring an old workspace
You only need to complete this step if your workspace was created before February 2023. If you are unsure about when your workspace was created, repeating these steps will not break anything - so you are safe to repeat this portion if needed.
If you are on a an older Windows workspace, you will may need to open an Anaconda PowerShell prompt. Under Ubuntu workspaces, any terminal window should work fine. This instructs your conda environment to connect to the HIC conda proxy, rather than trying to reach out to the internet directly.
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conda install -c http://conda.hic-tre.dundee.ac.uk/conda-forge/ --override-channels numpy |
☣️ Enabling bioconda
As of August 2024, we also allow package installation from the bioconda repository. You will need to manually enable this channel.
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$ conda config --append channels http://conda.hic-tre.dundee.ac.uk/bioconda/ |
\uD83D\uDCD8 Instructions
Installation of packages should be as you are used to with conda. For example, to install numpy, you would simply run:
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$ conda install numpy |
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\uD83D\uDCCB Related articles
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