How to install alphafold-multimer on a server that I don't have total permission?

01 January 1970 1 9K Report

I need a specific tutorial on how to install alphafold-multimer on a server that I don't have permission to (I can use conda and can not use docker. I install cuda 11, the nvcc version shows cuda 9.1.). Is there any tutorial on this simple installation?

install_colabbatch_linux.sh or download.sh In their github link alway end with error in this server.

If I can transport a prepared environment, with tools such as conda-pack, it will be great!

Kamel Khedhiri

Installing AlphaFold-Multimer on a server for which you don't have total permission can be challenging, as it typically requires administrative access to install the necessary software dependencies and configure the server. However, you may still be able to run AlphaFold-Multimer on such a server by following these steps:

Check with the Server Administrator: First, reach out to the server administrator or the person responsible for the server and explain your need to install AlphaFold-Multimer. They may be able to assist you with the installation or grant you the necessary permissions.

Use a Virtual Environment: If you can create a virtual environment or conda environment without administrative privileges, you can install some of the required dependencies there. This won't work for all dependencies, but it can help with some. You can create a Python virtual environment using the following command: bashCopy codepython -m venv myenv

Install Miniconda or Anaconda: If you don't have administrative access, you can install Miniconda or Anaconda in your home directory. These package managers allow you to create isolated environments without needing admin privileges. Download the Miniconda installer script and run it: bashCopy codewget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh bash Miniconda3-latest-Linux-x86_64.sh -b -p ~/miniconda3After installation, add Miniconda to your PATH by modifying your .bashrc or .bash_profile: bashCopy codeexport PATH=~/miniconda3/bin:$PATHThen, create and activate a conda environment for AlphaFold-Multimer: bashCopy codeconda create -n alphafold-multimer python=3.7 conda activate alphafold-multimer

Install AlphaFold-Multimer in the Conda Environment: Once you have your conda environment set up, you can install AlphaFold-Multimer and its dependencies within this environment. Follow the instructions provided in the AlphaFold documentation for installation.

Compile from Source: If you still face permission issues, you can try to compile AlphaFold-Multimer from source code within your home directory. Clone the AlphaFold repository and follow the build instructions provided in the documentation.

External Cloud Services: If you have restrictions on your server, consider using cloud-based services like Google Colab or AWS (Amazon Web Services) where you can run AlphaFold without worrying about server permissions.

Remember that the success of these methods may vary depending on the specific server setup and restrictions in place. Always respect server policies and guidelines and seek assistance from the server administrator when necessary.

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