Solving the 'x86_64-conda_cos6-linux-gnu-gcc': No such file or directory Error During Pysam Installation

If you’re a data scientist working with Python, you’ve likely come across the Pysam library. It’s a powerful tool for reading, manipulating, and writing genomic data sets. However, you might have encountered an error during installation: unable to execute ‘x86_64-conda_cos6-linux-gnu-gcc’: No such file or directory. This blog post will guide you through the steps to resolve this issue.

By Saturn Cloud | Tuesday, August 08, 2023 | Miscellaneous

Solving the ‘x86_64-conda_cos6-linux-gnu-gcc’: No such file or directory Error During Pysam Installation

If you’re a data scientist working with Python, you’ve likely come across the Pysam library. It’s a powerful tool for reading, manipulating, and writing genomic data sets. However, you might have encountered an error during installation: unable to execute 'x86_64-conda_cos6-linux-gnu-gcc': No such file or directory. This blog post will guide you through the steps to resolve this issue.

Understanding the Issue

The error message unable to execute 'x86_64-conda_cos6-linux-gnu-gcc': No such file or directory typically arises when you’re trying to install Pysam in a Conda environment. The problem is that the GCC compiler necessary for the installation isn’t found in the specified directory.

Prerequisites

Before we dive into the solution, ensure you have the following:

A working Conda environment. If you don’t have one, you can install it from here.
Basic knowledge of Python and Conda environments.

Step-by-Step Solution

Step 1: Update Conda

First, ensure your Conda environment is up-to-date. You can do this by running the following command:

conda update --all

Step 2: Install GCC

Next, install the GCC compiler in your Conda environment. Use the following command:

conda install gcc_linux-64

Step 3: Install Pysam

Now, try installing Pysam again. Use the following command:

pip install pysam

If the installation is successful, you’ve resolved the issue. If not, proceed to the next step.

Step 4: Create a New Conda Environment

If the error persists, it might be due to conflicts with other packages in your current Conda environment. In this case, create a new environment and install Pysam there. Use the following commands:

conda create --name new_env
conda activate new_env
pip install pysam

Conclusion

The unable to execute 'x86_64-conda_cos6-linux-gnu-gcc': No such file or directory error during Pysam installation can be a stumbling block. However, by following the steps outlined in this post, you should be able to resolve it and continue with your genomic data analysis.

Remember, the key is ensuring you have the correct GCC compiler installed in your Conda environment. If the problem persists, creating a new environment can help avoid conflicts with other packages.