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Installation

Execution environment

There are two main constraints with regards to the execution environment. These are that it must run on Linux/Unix and the Python version must be >=3.8 and <=3.10. This app was developed using Python version 3.9.

Python constraint

Python must be >=3.8 and <=3.10. This to accommodate the numpy version required by pbcore. Pre-built distributions of numpy==1.22.4 are only available for Python 3.8-3.10.

Linux/Unix constraint

Run on Linux/Unix. This is because there are no pre-built distributions of pysam (a dependency of pbcore) available for Windows.

Set up venv

Set up the virtual python environment using a supported (see above) python version. Use python -m venv venv to create the virtual environment, followed by pip install -r requirements.txt to install all required packages.

Troubleshooting

Problem: I'm building the virtual environment and pip is trying and failing to build packages.

Solution: This is a very generic Python issue. The basic problem is that a pre-built version of this package is not available. Availability of pre-built packages (a.k.a. "wheels") depends on your operating system and Python version.

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App for making SMRT Link datasets more accessible and shareable.

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