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Detailed Installation Guide

Installing Reconstructor consists of 2 (or 3) main steps:

  1. Install Reconstructor with pip
  2. (OPTIONAL) Install the DIAMOND sequence aligner
  3. Run tests and download resource files

These steps are discussed in more detail below.

Install Reconstructor python package

This can be done via pip in terminal on Mac, or a CMD.exe Prompt launched from Anaconda Navigator in Widnows:

pip install reconstructor

Note

You must be running >= Python 3.9

To determine your Python version you can use the following command:

python --version

Install DIAMOND (this step is optional)

If you want Reconstructor to use a version of DIAMOND other than the one that would be automatically downloaded, you can install DIAMOND manually. See the DIAMOND GitHub page for details on how to install DIAMOND. After installing DIAMOND, you must ensure that DIAMOND is discoverable on your PATH. Otherwise, Reconstructor will download its own copy.

Test suite (MUST RUN BEFORE USING RECONSTRUCTOR)

Caution

YOU MUST RUN THE TEST SUITE BEFORE PROCEEDING TO USE RECONSTRUCTOR

Run the following test to ensure reconstruction was installed correctly and is functional:

python -m reconstructor --test yes

This command also downloads a database file and a DIAMOND binary that are necessary for reconstructor to work. This series of tests should take about an hour to run, dependent on computer/processor speed. These are runtimes for Reconstructor on a 2020 MacBook Pro with a 1.4 GHz Quad-Core Intel Core i5 processor. You can speed the test suite up somewhat with the optional --cpu argument, which controls how many threads are used for blasting. For example, the following command would run the test suite with 4 threads for blasting:

python -m reconstructor --test yes --cpu 4

If you have a copy of DIAMOND on your PATH when you run the test suite, Reconstructor will default to using this copy of DIAMOND rather than downloading its own. If you would instead like Reconstructor to download and use its own copy of DIAMOND, you can use the --diamond option:

python -m reconstructor --test yes --diamond

This option also allows you specify a specific version of DIAMOND that you would like Reconstructor to download and use (provided that version is available for your specific system):

python -m reconstructor --test yes --diamond 2.1.13

If you do not have a version of DIAMOND in your PATH, but you do not want Reconstructor to download its own version of DIAMOND, you can use the --skip-diamond command:

python -m reconstructor --test yes --skip-diamond