expam 1.0.0

Metagenomic profiling using a reference phylogeny

Install.

From Bioconda (Recommended)

From PyPI

user@computer:~$ pip install expam

From GitLab source

To install from source, you need a local installation of Python >=3.8, as well as numpy and cython. There are some commonly encountered problems when installing on Linux, the most common of which are outlined in the FAQ section below.

First download the source code from the GitLab repository.

user@computer:~$ git clone [e-mail]:ssol0002/pam.git

This can then be installed locally by executing the following command from the source code root:

user@computer:~$ python3 setup.py install

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Documentation

View our online documentation!

https://expam.readthedocs.io/en/latest/index.html

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FAQ

Problems during installation

error: g++: Command not found

This is simply a matter of updating the compiler.

> sudo apt-get install build-essential

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fatal error: Python.h: No such file or directory

This simply means you need to install/update the Python development files for version 3.

> sudo apt-get install python3-dev

(Reference - SO)

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ete3 importing errors

For instance, ImportError: cannot import name 'NodeStyle'.

The ete3 module depends on Qt, and for Linux it may take some tweaking to get Python to recognise the local installation of Qt. The following seems to work for a broad collection of circumstances.

First update the local installation of Qt.

> sudo apt-get install qt5-default

Now double-check which version of Qt has been installed.

> dpkl -l | grep "pyqt5"

Install the corresponding Python interface to Qt.

> pip3 install pyqt5==5.12

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Commands

A complete list of available commands can by found by using the -h/--help flags.

user@computer:~$ expam --help
...

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Bug Reports

Please raise any bug reports at https://github.com/seansolari/expam/issues accompanied by any error messages, a rough description of the database/setup and parameters used to create the database.