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INSTALL.md

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Installation

Porechop_ABI can be installed using several methods, that can be separated in two categories:

  • Using package managers such as Conda or Pip.
  • Installing from sources using scripts or make.

Except for conda installation, all requirements described in README must be satisfied before install.

Table of Content

Install with Conda

Conda is a cross platform package / environment management system. Porechop_ABI was added as a package to the bioconda channel to make the installation easier.

If you do not have conda installed, you can get started here.

With Miniconda3 or Anaconda installed, it is recommended to keep conda up to date.

conda update conda

The different package required to install Porechop_ABI are scattered between the conda-forge and bioconda channels. You will need to add them both to your available channels:

conda config --add channels conda-forge
conda config --add channels bioconda

An alternative is to specify the channels during installation with -c flag after the package name.

With a fresh environment, install Porechop_ABI using either the Anaconda GUI, or the following command lines:

conda create -n my_env
conda activate my_env
conda install porechop_abi
porechop_abi -h

Fetching source code

All the following methods require you to either download and unzip this repository, or simply clone it:

git clone https://github.com/bonsai-team/Porechop_ABI.git
cd Porechop_ABI

Install with pip

If you are not using Conda but have pip installed, we recommand using pip to install Porechop_ABI, as it is the second easiest way.

In the Porechop_ABI folder, use pip as a python module.

python3.[X] -m pip install .
porechop_abi -h

Be sure the python version match the requirement (>= 3.6 and networkx installed)

Install from sources

You can also run the setup.py script yourself. It will compile the C++ components of Porechop_ABI and install a porechop_abi executable on your system. Depending on your permissions, you can install porechop_abi systemwide (root / sudo most likely required), or for yourself only.

After cloning the repository:

  • System wide install
python3.[x] setup.py install
porechop_abi -h
  • Local (user) install
python3.[x] setup.py install --user
porechop_abi -h

Build and run without installation

By simply running make in Porechop_ABI's directory, you can compile the C++ components but not install an executable. The program can then be executed by calling the porechop-abi-runner.py script.

cd Porechop_ABI
make release
./porechop-abi-runner.py -h

Troubleshooting

  • When installing from sources, you may in some cases get a "could not find cpp_function.so" or similar error. If that happens, you need to manually add execution permission to the impacted compiled objects. chmod +x <your_install folder>/<files that are "not found">

  • For user install (from sources), if you get a strange "can't combine user with prefix" error, read this.

  • You may want / need to install Porechop_ABI to a specific location. You can specify the installation path using --prefix: python3 setup.py install --prefix=$HOME/.local

  • If you'd like to specify which compiler to use, set the CXX environnemnt variable before installation. Ex: export CXX=g++-6

  • Porechop includes ez_setup.py for users who don't have setuptools installed, though that script is deprecated. So if you run into any installation problems, make sure setuptools is installed on your computer: python3.[x] -m pip install setuptools

  • If you have already the original Porechop installed, Porechop_ABI will not replace it. Despite having the same abilities, Porechop_ABI is a different software. It must be run using the porechop_abi command, and not just porechop.