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Installation
============
Requirements
------------
- Python 3.x
- Python packages `numpy` and `click`
- Command-line utilities `sort` (the Unix version), `bgzip` (shipped with `samtools`)
and `samtools`. If available, `pairtools` can compress outputs with `bgzip`, `pbgzip` and `lz4`.
Install using conda
-------------------
We highly recommend using the `conda` package manager to install pre-compiled
`pairtools` together with all its dependencies. To get it, you can either
install the full `Anaconda <https://www.continuum.io/downloads>`_ Python
distribution or just the standalone
`conda <http://conda.pydata.org/miniconda.html>`_ package manager.
With `conda`, you can install pre-compiled `pairtools` and all of its
dependencies from the `bioconda <https://bioconda.github.io/index.html>`_ channel:
.. code-block:: bash
$ conda install -c conda-forge -c bioconda pairtools
Install using pip
-----------------
Alternatively, compile and install `pairtools` and its Python dependencies from
PyPI using pip:
.. code-block:: bash
$ pip install pairtools
Install the development version
-------------------------------
Finally, you can install the latest development version of `pairtools` from
github. First, make a local clone of the github repository:
.. code-block:: bash
$ git clone https://github.com/open2c/pairtools
Then, you can compile and install `pairtools` in
`the development mode <https://setuptools.readthedocs.io/en/latest/setuptools.html#development-mode>`_,
which installs the package without moving it to a system folder and thus allows
immediate live-testing any changes in the python code. Please, make sure that you
have `cython` and `pysam` installed!
.. code-block:: bash
$ pip install cython pysam numpy
$ cd pairtools
$ pip install -e ./ --no-build-isolation
A few notes on the installation:
- `pairtools` have to use `--no-build-isolation`, because it extends `pysam` via Cython and
re-compiles it during the build process. When build isolation is enabled, these `pysam` objects
get lost after the build.
- Because of the `--no-build-isolation` flag, build does not install build-requires, so you have to
install `cython`, `pysam` and `numpy` manually before the build.
Building on MacOS is not fully supported yet, but this tentative solution seems to work:
.. code-block:: bash
$ pip install build cython pysam numpy delocate
$ cd pairtools
$ python -m build -n
$ DYLD_LIBRARY_PATH=$(python -c 'import pysam, os; print(os.path.dirname(pysam.get_libraries()[0]))') delocate-wheel -v dist/{wheel_name}.whl
$ pip install dist/{wheel_name}.whl
Note that you need to change the `{wheel_name}` to the actual name of the wheel file.
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