@@ -45,54 +45,58 @@ and ``gzip`` modules from the stdlib (with some minor exceptions, see below).
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Installation
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------------
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- Recommended installation via conda
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- ..................................
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- The recommended installation is an installation via Conda. For example using
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- the `miniconda <https://docs.conda.io/en/latest/miniconda.html >`_ installer
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- with a properly setup `conda-forge
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- <https://conda-forge.org/docs/user/introduction.html#how-can-i-install-packages-from-conda-forge> `_
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- channel. When used with bioinformatics tools setting up `bioconda
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- <http://bioconda.github.io/user/install.html#install-conda> `_
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- provides a clear set of installation instructions for conda.
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-
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- python-isal is available on conda-forge and can be installed with
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+ Installation with pip
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+ .....................
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+ Python-isal can be installed with:
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.. code-block ::
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- conda install python- isal
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+ pip install isal
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- This will automatically install the isa-l library dependency as well, since
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- it is available on conda-forge .
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+ On linux this will install a wheel that has a statically linked version of
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+ isa-l (version 2.30.0) included .
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- Installation with pip
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- .....................
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- isa-l version 2.26.0 or higher is needed on your system. This includes bindings
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- for the adler32 function.
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+ The latest development version of python-isal can be installed with
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+
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+ .. code-block ::
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+
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+ pip install git+https://github.com/rhpvorderman/python-isal.git
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+
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+ Installing from source will dynamically link isa-l if already available
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+ on the system. This will speed up the installation process.
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isa-l is available in numerous Linux distro's as well as on conda via the
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conda-forge channel. Checkout the `ports documentation
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<https://github.com/intel/isa-l/wiki/Ports--Repos> `_ on the isa-l project wiki
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- to find out how to install it. It is important that the development headers
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+ to find out how to install it. It is important that the development headers
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are also installed.
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On debian and ubuntu the isa-l libraries (including the development headers)
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- can be installed with:
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+ can be installed with:
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.. code-block ::
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sudo apt install libisal-dev
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- python-isal can be installed via pypi with:
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+ Installation via conda
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+ ..................................
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+ Python-isal can be installed via conda, for example using
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+ the `miniconda <https://docs.conda.io/en/latest/miniconda.html >`_ installer
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+ with a properly setup `conda-forge
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+ <https://conda-forge.org/docs/user/introduction.html#how-can-i-install-packages-from-conda-forge> `_
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+ channel. When used with bioinformatics tools setting up `bioconda
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+ <http://bioconda.github.io/user/install.html#install-conda> `_
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+ provides a clear set of installation instructions for conda.
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+
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+ python-isal is available on conda-forge and can be installed with
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.. code-block ::
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- pip install isal
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-
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- The latest development version of python-isal can be installed with
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+ conda install python-isal
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- .. code-block ::
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+ This will automatically install the isa-l library dependency as well, since
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+ it is available on conda-forge.
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- pip install git+https://github.com/rhpvorderman/python-isal.git
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Usage
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-----
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