Permalink
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
117 lines (72 sloc) 3.63 KB

Installation

nmrml2isa is available on PyPI, so if pip is installed on your machine installing nmrml2isa should be quite straightforward, without the need to worry about dependencies. It is also possible to install nmrml2isa development version from its GitHub repository. Please note that the GitHub version of the program may fix bugs but also introduce new bugs, and that it might not work on your files.

Windows

Windows users can either install mzml2isa as described below or use a 'ready to go' Windows executable (no python install required). The executables be found on the nmrml2isa Github release section. See file nmrml2isa_cli.exe.

Dependencies

Warning

Without pip you'll have to install the requirements yourself, otherwise running setup.py will fail when trying to import nmrml2isa for the first time.

Requirements

pronto
an interface to ontology files (used to import the MS controlled vocabulary)
chainmap (required for Python 2 or PyPy)
a polyfill implementation of collections.ChainMap (available in Python 3 stdlib)

Extras

lxml

an XML parser generally quicker than the builtin python xml.cElementTree (used as an alternative to parse the nmrML files)

Note

If installing lxml on windows, you can either:

  1. Compile it directly (requires Microsoft Visual C++ to be installed on the Windows machine): run the command set STATICBUILD=true && pip install lxml
  2. Install the unofficial windows binaries (whls)

PyPI (stable version) PyPI version

With pip

Just run one the following commands in a terminal:

pip install nmrml2isa        # install for all users, needs super-user rights
pip install nmrml2isa --user # install only for the current user, no rights needed

Without pip

This requires the python setuptools module to be installed, as well as the dependencies listed above. Download the latest stable release from the PyPI repository, unpack it and install it by running the following commands:

tar xf nmrml2isa-xx.yy.zz.tar.gz # replace with whatever version you downloaded
cd nmrml2isa-xx.yy.zz.tar.gz
python setup.py install          # will require super-user rights

GitHub (development version) Build Status

Warning

Please check the current version of the program passes the Travis CI validation beforehand, or else you're likely to install a non-functioning version of the program ! The program is working if the badge above displays Passing build .

With pip

pip install git+git://github.com/ISA-tools/nmrml2isa

Without pip

git clone https://github.com/ISA-tools/nmrml2isa
cd nmrml2isa
python setup.py install