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 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.
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.
- 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)
an XML parser generally quicker than the builtin python xml.cElementTree (used as an alternative to parse the nmrML files)
If installing lxml on windows, you can either:
- Compile it directly (requires Microsoft Visual C++ to be installed on the Windows machine):
run the command
set STATICBUILD=true && pip install lxml
- Install the unofficial windows binaries (whls)
- Compile it directly (requires Microsoft Visual C++ to be installed on the Windows machine): run the command
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
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
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 .
pip install git+git://github.com/ISA-tools/nmrml2isa
git clone https://github.com/ISA-tools/nmrml2isa cd nmrml2isa python setup.py install