mzml2isa is available on PyPI, so if
pip is installed on your
machine, installing mzml2isa should be quite straightforward, without
the need to worry about dependencies. It is also possible to install
mzml2isa development version directly from the mzml2isa GitHub repository.
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 mzml2isa Github release section. See file mzml2isa_cli.exe.
Without pip you'll have to install the requirements yourself, otherwise running
setup.py will fail when trying to import mzml2isa for the first time.
- an interface to ontology files (used to import the MS controled vocabulary)
an XML parser generally quicker than the builtin python xml.cElementTree (used as an alternative to parse the mzML 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 of the following commands in a terminal:
pip install mzml2isa # install in /usr, needs super-user rights pip install mzml2isa --user # install in ~/.local/
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 of mzml2isa ,
unpack it and install it by running the following commands:
tar xf mzml2isa-xx.yy.zz.tar.gz # replace with whatever version you downloaded cd mzml2isa-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 you could be installing a non-functional version of the program ! The program is working if the badge above displays .
pip install git+git://github.com/ISA-tools/mzml2isa
git clone https://github.com/ISA-tools/mzml2isa cd mzml2isa python setup.py install