sgs-utils 0.53

SGS toolbox

sgs-utils is a collection of python libraries that allows to manipulate SGS related files, especially the input and output of shogen.

Requirement

• a compatible shell (bash is ok, dash is not)

• awk, sort

• libsbml

• python 2.7 (optional: pip)

  • sgs-utils

    • python-libsbml (≥ 5.12.0)

    • networkx

  • shogen

    • pyasp (= 1.3.x, the python 2.7 branch of pyasp)

How to install

When installing sgs-utils, all needed python depencies will be automatically installed.

Warning

If you have already installed a version of pyasp somewhere in your system (system wide, user wide or virtualenv installation) and you when to install sgs-utils (and shogen) elsewhere, the setup.py script may not download and install the clasp and gringo binaries in the new installation. This problem is related to the way setuptools and pip manage the installation cache. There is no automatic workaround.

You can check that clasp and gringo binaries are installed by looking if they exist in the pyasp binary directory which is something like ${PYTHONPATH}/lib/python2.7/site-packages/pyasp-1.3.x-py2.7.egg/pyasp/bin/.

A solution to solve this issue is to reinstall pyasp with the --no-cache-dir option that force pip and setuptools to ignore the cache.

pip install pyasp==1.3.3 --user --ignore-installed --no-cache-dir

Alternatively, you can compile clasp and gringo3 or download their binaries from here and copy/link them respectively as clasp and gringo files in the pyasp binary directory.

Install with pip

pip install --user sgs-utils

Manual install

Download sgs-utils-x.yz.tar.gz From the pypi website and then do the following commands.

tar xvf sgs-utils-x.yz.tar.gz
cd sgs-utils-x.yz
python setup.py --user install
cd ..
rm -r sgs-utils-x.yz

Acknowledgement

This work was supported by grants Fondap 15090007, Basal program PFB-03 CMM, IntegrativeBioChile INRIA Assoc. Team, ANR-10-BLANC-0218 and CIRIC-INRIA Chile (line Natural Resources).