1 file was added to this release more than 14 days after its initial publication. Inspect the release files before installing.
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-dirAlternatively, 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-utilsManual 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.yzAcknowledgement
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).
1 maintainer
Release files for sgs-utils 0.53
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File added late
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Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| sgs-utils-0.53.tar.gz | 61.7 kB | Details |
Release files / sgs-utils-0.53.tar.gz
File added late
This file was uploaded more than 14 days after the first file in this release.
While project maintainers occasionally add legitimate files to an existing release, late additions can also indicate a security compromise.
We recommend inspecting the release file before installing.
| Download URL | sgs-utils-0.53.tar.gz |
|---|---|
| Size | 61.7 kB |
| Tags | Source |
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