Installation

MacSyFinder dependencies

MacSyFinder has two dependencies:
  • the formatdb (>=2.2.26) or makeblastdb (>=2.2.28) tools provided with the Blast suite of programs
(http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download)

formatdb or makeblastdb and hmmsearch programs should be installed (e.g., in the PATH) in order to use MacSyFinder. Otherwise, the paths to these executables must be specified in the command-line: see the command-line options.

Python version 2.7 is required to run MacSyFinder: https://docs.python.org/2.7/index.html

Installation procedure

First unarchive the source codes package, and enter the extracted folder:

tar -xzvf macsyfinder-x.x.tar.gz
cd macsyfinder-x.x

MacSyFinder installation follows classical “pythonic” installation procedure (see http://docs.python.org/2/install/):

python setup.py build
(sudo) python setup.py install

It is highly recommanded to run tests before performing the full installation:

python setup.py build
python setup.py test -vv
(sudo) python setup.py install

Note

Super-user privileges (i.e., sudo) are necesserary if you want to install the program in the general file architecture.

Note

If you do not have the privileges, or if you do not want to install MacSyFinder in the Python libraries of your system, you can install MacSyFinder in a virtual environment (http://www.virtualenv.org/).

Procedures specific to MacSyFinder can be used instead of default. Please run the command for full options:

python setup.py --help

The main ones are:

python setup.py install --prefix /usr/local/home/bob/my_programs # Specifies an installation path

=> It will install MacSyFinder and required data (profiles folder and systems definition folders) in the Home directory of “bob”, in the “my_progams” folder (useful if you do not have super-user privileges).

Warning

When installing a new version of MacSyFinder, do not forget to uninstall the previous version installed !

Uninstalling MacSyFinder

To uninstall MacSyFinder (the last version installed), run:

(sudo) python setup.py uninstall