MacSyFinder dependencies

MacSyFinder has two dependencies:
  • the formatdb (>=2.2.26) or makeblastdb (>=2.2.28) tools provided with the Blast suite of programs

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:

Installation procedure

It is recommended to use the MacSyFinder package instead of the git repository.

Archive overview

  • bin => contain the executables (macsyfinder)
  • data => the hmm profiles and the systems definitions
  • doc => the documentation in html and pdf
  • etc => a template of macsyfinder configuration file
  • test => all needed for unit tests
  • macsypy => the macsyfinder python library
  • => the installation script

Installation steps:

Make sure every required dependence/software is present.

By default MacSyFinder will search if makeblastdb is on your PATH if not it will looking for formatdb. if neither makeblastdb nor formatdb are in your path you have to set the absolute path toward one of these tools in the configuration file. by default MacSyFinder will try to use hmmsearch in your PATH, if hmmsearch is not in the PATH, you have to set the absolute path to the hmmsearch in configuration. If the tools are not in the path, some test will be skipped and a warning will be raised.

Perform the installation.

Uncompress the archive
sudo python install
tar -xzf macsyfinder-x.x.tar.gz
cd macsyfinder-x.x
Build MacSyFinder

macsyfinder installation follows classical “pythonic” installation procedure (see

python build
Test MacSyFinder

It is highly recommended to run tests before performing the full installation. To test the libraries you just build:

python test -vv
sudo python install

If you have not the privileges to perform a system wide installation, you can use a [virtual environment](

vitualenv macsyfinder
source macsyfinder/bin/activate
mkdir macsyfinder/src
cd macsyfinder/src

and follow the “regular” procedure:

  • uncompress the archive
  • build MacSyFinder
  • test MacSyFinder

for installation do not use neither –prefix nor sudo

python install

To exit the virtualenv just execute the deactivate command. To run macsyfinder, you need to activate the virtualenv:

source macsyfinder/bin/activate

Then run macsyfinder/macsyview

You can access all general cmd with

python --help

or specific options with

python cmd --help


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


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 (

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

python --help

The main ones are:

python 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).


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 uninstall

If You want to install from the git repository

virtualenv macsytest
mkdir macsytest/src
source macsytest/bin/activate
cd macsytest/src
git clone
cd macsyfinder/
python build
python install --no-viewer