gempasteur/macsyfinder repository overview

⁠MacSyFinder

MacSyFinder - Detection of macromolecular systems in protein datasets using systems modelling and similarity search.

⁠Availability

MacSyFinder Homepage : https://github.com/gem-pasteur/macsyfinder⁠

MacSyFinder Distribution:

⁠Citation

Néron, Bertrand; Denise, Rémi; Coluzzi, Charles; Touchon, Marie; Rocha, Eduardo P.C.; Abby, Sophie S.
MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes.
Peer Community Journal, Volume 3 (2023), article no. e28. doi : 10.24072/pcjournal.250.
https://peercommunityjournal.org/articles/10.24072/pcjournal.250/⁠

⁠how to use macsyfinder in container

⁠with docker

The computations are performed under msf user in /home/msf inside the container. So You have to mount a directory from the host in the container to exchange data (inputs data, and results) from the host and the container. The shared directory must be writable by the msf user or overwrite the user in the container by your id (see example below)

Furthermore the models are no longer packaged along macsyfinder. So you have to install them by yourself. For that we provide a command line tool macsydata which is inspired by pip.

 msf_data search PACKNAME
 msf_data install PACKNAME== or >=, or ... VERSION

To work with Docker you have to install models in a directory which will be mounted in the image at run time

mkdir shared_dir
cd shared_dir

# install desired models in my_models directory
mkdir my_models
docker run -v ${PWD}/:/home/msf -u $(id -u ${USER}):$(id -g ${USER})  gempasteur/macsyfinder:<tag> msf_data install --target /home/msf/my_models <MODELS_PACK>

# run msf against all models contains in <MODELS_PACK>
docker run -v ${PWD}/:/home/msf -u $(id -u ${USER}):$(id -g ${USER})  gempasteur/macsyfinder:<tag> macsyfinder --db-type unordered_replicon --models-dir=/home/msf/my_models/ --models  <MODELS_PACK>  all --sequence-db my_genome.fasta -w 12

⁠with apptainer (formely singularity https://apptainer.org/news/community-announcement-20211130/⁠ )

As the docker image is registered in docker hub you can also use it directly with Apptainer. Unlike docker you have not to worry about shared directory, your HOME and /tmp are automatically shared.

# install desired models in my_models directory
apptainer run -H ${HOME} docker://gempasteur/macsyfinder:<tag> msf_data install --target my_models <MODELS_PACK>

# run msf against all models contains in <MODELS_PACK>
apptainer run -H ${HOME} docker://gempasteur/macsyfinder:<tag> macsyfinder --db-type unordered_replicon --models-dir=my_models --models <MODELS_PACK> all --sequence-db my_genome.fasta -w 12

⁠Licence:

MacSyFinder is developed and released under