gempasteur/satellite_finder repository overview

⁠SatelliteFinder

SatelliteFinder - Detection of four families of phage satellites: P4-like, PICI, cfPICI and PLE in protein datasets using systems modelling and similarity search.

⁠Availability

• These Docker images
• on galaxy server @ pasteur.fr :

⁠how to use SatelliteFinder 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)

⁠you have the choice to run against models 'cfPICI', 'PICI', 'P4', 'PLE'

  docker run -v ${PWD}/:/home/msf -u $(id -u ${USER}):$(id -g ${USER})  gempasteur/satellite_finder:0.9.1  --db-type ordered_replicon --models  <cfPICI | PICI | P4 | PLE> --sequence-db my_protein_dataset.fasta -w 12 --out-dir <result_dir>

my_protein_dataset.fasta is a file containing all genes of a replicon translated in proteins. For ordered_replicon the order of sequences in the file is the same as along the replicon.

⁠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.

apptainer run -H ${HOME} docker://gempasteur/satellite_finder:0.9.1  --db-type ordered_replicon  --models  <cfPICI | PICI | P4 | PLE>  --sequence-db my_protein_dataset.fasta -w 12

# for instance to run satellite_finder to find phage satellite of P4 family

apptainer run -H ${HOME} docker://gempasteur/satellite_finder:0.9.1 --db-type ordered_replicon --models P4 --sequence-db my_protein_dataset.fasta -w 12