Install with Conda

Check what is the latest version of ICEscreen available on Conda

Visit the following URL: https://anaconda.org/search?q=icescreen

System prerequisites for ICEscreen

  • Linux or MacOS.
  • More than 8 Go RAM. Insufficient memory allocation will kill the process during the initialization (conda installation).
  • Disk space for installation: the source code and test dataset require about 30 MB ; the package dependencies of the software (installed through Conda) require about 140 MB.
  • Disk space for analysis: the output files generated by the pipeline usually take about 20M per genbank file to analyse (not taking into account the disk space of the original genbank files to analyse).

Dependencies

  • git
  • installer for Conda and/or Mamba, such as Miniforge, Micromamba, Pixi, or Miniconda. Please check the conda installer system requirements before installing. Disk space for installing Conda may requires up to 2.5 GB. The installation of the other package dependencies (Snakemake, HMMER, NCBI BLAST+, Bioperl, Python 3, Biopython, ect.) will be automatically managed through Conda.

[!NOTE] A note on Conda and licencing: ICEscreen only relies on packages and dependencies that are in the public repositories of packages (channels) conda-forge and bioconda where the license is free for all. ICEscreen does not relies on packages and dependencies that are in anaconda’s public repository of packages which is subject to a paid license for larger organizations. Some installer for Conda such as Miniforge do not include anaconda’s public repository of packages as default. The Miniconda installer does include anaconda’s public repository of packages as default but this repository can be bypassed with the following conda create options: -c nodefaults, --override-channels, and --strict-channel-priority. Within the Conda environment, use the command conda list --explicit to check for the repository origin of all the dependencies.

How to install ICEscreen locally with Conda

In order to install ICEscreen, the conda-forge and bioconda channels both must be specified to Conda (-c conda-forge -c bioconda). To install ICEscreen in a specific and isolated Conda environment, run the following command:

conda create -y --name icescreen_env_1-3-2 icescreen -c conda-forge -c bioconda

You will then need to activate this specific icescreen_env_1-3-2 Conda environment to access the tool (see below). Installing ICEscreen in your base Conda environment (conda install -c conda-forge -c bioconda icescreen) is not recommended as the version of the tool’s dependencies might be updated by other Conda installations and lead to errors at runtime.

Testing your local installation

To ensure that your local version of the software performs correctly, you can run the following tests on your computer.

  • First to access the tool installed from Conda, you need to activate the icescreen_env_1-3-2 Conda environment:
conda activate icescreen_env_1-3-2
  • If you have root privileges, you can test whether the installation of the dependencies and the compiling of the resources were successful:
icescreen --test_installation

You should see the message The installation of ICEscreen is successful.

  • Regardless of privileges, you can run ICEscreen on an example dataset downloaded from NCBI:
mkdir -p ~/tmp/test_icescreen
cd ~/tmp/test_icescreen
mkdir genbank_files
i=NC_004668
curl -s  "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=${i}&rettype=gbwithparts&retmode=txt" > genbank_files/$i.gbk
i=NZ_CP026548
curl -s  "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=${i}&rettype=gbwithparts&retmode=txt" > genbank_files/$i.gbk
icescreen -g ~/tmp/test_icescreen/genbank_files -o ~/tmp/test_icescreen/ --phylum bacillota
head ~/tmp/test_icescreen/ICEscreen_results/results/NC_004668/icescreen_detection_ME/NC_004668_detected_ME.summary
head ~/tmp/test_icescreen/ICEscreen_results/results/NZ_CP026548/icescreen_detection_ME/NZ_CP026548_detected_ME.summary
rm -rf ~/tmp/test_icescreen

Looking at the header of the .summary file, you should see that ICEscreen has found some ICEs and IMEs.

  • Once your analysis with ICEscreen is completed, you can deactivate the conda environment specific for the tool:
conda deactivate

How to update ICEscreen with Conda

We recommend installing the newer version of ICEscreen (see the section How to install ICEscreen locally from source), testing it, and then uninstalling the older version of ICEscreen (see the section How to uninstall ICEscreen installed from source).

How to uninstall ICEscreen with Conda

  • Conda environment:

You can remove the conda environment associated with the version of ICEscreen you want to uninstall. To know which conda icescreen_env to remove (i.e. if you have multiple versions of ICEscreen on the same machine), you can list all the conda icescreen_env installed on your system as follow:

conda info --envs | grep 'icescreen_env'

Once you have identified the version of the icescreen_env you want to remove, you can then use the conda env remove -n command, for example :

conda deactivate
conda env remove -n icescreen_env_X-X-X

Updated on 25 Jan 2024