Installing InSilicoSeq

Using pip

InSilicoSeq requires python>=3.5. To install InSilicoSeq, type the following in your terminal:

pip install InSilicoSeq

It will install InSilicoSeq as well as the following dependencies:

  • biopython
  • joblib
  • numpy
  • pysam
  • scipy

Other installation options

  • With conda:
conda install -c bioconda insilicoseq
  • Upgrading InSilicoSeq to the latest version:
pip install --upgrade InSilicoSeq
  • If you don’t have administration rights on your machine:
pip3 install --user InSilicoSeq
  • if you wish to install InSilicoSeq at a custom location (i.e with a module system):
pip install --install-option="--prefix=/$prefix" InSilicoSeq

then add $prefix/bin to your PATH, and $prefix/lib/python3.X/site-packages to your PYTHONPATH (replacing python3.X with your python version)

Using docker

If you wish to use InSilicoSeq using docker

docker pull hadrieng/insilicoseq:latest

To use InSilicoSeq with docker, you need to provide a volume to the docker run command. Given with the -v option, the volume is your way of exchanging data (in this case, your input and output files) with the docker container.

docker run -v /Users/hadrien/data:/mnt/data -it --rm \
    hadrieng/insilicoseq iss generate \
    --genomes /mnt/data/genomes.fasta -m miseq \
    -o /mnt/data/reads

The above command will mount the local folder /Users/hadrien/data onto /mnt/data on the docker side. The output reads will be located in /Users/hadrien/data when InSilicoSeq has finished running.