Installing InSilicoSeq¶
Using pip¶
To install InSilicoSeq, type the following in your terminal:
pip install InSilicoSeq
It will install InSilicoSeq as well as the following dependencies:
- biopython
- numpy
- pysam
- scipy
Advanced options¶
- If you don’t have administration rights on your machine:
pip install --user InSilicoSeq
- if you wish to install InSilicoSeq at a custom location (i.e with a
mdoule system):
prefix="/path/to/install/prefix"
pip install --install-option="--prefix=/$prefix" InSilicoSeq
then add $prefix/bin
to your PATH
, and
$prefix/lib/pythonX.X/site-packages
to your PYTHONPATH
(replacing
pythonX.X with your python version)
Using docker¶
If you wish to use InSilicoSeq using docker
docker pull hadrieng/insilicoseq:0.8.1
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
to 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:0.8.0 iss generate \
--genomes /mnt/data/ecoli.fasta -f MiSeq \
-o /mnt/data/reads_ecoli_miseq
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.