README.md

Dockerfile for building olivar with dependancies

Olivar Gitlab Repository

Packages and Dependencies installed in compile-image.

Python modules from requirements.txt file

• certifi==2020.4.5.1
• chardet==3.0.4
• docopt==0.6.2
• idna==2.9
• pipdeptree==0.13.2
• pipreqs==0.4.10
• requests==2.23.0
• urllib3==1.25.9
• yarg==0.1.9
• biopython==1.77
• pandas==1.0.4
• jinja2==2.11.2
• pysam==0.15.4
• pyvcf==0.6.8

Items manually installed

• Parsnp -https://github.com/marbl/parsnp - Download
• Primer3 - http://sourceforge.net/projects/primer3/files/primer3 - Download - Source
• Blast - https://blast.ncbi.nlm.nih.gov/Blast.cgi - Download
• Samtools - https://github.com/samtools/samtools - Source
• HTSlib - https://github.com/samtools/htslib - Source
• Minimap2 - https://lh3.github.io/minimap2 - Source
• Bowtie2 - http://bowtie-bio.sourceforge.net/bowtie2/index.shtml - Source
• Lofreq - https://csb5.github.io/lofreq/ - Source

Packages and Dependencies installed in build-image (2nd pass)

• MAFFT - https://mafft.cbrc.jp/alignment/software/mafft_7.450-1_amd64.deb

To build image

git clone [email protected]:deigaard/olivar-container.git

cd olivar-container

docker build -t deigaard/olivar-container .

To use image that you built above

Interactive use

docker run -it --rm \
    -v "${HOME}:${HOME}:ro" \
    -v "$(pwd):/opt/olivar" \
    -v /tmp:/tmp \
    --workdir /opt/olivar \
    --log-driver none \
    deigaard/olivar-container

Command-line use

docker run -it --rm \
    -v "${HOME}:${HOME}:ro" \
    -v "$(pwd):/opt/olivar" \
    -v /tmp:/tmp \
    --workdir /opt/olivar \
    --log-driver none \
    deigaard/olivar-container ./command and/or -args

Or, handy bash function:

. bashfunc
git clone [email protected]:treangenlab/olivar.git
cd olivar
olivar python ./olivar.py /path/to/reference.fasta /path/to/input_genomes/

olivar bash

olivar

To use pre-built image

. bashfunc-prebuilt

git clone [email protected]:treangenlab/olivar.git
cd olivar
olivar python ./olivar.py /path/to/reference.fasta /path/to/input_genomes/