Docker - Update base container

[marchoeppner]

Hi,

so I noticed that the Docker build is a tiny bit too minimal for my needs (I need 'ps' to be available); the base container that you guys use is also a l little on the older side and adding stuff via e.g. apt-get no longer works since the base OS is so old).

This worked for me (for 5.2.1):

FROM conda/miniconda3-centos7

WORKDIR /app

RUN conda install -c etetoolkit -c anaconda -c bioconda -c conda-forge -c defaults procps-ng biopython=1.77 cgmlst-dists=0.4.0 ete3 grapetree=2.1 numba=0.55.1 numpy=1.19.2 numpy-base=1.19.5 pandas=1.1.3 python=3.8 scikit-learn snp-sites=2.5.1 treecluster=1.0.3 zip pytest git --yes

RUN git clone -b v2.5.1 https://github.com/insapathogenomics/ReporTree && chmod 755 ReporTree/reportree.py && chmod 755 ReporTree/scripts/partitioning_grapetree.py && chmod 755 ReporTree/scripts/partitioning_HC.py && chmod 755 ReporTree/scripts/partitioning_treecluster.py && chmod 755 ReporTree/scripts/alignment_processing.py && chmod 755 ReporTree/scripts/metadata_report.py && cd ReporTree/scripts/ && git clone https://github.com/insapathogenomics/ComparingPartitions.git && git clone https://github.com/insapathogenomics/GrapeTree.git && git clone https://github.com/insapathogenomics/vcf2mst.git && cd ComparingPartitions && chmod 755 comparing_partitions_v2.py

ENV PATH="/app/ReporTree:/app/ReporTree/scripts:/app/ReporTree/scripts/ComparingPartitions:${PATH}"