Dockerfile for eukcc 2.1.3 via pip

[KateSakharova]

That one is quite urgly, but it seems working... It didn't build on my Mac, but @vagkaratzas built it sucessfully on linux

[mberacochea]

mysql?

[mberacochea]

Why do we need ti skip the certificates?

[mberacochea]

I have simpler solution (BUT I haven't tested other than eukcc --version)

Dockerfile:

FROM mambaorg/micromamba:2.0.5

COPY --chown=$MAMBA_USER:$MAMBA_USER env.yml /tmp/env.yml

RUN micromamba install -y -n base -f /tmp/env.yml \
    && micromamba install -y -n base conda-forge::procps-ng \
    && micromamba env export --name base --explicit > environment.lock \
    && cat environment.lock \
    && micromamba clean -a -y

ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"

env.yml

  - bioconda
  - conda-forge
dependencies:
  - metaeuk=4.a0f584d
  - pplacer
  - epa-ng=0.3.8
  - python=3.8
  - hmmer=3.3
  - minimap2
  - bwa
  - pysam
  - biopython
  - samtools=1.12
  - six
  - pip
  - pip:
      - jsonpickle>=4.0.0
      - numpy>=1.24.4
      - ete3>=3.1.3
      - eukcc==2.1.3