FROM python:3

WORKDIR /usr/src/app

COPY FastQC/ /FastQC/
COPY kegg_annotation/ /kegg_annotation/
COPY Read_files/ /Read_files/
COPY sample_input_files/ /sample_input_files/
COPY sample_output_files/ /sample_output_files/
COPY sra_files/ /sra_files/
COPY 2.1.26.pe.100.0065.ann .
COPY 2.1.26.se.100.005.ann .
COPY camamed_data_normalization.py .
COPY camamed_kegg_annotation.py .
COPY camamed_mapping_mosaik.py .
COPY camamed_metaphlan_profiling.py .
COPY camamed_pre_processing.py .
COPY camamed_quality_control.py .
COPY camamed_statistical_test.py .
COPY cumNormMat.py .
COPY fastqc_samlpe.sh .
COPY metaphlan_samlpe.sh .
COPY MosaikAligner .
COPY MosaikBuild .
COPY mosaik_build_ref.sh .
COPY MosaikJump .
COPY mosaik_read_aligner.sh . 
COPY seqkit .
COPY seqkit_samlpe.sh .
COPY sra_samlpe.sh .

RUN apt-get update && apt-get install -y \
    fastqc \
    sra-toolkit \
    samtools \
    cd-hit \
    metaphlan2


COPY requirements.txt .
RUN pip install --no-cache-dir -r requirements.txt
