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| Original file line number | Diff line number | Diff line change |
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| # Use the official Ubuntu image as a base | ||
| FROM ubuntu:24.04 | ||
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| # Set environment variables | ||
| ENV DEBIAN_FRONTEND=noninteractive | ||
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| # Update and install required packages | ||
| RUN apt update && \ | ||
| apt install -y wget git default-jre | ||
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| # create user | ||
| RUN useradd -ms /bin/bash participant | ||
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| # switch to participant | ||
| USER participant | ||
| WORKDIR /home/participant | ||
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| # Install Miniforge | ||
| RUN wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-$(uname -m).sh" && \ | ||
| bash Miniforge3-Linux-$(uname -m).sh -b -p /home/participant/miniforge3 && \ | ||
| rm Miniforge3-Linux-$(uname -m).sh && \ | ||
| /home/participant/miniforge3/bin/mamba init | ||
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| ENV PATH="/home/participant/miniforge3/bin:$PATH" | ||
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| # Setup Conda channels and config | ||
| RUN conda config --add channels defaults && \ | ||
| conda config --add channels bioconda && \ | ||
| conda config --add channels conda-forge && \ | ||
| conda config --set remote_read_timeout_secs 1000 | ||
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| # Install conda packages and create environments | ||
| RUN mamba install -y -n base pandas && \ | ||
| mamba create -y -n bakta bakta && \ | ||
| mamba create -y -n gubbins gubbins && \ | ||
| mamba create -y -n iqtree iqtree snp-sites biopython && \ | ||
| mamba create -y -n mlst mlst && \ | ||
| mamba create -y -n nextflow nextflow && \ | ||
| mamba create -y -n pairsnp pairsnp && \ | ||
| mamba create -y -n panaroo python=3.9 panaroo>=1.3 snp-sites && \ | ||
| mamba create -y -n poppunk python=3.10 poppunk && \ | ||
| mamba create -y -n remove_blocks python=2.7 && \ | ||
| /home/participant/miniforge3/envs/remove_blocks/bin/pip install git+https://github.com/sanger-pathogens/remove_blocks_from_aln.git && \ | ||
| mamba create -y -n seqtk seqtk pandas && \ | ||
| mamba create -y -n tb-profiler tb-profiler pandas && \ | ||
| mamba create -y -n treetime treetime seqkit biopython | ||
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| # Setup Nextflow config | ||
| RUN mkdir -p /home/participant/.nextflow && \ | ||
| echo "\ | ||
| conda { \ | ||
| conda.enabled = true \ | ||
| singularity.enabled = false \ | ||
| docker.enabled = false \ | ||
| useMamba = true \ | ||
| createTimeout = '4 h' \ | ||
| cacheDir = '/home/participant/.nextflow-conda-cache/' \ | ||
| } \ | ||
| singularity { \ | ||
| singularity.enabled = true \ | ||
| conda.enabled = false \ | ||
| docker.enabled = false \ | ||
| pullTimeout = '4 h' \ | ||
| cacheDir = '/home/participant/.nextflow-singularity-cache/' \ | ||
| } \ | ||
| docker { \ | ||
| docker.enabled = true \ | ||
| singularity.enabled = false \ | ||
| conda.enabled = false \ | ||
| }" >> /home/participant/.nextflow/config | ||
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| # Set the default command | ||
| CMD ["/bin/bash"] |
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| #!/bin/bash | ||
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| # exit on error | ||
| set -e | ||
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| # check for amrfinder_update | ||
| if ! command -v "amrfinder_update" &> /dev/null; then | ||
| echo "Error: amrfinder_update is not available on the PATH. You can install it with: mamba create -n bakta bakta" >&2 | ||
| exit 1 | ||
| fi | ||
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| # Download and extract course data | ||
| echo "Downloading and extracting course files" | ||
| wget -O bact-data.tar.gz "https://www.dropbox.com/scl/fi/osjpmst8i2919fv3by3eh/bact-data.tar.gz?rlkey=iddkexnnm6ccsx8prfcay259u&dl=1" | ||
| tar -xzf bact-data.tar.gz | ||
| rm bact-data.tar.gz | ||
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| # Download and extract public databases | ||
| mkdir databases | ||
| cd databases | ||
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| # kraken2 | ||
| echo "Downloading and extracting Kraken2 database" | ||
| wget https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20240605.tar.gz | ||
| mkdir k2_standard_08gb_20240605 | ||
| tar -xzf k2_standard_08gb_20240605.tar.gz -C k2_standard_08gb_20240605 | ||
| rm k2_standard_08gb_20240605.tar.gz | ||
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| # bakta | ||
| echo "Downloading and extracting Bakta database" | ||
| wget https://zenodo.org/records/10522951/files/db-light.tar.gz | ||
| tar -xzf db-light.tar.gz | ||
| mv db-light bakta_light_20240119 | ||
| rm db-light.tar.gz | ||
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| # update amrfinder database | ||
| amrfinder_update --force_update --database bakta_light_20240119/amrfinderplus-db/ | ||
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| # checkm2 | ||
| echo "Downloading and extracting CheckM2 database" | ||
| wget https://zenodo.org/records/5571251/files/checkm2_database.tar.gz | ||
| tar -xzf checkm2_database.tar.gz | ||
| mv CheckM2_database checkm2_v2_20210323 | ||
| rm checkm2_database.tar.gz CONTENTS.json | ||
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| # poppunk | ||
| echo "Downloading and extracting PopPunk database" | ||
| wget https://gps-project.cog.sanger.ac.uk/GPS_v8_ref.tar.gz | ||
| mkdir poppunk | ||
| tar -xzf GPS_v8_ref.tar.gz -C poppunk | ||
| rm GPS_v8_ref.tar.gz | ||
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| wget -O poppunk/GPS_v8_external_clusters.csv https://gps-project.cog.sanger.ac.uk/GPS_v8_external_clusters.csv |