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Merge branch 'rc5.0.0' of github.com:Clinical-Genomics/microSALT into rc5.0.0
2 parents 4ddf050 + 7f0bbb0 commit 5ec64e3

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‎.python_version‎

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‎README.md‎

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## Usage
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- `microSALT analyse` contains functions to start sbatch job(s) & produce
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- `microsalt analyse` contains functions to start sbatch job(s) & produce
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output to `folders['results']`. Afterwards the parsed results are uploaded
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to the SQL back-end and produce reports (HTML), which are then automatically
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e-mailed to the user.
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- `microSALT utils` contains various functionality, including generating the
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- `microsalt utils` contains various functionality, including generating the
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sample description json, manually adding new reference organisms and
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re-generating reports.
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‎configExample.json‎

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"_comment": "Download path for NCBI genomes, for alignment usage",
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"genomes": "/tmp/MLST/references/genomes",
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"_comment": "Credentials",
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"credentials": "/tmp/MLST/credentials"
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"credentials": "/tmp/MLST/credentials",
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"_comment": "Trimmomatic adapter FASTA files directory",
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"adapters": "/path/to/trimmomatic/adapters/"
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},
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"_comment": "Database/Flask configuration",
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"database": {
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"pasteur": {
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"client_id": "",
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"client_secret": ""
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},
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"_comment": "Singularity runtime configuration",
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"singularity": {
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"binary": "/usr/bin/singularity",
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"_comment": "Paths that must be visible inside every container (passed as --bind)",
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"bind_paths": ["/data"],
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"_comment": "Adapter path inside the trimmomatic container (bioconda default)",
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"trimmomatic_adapters": "/opt/conda/share/trimmomatic/adapters/"
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},
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"_comment": "Absolute paths to pre-built Singularity SIF images on the cluster",
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"containers": {
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"skesa": "/fs1/resources/containers/skesa_2.5.1.sif",
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"blast": "/fs1/resources/containers/blast_2.12.0.sif",
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"bwa": "/fs1/resources/containers/bwa_0.7.17.sif",
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"samtools": "/fs1/resources/containers/samtools_1.13.sif",
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"picard": "/fs1/resources/containers/picard_2.20.3.sif",
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"trimmomatic": "/fs1/resources/containers/trimmomatic_0.39.sif",
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"quast": "/fs1/resources/containers/quast_5.3.0.sif"
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}
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}

‎containers/Dockerfile.blast‎

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# NCBI BLAST 2.12.0 — nucleotide BLAST search and database indexing
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# Build: docker build -f Dockerfile.blast -t blast:2.12.0 .
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# Convert: singularity pull --name blast_2.12.0.sif docker://your-repo/blast:2.12.0
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FROM mambaorg/micromamba:1-bookworm-slim
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ARG MAMBA_DOCKERFILE_ACTIVATE=1
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USER root
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RUN apt-get update \
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&& apt-get upgrade -y \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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USER $MAMBA_USER
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RUN micromamba install -y -n base -c conda-forge -c bioconda \
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blast=2.12.0 \
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&& micromamba clean -afy

‎containers/Dockerfile.bwa‎

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# BWA 0.7.17 — short read aligner (mem mode) and reference indexing
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# Build: docker build -f Dockerfile.bwa -t bwa:0.7.17 .
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# Convert: singularity pull --name bwa_0.7.17.sif docker://your-repo/bwa:0.7.17
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FROM mambaorg/micromamba:1-bookworm-slim
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ARG MAMBA_DOCKERFILE_ACTIVATE=1
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USER root
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RUN apt-get update \
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&& apt-get upgrade -y \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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USER $MAMBA_USER
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RUN micromamba install -y -n base -c conda-forge -c bioconda \
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bwa=0.7.17 \
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&& micromamba clean -afy

‎containers/Dockerfile.picard‎

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# Picard 2.20.3 — duplicate marking and insert size metrics
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# Build: docker build -f Dockerfile.picard -t picard:2.20.3 .
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# Convert: singularity pull --name picard_2.20.3.sif docker://your-repo/picard:2.20.3
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#
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# The bioconda picard package installs a wrapper script that calls the JAR via
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# the bundled Java runtime; no separate openjdk install is needed.
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FROM mambaorg/micromamba:1-bookworm-slim
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ARG MAMBA_DOCKERFILE_ACTIVATE=1
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USER root
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RUN apt-get update \
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&& apt-get upgrade -y \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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USER $MAMBA_USER
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RUN micromamba install -y -n base -c conda-forge -c bioconda \
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picard=2.20.3 \
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r-base=4.1.1 \
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&& micromamba clean -afy

‎containers/Dockerfile.quast‎

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# QUAST 5.3.0 — assembly quality assessment
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# Build: docker build -f Dockerfile.quast -t quast:5.3.0 .
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# Convert: singularity pull --name quast_5.3.0.sif docker://your-repo/quast:5.3.0
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#
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# The entry point is quast.py (as installed by bioconda).
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FROM mambaorg/micromamba:1-bookworm-slim
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ARG MAMBA_DOCKERFILE_ACTIVATE=1
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USER root
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RUN apt-get update \
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&& apt-get upgrade -y \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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USER $MAMBA_USER
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RUN micromamba install -y -n base -c conda-forge -c bioconda \
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quast=5.3.0 \
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&& micromamba clean -afy

‎containers/Dockerfile.samtools‎

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# SAMtools 1.13 — SAM/BAM processing, indexing, and statistics
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# Build: docker build -f Dockerfile.samtools -t samtools:1.13 .
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# Convert: singularity pull --name samtools_1.13.sif docker://your-repo/samtools:1.13
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FROM mambaorg/micromamba:1-bookworm-slim
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ARG MAMBA_DOCKERFILE_ACTIVATE=1
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USER root
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RUN apt-get update \
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&& apt-get upgrade -y \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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USER $MAMBA_USER
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RUN micromamba install -y -n base -c conda-forge -c bioconda \
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samtools=1.13 \
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&& micromamba clean -afy

‎containers/Dockerfile.skesa‎

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# SKESA 2.5.1 — de novo assembler
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# Build: docker build -f Dockerfile.skesa -t skesa:2.5.1 .
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# Convert: singularity pull --name skesa_2.5.1.sif docker://your-repo/skesa:2.5.1
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FROM mambaorg/micromamba:1-bookworm-slim
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ARG MAMBA_DOCKERFILE_ACTIVATE=1
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USER root
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RUN apt-get update \
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&& apt-get upgrade -y \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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USER $MAMBA_USER
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RUN micromamba install -y -n base -c conda-forge -c bioconda \
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skesa=2.5.1 \
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&& micromamba clean -afy

‎containers/Dockerfile.trimmomatic‎

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# Trimmomatic 0.39 — quality trimming for paired-end Illumina reads
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# Build: docker build -f Dockerfile.trimmomatic -t trimmomatic:0.39 .
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# Convert: singularity pull --name trimmomatic_0.39.sif docker://your-repo/trimmomatic:0.39
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#
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# Adapter files are located inside the container at:
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# /opt/conda/share/trimmomatic/adapters/
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# Set singularity.trimmomatic_adapters in your config to this path.
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FROM mambaorg/micromamba:1-bookworm-slim
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ARG MAMBA_DOCKERFILE_ACTIVATE=1
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USER root
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RUN apt-get update \
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&& apt-get upgrade -y \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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USER $MAMBA_USER
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RUN micromamba install -y -n base -c conda-forge -c bioconda \
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trimmomatic=0.39 \
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&& micromamba clean -afy

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