microSALT v.5.0.0

.github/workflows/run_tests.yml

@@ -3,39 +3,24 @@ name: Tests
 on: [push]
 
 
-env:
-  CONDA_PREFIX: /home/runner/work/microSALT/microSALT/tests
-  COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
-
 jobs:
   build-linux:
     runs-on: ubuntu-latest
-    container:
-      image: python:3.6-slim
-
+
     steps:
     - uses: actions/checkout@v4
-
-    - name: Create conda/mamba environment using micromamba
-      uses: mamba-org/setup-micromamba@v1
-      with:
-        environment-file: environment.yml
-        cache-downloads: true
-    - name: Install microSALT
-      run: |
-        mkdir ~/.microSALT && cp configExample.json ~/.microSALT/config.json
-        GITHUB_BRANCH=${GITHUB_REF##*/}
-        pip install -r requirements.txt -r requirements-dev.txt
-        pip install -U .
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+    - name: Set up Python
+      run: uv python install
+    - name: Install microSALT and dev dependencies
+      run: uv sync --dev
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        uv run flake8 . --exclude=.venv --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        uv run flake8 . --exclude=.venv --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        pytest --cov=microSALT tests
-    - name: Run Coveralls
-      run: |
-        coveralls
+        uv run pytest tests

.gitignore

@@ -4,7 +4,7 @@ microSALT/__pycache__
 microSALT.log
 instance/sqlalchemy_config.py
 instance/paths.yml
-unique_references/*.n*
+microSALT/unique_references/*.n*
 .pytest_cache/
 *.egg-info
 *pyc
@@ -16,3 +16,4 @@ tmp.json
 .venv/
 .vscode*
 .markdownlint.jsonc
+build

.python-version

@@ -0,0 +1 @@
+3.12

README.md

@@ -1,10 +1,9 @@
 [![Build status](https://github.com/clinical-genomics/microsalt/actions/workflows/run_tests.yml/badge.svg)](https://github.com/clinical-genomics/microsalt/actions/workflows/run_tests.yml)
-[![Coverage Status](https://coveralls.io/repos/github/Clinical-Genomics/microSALT/badge.svg?branch=master)](https://coveralls.io/github/Clinical-Genomics/microSALT?branch=master)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4026043.svg)](https://doi.org/10.5281/zenodo.4026043)
 
 <p align="center">
-  <a href="https://github.com/sylvinite/microSALT">
-    <img width="1000" height="250" src="artwork/microsalt.jpg"/>
+  <a href="https://github.com/Clinical-Genomics/microSALT">
+    <img width="1000" height="250" src="microSALT/artwork/microsalt.jpg"/>
   </a>
 </p>
 
@@ -16,16 +15,20 @@ sample, determines a sample's organism specific sequence type, and its
 resistance pattern. microSALT also provides a database storage solution and
 report generation of these results._
 
-_microSALT uses a combination of python, sqLite and flask. Python is used for
-the majority of functionality, the database is handled through sqLite and the
-front-end is handled through flask. All analysis activity by microSALT requires
-a SLURM cluster._
+_microSALT uses a combination of Python, MySQL and Jinja2. Python is used for
+the majority of functionality, the database is handled through MySQL via
+SQLAlchemy and reports are rendered through Jinja2. All analysis activity by
+microSALT requires a SLURM cluster._
 
 ## Quick installation
 
-1. `yes | bash <(curl https://raw.githubusercontent.com/Clinical-Genomics/microSALT/master/install.sh)`
-2. `cp configExample.json $HOME/.microSALT/config.json`
-3. `vim $HOME/.microSALT/config.json`
+> [!IMPORTANT]
+> This install requires `uv` to be installed on the system. For installation instructions, see [https://docs.astral.sh/uv/getting-started/installation/](https://docs.astral.sh/uv/getting-started/installation/).
+
+1. `bash <(curl https://raw.githubusercontent.com/Clinical-Genomics/microSALT/master/install.sh)`
+2. `source microSALT/.venv/bin/activate`
+3. `cp microSALT/configExample.json $HOME/.microSALT/config.json`
+4. `vim $HOME/.microSALT/config.json`
 
 ## Configuration
 
@@ -46,11 +49,11 @@ export MICROSALT_CONFIG=/MY/FAV/FOLDER/config.json
 
 ## Usage
 
-- `microSALT analyse` contains functions to start sbatch job(s) & produce
+- `microsalt analyse` contains functions to start sbatch job(s) & produce
   output to `folders['results']`. Afterwards the parsed results are uploaded
   to the SQL back-end and produce reports (HTML), which are then automatically
   e-mailed to the user.
-- `microSALT utils` contains various functionality, including generating the
+- `microsalt utils` contains various functionality, including generating the
   sample description json, manually adding new reference organisms and
   re-generating reports.
 
@@ -72,13 +75,12 @@ Any definitions will work, as long as they retain the same formatting.
 ### Hardware
 
 - A [SLURM](https://slurm.schedmd.com) enabled HPC system
-- A (clarity) LIMS server
 
 ### Software
 
-- [Conda](https://conda.io) >= 3.6
-- Python 3.6
-- [SQLite](https://www.sqlite.org)
+- [uv](https://docs.astral.sh/uv) >= 0.4
+- Python >= 3.10
+- [MySQL](https://www.mysql.com) server
 
 ## Contributing to this repo
 

configExample.json

@@ -21,8 +21,6 @@
     "results": "/tmp/MLST/results/",
     "_comment": "Report collection folder",
     "reports": "/tmp/MLST/reports/",
-    "_comment": "Log file position and name",
-    "log_file": "/tmp/microsalt.log",
     "_comment": "Root folder for input fasta sequencing data",
     "seqdata": "/tmp/projects/",
     "_comment": "ST profiles. Each ST profile file under 'profiles' have an identicial folder under references",
@@ -69,12 +67,6 @@
     "bp_50x_warn": 50,
     "bp_100x_warn": 20
   },
-  "_comment": "Genologics temporary configuration file",
-  "genologics": {
-    "baseuri": "https://lims.facility.se/",
-    "username": "limsuser",
-    "password": "mypassword"
-  },
   "_comment": "Credentials",
   "pubmlst": {
     "client_id": "",
@@ -83,5 +75,24 @@
   "pasteur": {
     "client_id": "",
     "client_secret": ""
+  },
+  "_comment": "Singularity runtime configuration",
+  "singularity": {
+    "binary": "/usr/bin/singularity",
+    "_comment": "Paths that must be visible inside every container (passed as --bind)",
+    "bind_paths": ["/data"],
+    "_comment": "Adapter path inside the trimmomatic container (bioconda default)",
+    "trimmomatic_adapters": "/opt/conda/share/trimmomatic/adapters/"
+  },
+  "_comment": "Absolute paths to pre-built Singularity SIF images on the cluster",
+  "containers": {
+    "skesa": "/fs1/resources/containers/skesa_2.5.1.sif",
+    "blast": "/fs1/resources/containers/blast_2.12.0.sif",
+    "bwa": "/fs1/resources/containers/bwa_0.7.17.sif",
+    "samtools": "/fs1/resources/containers/samtools_1.13.sif",
+    "picard": "/fs1/resources/containers/picard_2.20.3.sif",
+    "trimmomatic": "/fs1/resources/containers/trimmomatic_0.39.sif",
+    "quast": "/fs1/resources/containers/quast_5.3.0.sif"
   }
-}
+}
+

containers/Dockerfile.blast

@@ -0,0 +1,19 @@
+# NCBI BLAST 2.12.0 — nucleotide BLAST search and database indexing
+# Build: docker build -f Dockerfile.blast -t blast:2.12.0 .
+# Convert: singularity pull --name blast_2.12.0.sif docker://your-repo/blast:2.12.0
+FROM mambaorg/micromamba:1-bookworm-slim
+
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+USER root
+RUN apt-get update \
+    && apt-get upgrade -y \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+USER $MAMBA_USER
+
+RUN micromamba install -y -n base -c conda-forge -c bioconda \
+        blast=2.12.0 \
+    && micromamba clean -afy
+
+ENV PATH="/opt/conda/bin:$PATH"

containers/Dockerfile.bwa

@@ -0,0 +1,19 @@
+# BWA 0.7.17 — short read aligner (mem mode) and reference indexing
+# Build: docker build -f Dockerfile.bwa -t bwa:0.7.17 .
+# Convert: singularity pull --name bwa_0.7.17.sif docker://your-repo/bwa:0.7.17
+FROM mambaorg/micromamba:1-bookworm-slim
+
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+USER root
+RUN apt-get update \
+    && apt-get upgrade -y \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+USER $MAMBA_USER
+
+RUN micromamba install -y -n base -c conda-forge -c bioconda \
+        bwa=0.7.17 \
+    && micromamba clean -afy
+
+ENV PATH="/opt/conda/bin:$PATH"

containers/Dockerfile.picard

@@ -0,0 +1,23 @@
+# Picard 2.20.3 — duplicate marking and insert size metrics
+# Build: docker build -f Dockerfile.picard -t picard:2.20.3 .
+# Convert: singularity pull --name picard_2.20.3.sif docker://your-repo/picard:2.20.3
+#
+# The bioconda picard package installs a wrapper script that calls the JAR via
+# the bundled Java runtime; no separate openjdk install is needed.
+FROM mambaorg/micromamba:1-bookworm-slim
+
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+USER root
+RUN apt-get update \
+    && apt-get upgrade -y \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+USER $MAMBA_USER
+
+RUN micromamba install -y -n base -c conda-forge -c bioconda \
+        picard=2.20.3 \
+        r-base=4.1.1 \
+    && micromamba clean -afy
+
+ENV PATH="/opt/conda/bin:$PATH"

containers/Dockerfile.quast

@@ -0,0 +1,21 @@
+# QUAST 5.3.0 — assembly quality assessment
+# Build: docker build -f Dockerfile.quast -t quast:5.3.0 .
+# Convert: singularity pull --name quast_5.3.0.sif docker://your-repo/quast:5.3.0
+#
+# The entry point is quast.py (as installed by bioconda).
+FROM mambaorg/micromamba:1-bookworm-slim
+
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+USER root
+RUN apt-get update \
+    && apt-get upgrade -y \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+USER $MAMBA_USER
+
+RUN micromamba install -y -n base -c conda-forge -c bioconda \
+        quast=5.3.0 \
+    && micromamba clean -afy
+
+ENV PATH="/opt/conda/bin:$PATH"

containers/Dockerfile.samtools

@@ -0,0 +1,19 @@
+# SAMtools 1.13 — SAM/BAM processing, indexing, and statistics
+# Build: docker build -f Dockerfile.samtools -t samtools:1.13 .
+# Convert: singularity pull --name samtools_1.13.sif docker://your-repo/samtools:1.13
+FROM mambaorg/micromamba:1-bookworm-slim
+
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+USER root
+RUN apt-get update \
+    && apt-get upgrade -y \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+USER $MAMBA_USER
+
+RUN micromamba install -y -n base -c conda-forge -c bioconda \
+        samtools=1.13 \
+    && micromamba clean -afy
+
+ENV PATH="/opt/conda/bin:$PATH"

containers/Dockerfile.skesa

@@ -0,0 +1,19 @@
+# SKESA 2.5.1 — de novo assembler
+# Build: docker build -f Dockerfile.skesa -t skesa:2.5.1 .
+# Convert: singularity pull --name skesa_2.5.1.sif docker://your-repo/skesa:2.5.1
+FROM mambaorg/micromamba:1-bookworm-slim
+
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+USER root
+RUN apt-get update \
+    && apt-get upgrade -y \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+USER $MAMBA_USER
+
+RUN micromamba install -y -n base -c conda-forge -c bioconda \
+        skesa=2.5.1 \
+    && micromamba clean -afy
+
+ENV PATH="/opt/conda/bin:$PATH"

containers/Dockerfile.trimmomatic

@@ -0,0 +1,23 @@
+# Trimmomatic 0.39 — quality trimming for paired-end Illumina reads
+# Build: docker build -f Dockerfile.trimmomatic -t trimmomatic:0.39 .
+# Convert: singularity pull --name trimmomatic_0.39.sif docker://your-repo/trimmomatic:0.39
+#
+# Adapter files are located inside the container at:
+#   /opt/conda/share/trimmomatic/adapters/
+# Set singularity.trimmomatic_adapters in your config to this path.
+FROM mambaorg/micromamba:1-bookworm-slim
+
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+USER root
+RUN apt-get update \
+    && apt-get upgrade -y \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+USER $MAMBA_USER
+
+RUN micromamba install -y -n base -c conda-forge -c bioconda \
+        trimmomatic=0.39 \
+    && micromamba clean -afy
+
+ENV PATH="/opt/conda/bin:$PATH"

environment.yml

@@ -1,19 +1,3 @@
 name: P_microSALT
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
 dependencies:
-  - python=3.6
-  - blast=2.12.0
-  - bwa=0.7.17
-  - picard=2.20.3
-  - pigz>=2.4
-  - quast=5.0.2
-  - samtools=1.13
-  - trimmomatic=0.39
-  - r-base=4.1.1
-  - openjdk=11.0.9.1
-  - pytest=6.2.5
-  - pytest-cov=2.12.1
-  - skesa=2.5.1
+  - python=3.12