updating freyja to 1.5.2

.github/workflows/update_freyja.yml

@@ -9,7 +9,7 @@ name: Update Freyja
 on: 
   workflow_dispatch:
   schedule:
-    - cron: '30 7 1 * *'
+    - cron: '30 7 * * 1'
 
 run-name: Updating Freyja
 
@@ -23,7 +23,7 @@ jobs:
       - name: set freyja version
         id: latest_version
         run: |
-          version=1.5.1
+          version=1.5.2
           echo "version=$version" >> $GITHUB_OUTPUT 
 
           file=freyja/$version/Dockerfile

README.md

@@ -170,7 +170,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [Filtlong](https://hub.docker.com/r/staphb/filtlong) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/filtlong)](https://hub.docker.com/r/staphb/filtlong) | <ul><li>0.2.0</li><li>0.2.1</li></ul> | https://github.com/rrwick/filtlong |
 | [FLASH](https://hub.docker.com/r/staphb/flash) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/flash)](https://hub.docker.com/r/staphb/flash) | <ul><li>1.2.11</li></ul> | http://ccb.jhu.edu/software/FLASH |
 | [Flye](https://hub.docker.com/r/staphb/flye) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/flye)](https://hub.docker.com/r/staphb/flye) | <ul><li>[2.5](flye/2.5/)</li><li>[2.7](flye/2.7/)</li><li>[2.8](flye/2.8/)</li><li>[2.9](flye/2.9/)</li><li>[2.9.1](flye/2.9.1/)</li><li>[2.9.2](flye/2.9.2/)</li><li>[2.9.3](flye/2.9.3/)</li><li>[2.9.4](flye/2.9.4/)</li></ul> | https://github.com/fenderglass/Flye |
-| [Freyja](https://hub.docker.com/r/staphb/freyja) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/freyja)](https://hub.docker.com/r/staphb/freyja) | <ul><li>[1.2](./freyja/1.2/)</li><li>[1.2.1](./freyja/1.2.1/)</li><li>[1.3.1](./freyja/1.3.1/)</li><li>[1.3.2](./freyja/1.3.2/)</li><li>[1.3.4](./freyja/1.3.4/)</li><li>[1.3.7](./freyja/1.3.7/)</li><li>[1.3.8](./freyja/1.3.8/)</li><li>[1.3.9](./freyja/1.3.9/)</li><li>[1.3.10](./freyja/1.3.10/)</li><li>[1.3.11](./freyja/1.3.11/)</li><li>[1.3.12](./freyja/1.3.12/)</li><li>[1.4.2](./freyja/1.4.2/)</li><li>[1.4.3](freyja/1.4.3/)</li><li>[1.4.4](freyja/1.4.4/)</li><li>[1.4.5](freyja/1.4.5/)</li><li>[1.4.7](freyja/1.4.7/)</li><li>[1.4.8](freyja/1.4.8/)</li><li>[1.4.9](freyja/1.4.9/)</li><li>[1.5.0](freyja/1.5.0/)</li><li>[1.5.1](freyja/1.5.1/)</li></ul> | https://github.com/andersen-lab/Freyja |
+| [Freyja](https://hub.docker.com/r/staphb/freyja) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/freyja)](https://hub.docker.com/r/staphb/freyja) | <ul><li>[1.2](./freyja/1.2/)</li><li>[1.2.1](./freyja/1.2.1/)</li><li>[1.3.1](./freyja/1.3.1/)</li><li>[1.3.2](./freyja/1.3.2/)</li><li>[1.3.4](./freyja/1.3.4/)</li><li>[1.3.7](./freyja/1.3.7/)</li><li>[1.3.8](./freyja/1.3.8/)</li><li>[1.3.9](./freyja/1.3.9/)</li><li>[1.3.10](./freyja/1.3.10/)</li><li>[1.3.11](./freyja/1.3.11/)</li><li>[1.3.12](./freyja/1.3.12/)</li><li>[1.4.2](./freyja/1.4.2/)</li><li>[1.4.3](freyja/1.4.3/)</li><li>[1.4.4](freyja/1.4.4/)</li><li>[1.4.5](freyja/1.4.5/)</li><li>[1.4.7](freyja/1.4.7/)</li><li>[1.4.8](freyja/1.4.8/)</li><li>[1.4.9](freyja/1.4.9/)</li><li>[1.5.0](freyja/1.5.0/)</li><li>[1.5.1](freyja/1.5.1/)</li><li>[1.5.2](freyja/1.5.2/)</li></ul> | https://github.com/andersen-lab/Freyja |
 | [GAMBIT](https://hub.docker.com/r/staphb/gambit) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/gambit)](https://hub.docker.com/r/staphb/gambit) | <ul><li>0.3.0</li><li>0.4.0</li><li>0.5.0</li><li>1.0.0</li></ul> | https://github.com/jlumpe/gambit |
 | [GAMMA](https://hub.docker.com/r/staphb/gamma) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/gamma)](https://hub.docker.com/r/staphb/gamma) | <ul><li>1.4</li><li>2.1</li><li>2.2</li></ul> | https://github.com/rastanton/GAMMA/ |
 | [GenoFLU](https://hub.docker.com/r/staphb/genoflu) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/genoflu)]() | <ul><li>[1.03](genoflu/1.03/)</li></ul> | https://github.com/USDA-VS/GenoFLU |

freyja/1.5.2/Dockerfile

@@ -0,0 +1,103 @@
+FROM mambaorg/micromamba:1.5.8 as app
+
+# Version arguments
+# ARG variables only persist during build time
+ARG FREYJA_SOFTWARE_VERSION="1.5.2"
+ARG IVAR_VER="1.4.3"
+ARG SAMTOOLS_VER="1.21"
+ARG USHER_VER="0.6.3"
+
+
+# build and run as root users since micromamba image has 'mambauser' set as the $USER
+USER root
+# set workdir to default for building; set to /data at the end
+WORKDIR /
+
+LABEL base.image="mambaorg/micromamba:1.5.8"
+LABEL dockerfile.version="1"
+LABEL software="Freyja"
+LABEL software.version=${FREYJA_SOFTWARE_VERSION}
+LABEL description="Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference)"
+LABEL website="https://github.com/andersen-lab/Freyja"
+LABEL license="https://github.com/andersen-lab/Freyja/blob/main/LICENSE"
+LABEL maintainer="Kevin Libuit"
+LABEL maintainer.email="[email protected]"
+LABEL maintainer2="Curtis Kapsak"
+LABEL maintainer2.email="[email protected]"
+LABEL maintainer3="Erin Young"
+LABEL maintainer3.email="[email protected]"
+
+# install dependencies; cleanup apt garbage
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    procps \
+    git && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# Create Freyja conda environment called freyja-env from bioconda recipe
+# clean up conda garbage
+RUN micromamba create -n freyja-env -c conda-forge -c bioconda -c defaults \
+    ivar=${IVAR_VER} \
+    usher=${USHER_VER} \
+    samtools=${SAMTOOLS_VER} \
+    pip \
+    biopython \
+    click \
+    cvxpy \
+    epiweeks \
+    joblib \
+    matplotlib-base \
+    numpy \
+    pandas \
+    plotly \
+    pyarrow \
+    pysam \
+    pyyaml \
+    requests \
+    seaborn \
+    tqdm && \
+    micromamba clean -a -y -f 
+
+# set the environment, put new conda env in PATH by default
+ENV PATH="/opt/conda/envs/freyja-env/bin:/opt/conda/envs/env/bin:${PATH}" \
+    LC_ALL=C.UTF-8
+
+RUN wget -q https://github.com/andersen-lab/Freyja/archive/refs/tags/v${FREYJA_SOFTWARE_VERSION}.tar.gz && \
+    pip install --no-cache-dir v${FREYJA_SOFTWARE_VERSION}.tar.gz && \
+    rm v${FREYJA_SOFTWARE_VERSION}.tar.gz
+
+
+# update barcodes
+# NOTE: this will download the latest version of the `freyja/data/usher_barcodes.csv` file from GitHub
+RUN freyja update
+
+# set working directory to /data
+WORKDIR /data
+
+# default command is to pull up help options
+CMD [ "freyja", "--help" ]
+
+# new base for testing
+FROM app as test
+
+RUN freyja --help && freyja --version
+
+# Grab test data from Freyja version 1.3.4
+RUN wget -O /data/Freyja_WWSC2.bam https://github.com/StaPH-B/docker-builds/blob/master/freyja/1.3.4/tests/Freyja_WWSC2.bam?raw=true && \
+    wget -P /data https://raw.githubusercontent.com/StaPH-B/docker-builds/master/freyja/1.3.4/tests/Freyja_depths.tsv && \
+    wget -P /data https://raw.githubusercontent.com/StaPH-B/docker-builds/master/freyja/1.3.4/tests/Freyja_variants.tsv && \
+    wget -P /data https://raw.githubusercontent.com/StaPH-B/docker-builds/master/freyja/1.3.4/tests/nCoV-2019.reference.fasta
+
+# Run Freyja
+RUN freyja variants /data/Freyja_WWSC2.bam --variants /data/test_variants.tsv --depths /data/test_depths.tsv --ref /data/nCoV-2019.reference.fasta && \
+    freyja demix /data/test_variants.tsv /data/test_depths.tsv --output /data/test_demix.tsv
+
+# Check validity of outputs
+RUN head /data/test_variants.tsv && \
+    head /data/test_depths.tsv && \
+    head /data/test_demix.tsv && \
+    grep "Omicron" /data/test_demix.tsv
+
+# print barcode version and freyja version
+RUN freyja demix --version

freyja/1.5.2/README.md

@@ -0,0 +1,23 @@
+# freyja container
+
+Main tool & documentation: [freyja](https://github.com/andersen-lab/Freyja)
+
+Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference). The method uses lineage-determining mutational "barcodes" derived from the UShER global phylogenetic tree as a basis set to solve the constrained (unit sum, non-negative) de-mixing problem.
+
+## freyja barcodes
+
+This docker image was built on **2024-10-28** and the command `freyja update` is run as part of the build to retrieve the most up-to-date database. The barcode version included in this docker image is **`10_27_2024-01-41`** as reported by `freyja demix --version`
+
+This image is rebuilt every day on Dockerhub and Quay.io with the tag ${freyja version}-${freyja database version}-${data image was deployed}.
+
+## Example Usage
+
+```bash
+# run freyja variants to call variants from an aligned SC2 bam file
+freyja variants [bamfile] --variants [variant outfile name] --depths [depths outfile name] --ref [reference.fa]
+
+# run freyja demix to identify lineages based on called variants 
+freyja demix [variants-file] [depth-file] --output [output-file]
+```
+
+Warning: `freyja update` does not work under all conditions. You may need to specify an output directory (`freyja update --outdir /path/to/outdir`) for which your user has write privileges, such as a mounted volume.