Merge pull request #792 from laura-bankers/master

freyja v.1.4.7 docker workshop

README.md

@@ -150,7 +150,7 @@ 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</li><li>2.7</li><li>2.8</li><li>2.9</li><li>2.9.1</li><li>2.9.2</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</li><li>1.2.1</li><li>1.3.1</li><li>1.3.2</li><li>1.3.4</li><li>1.3.7</li><li>1.3.8</li><li>1.3.9</li><li>1.3.10</li><li>1.3.11</li><li>1.3.12</li><li>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></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</li><li>1.2.1</li><li>1.3.1</li><li>1.3.2</li><li>1.3.4</li><li>1.3.7</li><li>1.3.8</li><li>1.3.9</li><li>1.3.10</li><li>1.3.11</li><li>1.3.12</li><li>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></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/ |
 | [gfastats](https://hub.docker.com/r/staphb/gfastats) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/gfastats)](https://hub.docker.com/r/staphb/gfastats) | <ul><li>1.3.6</li></ul> | https://github.com/vgl-hub/gfastats |
@@ -320,4 +320,5 @@ Each Dockerfile lists the author(s)/maintainer(s) as a metadata `LABEL`, but the
   * [@Kincekara](https://github.com/Kincekara)
   * [@Haikelnb](https://github.com/Haikelnb)
   * [@kprus](https://github.com/kprus)
+  * [@laura-bankers](https://github.com/laura-bankers)
 

freyja/1.4.7/Dockerfile

@@ -0,0 +1,76 @@
+FROM mambaorg/micromamba:1.4.9 as app
+
+# Version arguments
+# ARG variables only persist during build time
+ARG FREYJA_SOFTWARE_VERSION="1.4.7"
+
+# build and run as root users since micromamba image has 'mambauser' set as the $USER
+USER root
+# set workdir to default for building; set to /data at the end
+WORKDIR /
+
+LABEL base.image="mambaorg/micromamba:1.4.9"
+LABEL dockerfile.version="1"
+LABEL software="Freyja"
+LABEL software.version=${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 && \
+    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 freyja=${FREYJA_SOFTWARE_VERSION} && \
+    micromamba clean -a -y
+
+# set the environment, put new conda env in PATH by default
+ENV PATH="/opt/conda/envs/freyja-env/bin:/opt/conda/envs/env/bin:${PATH}" \
+    LC_ALL=C.UTF-8
+
+# 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
+
+# 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
+
+# so that mamba/conda env is active when running below commands
+ENV ENV_NAME="freyja-env"
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+# 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 --version

freyja/1.4.7/README.md

@@ -0,0 +1,34 @@
+# 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.
+
+## Additional tools
+
+- biopython 1.81
+- ivar 1.4.2
+- mafft 7.520
+- matplotlib-base 3.7.2
+- pandas 2.0.3
+- samtools 1.17
+- scipy 1.11.1
+- seaborn 0.12.2
+- ucsc-fatovcf 448
+- usher 0.6.2
+
+## freyja barcodes
+
+This docker image was built on **2023-11-14** and the command `freyja update` is run as part of the build to retrieve the most up-to-date barcode file `freyja/data/usher_barcodes.csv` file from Freyja's GitHub repo. The barcode version included in this docker image is **`11_14_2023-00-57`** as reported by `freyja demix --version`
+
+## 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 priveleges, such as a mounted volume.