From f01806fcb229ede91b6d23e886c66d36018de4ec Mon Sep 17 00:00:00 2001 From: laura-bankers <73671005+laura-bankers@users.noreply.github.com> Date: Mon, 13 Nov 2023 23:03:40 +0000 Subject: [PATCH 1/4] Update README.md --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index a9b69bd3e..ac2114fa0 100644 --- a/README.md +++ b/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)
[![docker pulls](https://badgen.net/docker/pulls/staphb/filtlong)](https://hub.docker.com/r/staphb/filtlong) | | https://github.com/rrwick/filtlong | | [FLASH](https://hub.docker.com/r/staphb/flash)
[![docker pulls](https://badgen.net/docker/pulls/staphb/flash)](https://hub.docker.com/r/staphb/flash) | | http://ccb.jhu.edu/software/FLASH | | [Flye](https://hub.docker.com/r/staphb/flye)
[![docker pulls](https://badgen.net/docker/pulls/staphb/flye)](https://hub.docker.com/r/staphb/flye) | | https://github.com/fenderglass/Flye | -| [Freyja](https://hub.docker.com/r/staphb/freyja)
[![docker pulls](https://badgen.net/docker/pulls/staphb/freyja)](https://hub.docker.com/r/staphb/freyja) | | https://github.com/andersen-lab/Freyja | +| [Freyja](https://hub.docker.com/r/staphb/freyja)
[![docker pulls](https://badgen.net/docker/pulls/staphb/freyja)](https://hub.docker.com/r/staphb/freyja) | | https://github.com/andersen-lab/Freyja | | [GAMBIT](https://hub.docker.com/r/staphb/gambit)
[![docker pulls](https://badgen.net/docker/pulls/staphb/gambit)](https://hub.docker.com/r/staphb/gambit) | | https://github.com/jlumpe/gambit | | [GAMMA](https://hub.docker.com/r/staphb/gamma)
[![docker pulls](https://badgen.net/docker/pulls/staphb/gamma)](https://hub.docker.com/r/staphb/gamma) | | https://github.com/rastanton/GAMMA/ | | [gfastats](https://hub.docker.com/r/staphb/gfastats)
[![docker pulls](https://badgen.net/docker/pulls/staphb/gfastats)](https://hub.docker.com/r/staphb/gfastats) | | 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) From de13257ee44209b0c4de4be3fc59f333d6f9a978 Mon Sep 17 00:00:00 2001 From: laura-bankers <73671005+laura-bankers@users.noreply.github.com> Date: Mon, 13 Nov 2023 23:09:02 +0000 Subject: [PATCH 2/4] Create README.md create readme for freyja v.1.4.7 --- freyja/1.4.7/README.md | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 freyja/1.4.7/README.md diff --git a/freyja/1.4.7/README.md b/freyja/1.4.7/README.md new file mode 100644 index 000000000..27859ac77 --- /dev/null +++ b/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 **2023-11-13** 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_13_2023-00-47`** 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. From ec26edbab2bac57b52285b1b2c4a43131a7ebd8b Mon Sep 17 00:00:00 2001 From: laura-bankers <73671005+laura-bankers@users.noreply.github.com> Date: Mon, 13 Nov 2023 23:09:39 +0000 Subject: [PATCH 3/4] Add Dockerfile upload docker file for freyja v.1.4.7 --- freyja/1.4.7/Dockerfile | 76 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 freyja/1.4.7/Dockerfile diff --git a/freyja/1.4.7/Dockerfile b/freyja/1.4.7/Dockerfile new file mode 100644 index 000000000..e40cc43c0 --- /dev/null +++ b/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="kevin.libuit@theiagen.com" +LABEL maintainer2="Curtis Kapsak" +LABEL maintainer2.email="curtis.kapsak@theiagen.com" +LABEL maintainer3="Erin Young" +LABEL maintainer3.email="eriny@utah.gov" + +# 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 From 4a1960f395efacbe4caa0e3a6b7310945a84db75 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 14 Nov 2023 10:26:19 -0700 Subject: [PATCH 4/4] Update README.md --- freyja/1.4.7/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/freyja/1.4.7/README.md b/freyja/1.4.7/README.md index 27859ac77..3d12712f6 100644 --- a/freyja/1.4.7/README.md +++ b/freyja/1.4.7/README.md @@ -19,7 +19,7 @@ Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 sa ## freyja barcodes -This docker image was built on **2023-11-13** 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_13_2023-00-47`** as reported by `freyja demix --version` +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