diff --git a/Program_Licenses.md b/Program_Licenses.md index 784acebde..f94868838 100644 --- a/Program_Licenses.md +++ b/Program_Licenses.md @@ -59,6 +59,7 @@ The licenses of the open-source software that is contained in these Docker image | Freyja | BSD-2 | https://github.com/andersen-lab/Freyja/blob/main/LICENSE | | GAMBIT | GNU aGPLv3 | https://github.com/jlumpe/gambit/blob/master/LICENSE | | GAMMA | Apache 2.0 | https://github.com/rastanton/GAMMA/blob/main/LICENSE | +| GenoFlu | GNU GPL v3 | https://github.com/USDA-VS/GenoFLU/blob/main/LICENSE | | Genotyphi | GNU GPLv3 | https://github.com/katholt/genotyphi/blob/main/LICENSE | | geNomad | ACADEMIC, INTERNAL, RESEARCH & DEVELOPMENT, NON-COMMERCIAL USE ONLY | https://github.com/apcamargo/genomad/blob/main/LICENSE | | GenoVi | BY-NC-SA Creative Commons License | https://github.com/robotoD/GenoVi/blob/main/LICENSE.txt | diff --git a/README.md b/README.md index 81dafe4ca..5a3d42885 100644 --- a/README.md +++ b/README.md @@ -164,6 +164,7 @@ To learn more about the docker pull rate limits and the open source software pro | [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/ | +| [GenoFLU](https://hub.docker.com/r/staphb/genoflu)
[![docker pulls](https://badgen.net/docker/pulls/staphb/genoflu)]() | | https://github.com/USDA-VS/GenoFLU | | [geNomad](https://hub.docker.com/r/staphb/genomad)
[![docker pulls](https://badgen.net/docker/pulls/staphb/genomad)](https://hub.docker.com/r/staphb/genomad) | | https://github.com/apcamargo/genomad | | [GenoVi](https://hub.docker.com/r/staphb/genovi)
[![docker pulls](https://badgen.net/docker/pulls/staphb/genovi)](https://hub.docker.com/r/staphb/genovi) | | https://github.com/robotoD/GenoVi | | [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 | diff --git a/genoflu/1.03/Dockerfile b/genoflu/1.03/Dockerfile new file mode 100644 index 000000000..074535ea5 --- /dev/null +++ b/genoflu/1.03/Dockerfile @@ -0,0 +1,52 @@ +FROM mambaorg/micromamba:1.5.8 as app + +USER root +WORKDIR / + +ARG GENOFLU_VER="1.03-0" + +# LABEL instructions tag the image with metadata that might be important to the user +LABEL base.image="micromamba:1.5.8" +LABEL dockerfile.version="1" +LABEL software="genoflu" +LABEL software.version=$GENOFLU_VER +LABEL description="Uses BLAST to detect whole-genome flu genotype" +LABEL website="https://github.com/USDA-VS/GenoFLU" +LABEL license="https://github.com/USDA-VS/GenoFLU/blob/main/LICENSE" +LABEL maintainer="Sage Wright" +LABEL maintainer.email="sagemwright@gmail.com" + +# Install dependencies via apt-get; cleanup apt garbage +RUN apt-get update && apt-get install -y --no-install-recommends \ + wget \ + ca-certificates \ + procps && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +# install genoflu via bioconda; install into 'base' conda env +# genoflu is not recognized in micromamba by the version tag +RUN micromamba install --yes --name base --channel conda-forge --channel bioconda \ + genoflu=${GENOFLU_VER} && \ + micromamba clean --all --force-pkgs-dirs --yes + + +# ENV instructions set environment variables that persist from the build into the resulting image +# hardcode 'base' env bin into PATH, so conda env does not have to be "activated" at run time +ENV PATH="/opt/conda/bin:${PATH}" + +# WORKDIR sets working directory +WORKDIR /data + +# default command is to pull up help options for genoflu +CMD [ "genoflu.py", "--help" ] + +# A second FROM insruction creates a new stage +# We use `test` for the test image +FROM app as test + +# getting all the exectubles in bin +RUN genoflu.py --help && genoflu.py --version + +# testing a genome +RUN wget -q https://raw.githubusercontent.com/USDA-VS/GenoFLU/main/test/test-genome-A1.fasta && \ + genoflu.py -f test-genome-A1.fasta \ No newline at end of file diff --git a/genoflu/README.md b/genoflu/README.md new file mode 100644 index 000000000..f24fd2c97 --- /dev/null +++ b/genoflu/README.md @@ -0,0 +1,24 @@ +# GenoFLU container + +Main tool: [GenoFLU](https://github.com/USDA-VS/GenoFLU) + +Code repository: https://github.com/USDA-VS/GenoFLU + +Additional tools: + +Basic information on how to use this tool: + +- executable: genoflu.py +- help: --help +- version: --version +- description: "GenoFLU determines the genotype of a segmented flu sample by BLASTing a multi-segment FASTA against the BLAST database" + +Additional information: + +Full documentation: [https://github.com/USDA-VS/GenoFLU](https://github.com/USDA-VS/GenoFLU) + +## Example Usage + +```bash +genoflu.py -f input.fasta +```