Add GenoFLU 1.03 (#1020)

* add genoflu

* add readme

* add to license

* add --force-pkgs-dirs

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 |

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) <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 |
 | [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 |
 | [geNomad](https://hub.docker.com/r/staphb/genomad) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/genomad)](https://hub.docker.com/r/staphb/genomad) | <ul><li>[1.7.4](./genomad/1.7.4/)</li><li>[1.8.0](./genomad/1.8.0/)</li></ul> | https://github.com/apcamargo/genomad |
 | [GenoVi](https://hub.docker.com/r/staphb/genovi) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/genovi)](https://hub.docker.com/r/staphb/genovi) | <ul><li>[0.2.16](./genovi/0.2.16/)</li></ul> | https://github.com/robotoD/GenoVi |
 | [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](./gfastats/1.3.6/)</li><li>[1.3.7](./gfastats/1.3.7/)</li></ul> | https://github.com/vgl-hub/gfastats |

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=$GENOFLU_VER
+LABEL description="Uses BLAST to detect whole-genome flu genotype"
+LABEL website="https://github.com/USDA-VS/GenoFLU"
+LABEL license="https://github.com/USDA-VS/GenoFLU/blob/main/LICENSE"
+LABEL maintainer="Sage Wright"
+LABEL maintainer.email="[email protected]"
+
+# Install dependencies via apt-get; cleanup apt garbage
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    procps && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# install genoflu via bioconda; install into 'base' conda env
+# genoflu is not recognized in micromamba by the version tag
+RUN micromamba install --yes --name base --channel conda-forge --channel bioconda \
+    genoflu=${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 

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
+```