adding grandeur_ref 4.5 (#1116)

* adding grandeur 4.5

* added labels

* fixed quotation

* renamed to grandeur_ref

Program_Licenses.md

@@ -69,6 +69,7 @@ The licenses of the open-source software that is contained in these Docker image
 | 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 |
 | gfastats | MIT | https://github.com/vgl-hub/gfastats/blob/main/LICENSE |
+| Grandeur | GNU General Public License v3.0 | https://github.com/UPHL-BioNGS/Grandeur/blob/main/LICENSE |
 | Gubbins | GNU GPLv2 | https://github.com/nickjcroucher/gubbins/blob/master/LICENSE |
 | HeatCluster | GPL-3.0 | https://github.com/DrB-S/heatcluster/blob/main/LICENSE |
 | Hmmer | BSD-3 | http://eddylab.org/software/hmmer/Userguide.pdf |

README.md

@@ -178,6 +178,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [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><li>[1.8.1](./genomad/1.8.1/)</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 |
+| [grandeur_ref](https://hub.docker.com/r/staphb/grandeur_ref) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/grandeur_ref)](https://hub.docker.com/r/staphb/grandeur_ref) | <ul><li>[4.5](./grandeur_ref/4.5/)</li></ul> | Part of https://github.com/UPHL-BioNGS/Grandeur |
 | [Gubbins](https://hub.docker.com/r/staphb/gubbins) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/gubbins)](https://hub.docker.com/r/staphb/gubbins) | <ul><li>[3.3.3](./gubbins/3.3.3/)</li><li>[3.3.4](./gubbins/3.3.4/)</li><li>[3.3.5](./gubbins/3.3.5/)</li></ul> | https://github.com/nickjcroucher/gubbins |
 | [heatcluster](https://hub.docker.com/r/staphb/heatcluster) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/heatcluster)](https://hub.docker.com/r/staphb/heatcluster) | <ul><li>[1.0.2c](./heatcluster/1.0.2c/)</li></ul> | https://github.com/DrB-S/heatcluster/tree/main |
 | [hmmer](https://hub.docker.com/r/staphb/hmmer) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/hmmer)](https://hub.docker.com/r/staphb/hmmer) | <ul><li>[3.3](hmmer/3.3/)</li><li>[3.3.2](hmmer/3.3.2/)</li><li>[3.4](./hmmer/3.4/)</li></ul> | http://hmmer.org/ |

grandeur_ref/4.5/Dockerfile

@@ -0,0 +1,41 @@
+FROM staphb/ncbi-datasets:16.35.0 AS fasta
+
+WORKDIR /ref
+
+COPY accessions.txt rename.sh /ref/
+
+RUN grep -v ^# accessions.txt > ids.txt
+
+RUN datasets download genome accession --inputfile ids.txt
+
+RUN unzip *zip
+
+RUN mkdir prep && bash rename.sh
+
+FROM ubuntu:jammy as app
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="References for UPHL-BioNGS/Grandeur"
+LABEL software.version="4.5"
+LABEL description="Reference genomes for Grandeur"
+LABEL website="https://github.com/UPHL-BioNGS/Grandeur"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="[email protected]"
+
+WORKDIR /ref
+
+COPY --from=fasta /ref/prep /ref
+
+# install dependencies; cleanup apt garbage
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    procps && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /data
+
+CMD ls /ref
+
+FROM app AS test
+
+RUN ls /ref

grandeur_ref/4.5/README.md

@@ -0,0 +1,11 @@
+# Grandeur References container
+
+Main tool: Part of [UPHL-BioNGS/Grandeur](https://github.com/UPHL-BioNGS/Grandeur)
+
+Code repository: https://github.com/UPHL-BioNGS/Grandeur
+
+Basic information on how to use this tool:
+- executable: NA
+- help: NA
+- version: NA
+- description: Contains reference sequences that Grandeur uses by default. Not intended to be run separately.