Adding Dr. PRG

Program_Licenses.md

@@ -28,6 +28,7 @@ The licenses of the open-source software that is contained in these Docker image
 | datasets-sars-cov-2 | Apache 2.0 | https://github.com/CDCgov/datasets-sars-cov-2/blob/master/LICENSE |
 | dnaapler | MIT | https://github.com/gbouras13/dnaapler/blob/main/LICENSE |
 | dragonflye | GNU GPLv3 | https://github.com/rpetit3/dragonflye/blob/main/LICENSE |
+| drprg | MIT | https://github.com/mbhall88/drprg/blob/main/LICENSE |
 | DSK | GNU Affero GPLv3 | https://github.com/GATB/dsk/blob/master/LICENSE |
 | emboss | GNU GPLv3 | http://emboss.sourceforge.net/licence/ |
 | emmtyper | GNU GPLv3 | https://github.com/MDU-PHL/emmtyper/blob/master/LICENSE |

README.md

@@ -133,6 +133,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [datasets-sars-cov-2](https://github.com/CDCgov/datasets-sars-cov-2) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/datasets-sars-cov-2)](https://hub.docker.com/r/staphb/datasets-sars-cov-2) | <ul><li>0.6.2</li><li>0.6.3</li><li>0.7.2</li></ul> | https://github.com/CDCgov/datasets-sars-cov-2 |
 | [dnaapler](https://hub.docker.com/r/staphb/dnaapler) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dnaapler)](https://hub.docker.com/r/staphb/dnaapler) | <ul><li>[0.1.0](dnaapler/0.1.0/)</li></ul> | https://github.com/gbouras13/dnaapler |
 | [dragonflye](https://hub.docker.com/r/staphb/dragonflye) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dragonflye)](https://hub.docker.com/r/staphb/dragonflye) | <ul><li>1.0.14</li><li>[1.1.1](dragonflye/1.1.1/)</li></ul> | https://github.com/rpetit3/dragonflye |
+| [Dr. PRG ](https://hub.docker.com/r/staphb/drprg) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/drprg)](https://hub.docker.com/r/staphb/drprg) | <ul><li>[0.1.1](drprg/0.1.1/)</li></ul> | https://mbh.sh/drprg/ |
 | [DSK](https://hub.docker.com/r/staphb/dsk) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dsk)](https://hub.docker.com/r/staphb/dsk) | <ul><li>0.0.100</li></ul> | https://gatb.inria.fr/software/dsk/ |
 | [emboss](https://hub.docker.com/r/staphb/emboss) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/emboss)](https://hub.docker.com/r/staphb/emboss) | <ul><li>6.6.0 (no version)</li></ul> | http://emboss.sourceforge.net |
 | [emmtyper](https://hub.docker.com/r/staphb/emmtyper) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/emmtyper)](https://hub.docker.com/r/staphb/emmtyper) | <ul><li>0.2.0</li></ul> | https://github.com/MDU-PHL/emmtyper |

drprg/0.1.1/Dockerfile

@@ -0,0 +1,69 @@
+# 'FROM' defines the base docker image. This command has to come first in the file
+# The 'as' keyword lets you name the folowing stage. The production image uses everything to the 'app' stage.
+FROM mambaorg/micromamba:1.5.1 as app
+
+# List all software versions are ARGs near the top of the dockerfile
+# 'ARG' sets environment variables during the build stage
+ARG DRPRG_VER="0.1.1"
+ARG MTB_VER="20230308"
+
+# build and run as root users since micromamba image has 'mambauser' set as the $USER
+USER root
+# set workdir to default for building; set to /data at the end
+WORKDIR /
+
+# 'LABEL' instructions tag the image with metadata that might be important to the user
+
+LABEL base.image="mambaorg/micromamba:1.4.9"
+LABEL dockerfile.version="1"
+LABEL software="Dr. PRG"
+LABEL software.version="${DRPRG_VER}"
+LABEL description="Antimicrobial resistance prediction"
+LABEL website="https://github.com/mbhall88/drprg"
+LABEL license="https://github.com/mbhall88/drprg/blob/main/LICENSE"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="[email protected]"
+
+# 'RUN' executes code during the build
+# Install dependencies via apt-get or yum if using a centos or fedora base
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    wget \
+    ca-certificates \
+    procps && \
+    rm -rf /var/lib/apt/lists/* && apt-get autoclean
+
+# Install your desired software into the base conda/micromamba environment, pinning the version
+# clean up conda garbage
+# make /data to use as a working directory
+RUN micromamba install --name base -c conda-forge -c bioconda -c defaults drprg=${DRPRG_VER} && \
+    micromamba clean -a -y && \
+    mkdir /data
+
+# 'ENV' instructions set environment variables that persist from the build into the resulting image
+# set the environment, add base conda/micromamba bin directory into path
+# set locale settings to UTF-8
+ENV PATH="/opt/conda/bin/:${PATH}" \
+    LC_ALL=C.UTF-8
+
+# download MTB index and change the name
+RUN mkdir /drprg && \
+    drprg index --download mtb@${MTB_VER} --outdir /drprg && \
+    mv /drprg/mtb/mtb-${MTB_VER} /drprg/mtb/mtb
+
+CMD drprg --help
+
+WORKDIR /data
+
+FROM app as test
+
+WORKDIR /test
+
+RUN drprg --help
+
+# testing prediction
+RUN wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR230/005/SRR23086705/SRR23086705_1.fastq.gz && \
+    drprg predict -x /drprg/mtb/mtb -i SRR23086705_1.fastq.gz --illumina -o outdir/ && \
+    ls outdir/*
+
+# list available databases for download
+RUN drprg index --list

drprg/0.1.1/README.md

@@ -0,0 +1,48 @@
+<!-- 
+Please edit this readme with some basic information about the tool and how to use this container. 
+- Include information about databases and additional files that are included.
+- Keep it short - you don't need to recreate the documentation from the creators.
+- Do not just copy and paste the readme or help for the tool. 
+-->
+
+# Dr. PRG - Drug resistance Prediction with Reference Graphs️ container
+
+Main tool: [Dr. PRG](https://mbh.sh/drprg/)
+
+Code repository: https://github.com/mbhall88/drprg
+
+Basic information on how to use this tool:
+- executable: drprg
+- help: --help
+- version: --version  
+- description: Drug Resistance Prediction with Reference Graphs
+
+Additional information:
+
+Imagine contains the mtb@20230308 database located at `/drprg/mtb/mtb`.
+
+Full documentation: https://mbh.sh/drprg/guide/download.html
+
+## Example Usage
+
+Using the index in from the image
+
+```bash
+
+# prediction (paired-end fastq files much be contatenated together into one)
+drprg predict -x /drprg/mtb/mtb -i input.fastq.gz --illumina -o outdir/
+```
+
+Getting the latest index and using it
+
+```bash
+
+# download latest TB database
+drprg index --download mtb
+
+# list available indices
+drprg index --list
+
+# prediction (paired-end fastq files much be contatenated together into one)
+drprg predict -x mtb -i input.fastq.gz --illumina -o outdir/
+```