adding pbptyper version 2.0.0

README.md

@@ -229,7 +229,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [pasty](https://hub.docker.com/r/staphb/pasty) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pasty)](https://hub.docker.com/r/staphb/pasty) | <ul><li>1.0.2</li><li>[1.0.3](pasty/1.0.3/)</li><li>[2.2.1](./pasty/2.2.1/)</li></ul> | https://github.com/rpetit3/pasty |
 | [pbmm2](https://hub.docker.com/r/staphb/pbmm2) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pbmm2)](https://hub.docker.com/r/staphb/pbmm2) | <ul><li>[1.13.1](./pbmm2/1.13.1/)</li></ul> | https://github.com/PacificBiosciences/pbmm2 |
 | [Pavian](https://hub.docker.com/r/staphb/pavian) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pavian)](https://hub.docker.com/r/staphb/pavian) | <ul><li>[1.2.1](pavian/1.2.1/)</li></ul> | https://github.com/fbreitwieser/pavian |
-| [pbptyper](https://hub.docker.com/r/staphb/pbptyper) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pbptyper)](https://hub.docker.com/r/staphb/pbptyper) | <ul><li>1.0.0</li><li>1.0.1</li><li>1.0.4</li></ul> | https://github.com/rpetit3/pbptyper |
+| [pbptyper](https://hub.docker.com/r/staphb/pbptyper) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pbptyper)](https://hub.docker.com/r/staphb/pbptyper) | <ul><li>[1.0.0](./pbptyper/1.0.0/)</li><li>[1.0.1](./pbptyper/1.0.0/)</li><li>[1.0.4](./pbptyper/1.0.4/)</li><li>[2.0.0](./pbptyper/2.0.0/)</li></ul> | https://github.com/rpetit3/pbptyper |
 | [pbtk](https://hub.docker.com/r/staphb/pbtk) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pbtk)](https://hub.docker.com/r/staphb/pbtk) | <ul><li>[3.1.1](./pbtk/3.1.1/)</li></ul> | https://github.com/PacificBiosciences/pbtk |
 | [Phyml](https://hub.docker.com/r/staphb/phyml) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/phyml)](https://hub.docker.com/r/staphb/phyml) | <ul><li>3.3.20220408</li></ul> | https://github.com/stephaneguindon/phyml |
 | [phyTreeViz](https://hub.docker.com/r/staphb/phytreeviz) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/phytreeviz)](https://hub.docker.com/r/staphb/phytreeviz) | <ul><li>[0.1.0](./phytreeviz/0.1.0/)</li><li>[0.2.0](./phytreeviz/0.2.0/)</li></ul> | https://github.com/moshi4/phyTreeViz/ |

pbptyper/2.0.0/Dockerfile

@@ -0,0 +1,104 @@
+ARG PBPTYPER_VERSION="2.0.0"
+
+FROM mambaorg/micromamba:1.5.8 as app
+
+# Version arguments
+# ARG variables only persist during build time
+ARG PBPTYPER_VERSION
+
+# build and run as root users since micromamba image has 'mambauser' set as the $USER
+USER root
+# set workdir to default for building; set to /data at the end
+WORKDIR /
+
+LABEL base.image="mambaorg/micromamba:1.5.8"
+LABEL dockerfile.version="1"
+LABEL software="pbptyper"
+LABEL software.version="${PBPTYPER_VERSION}"
+LABEL description="In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies"
+LABEL website="https://github.com/rpetit3/pbptyper"
+LABEL license="https://github.com/rpetit3/pbptyper/blob/main/LICENSE"
+LABEL maintainer="Curtis Kapsak"
+LABEL maintainer.email="[email protected]"
+
+# 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/*
+
+# Install pbptyper into the base conda/micromamba environment, pinning the version
+# clean up conda garbage
+RUN micromamba install --name base -c conda-forge -c bioconda -c defaults pbptyper=${PBPTYPER_VERSION} && \
+    micromamba clean -a -f -y
+
+# set the environment, add base conda/micromamba bin directory into path
+# set locale settings to UTF-8
+ENV PATH="/opt/conda/bin/:${PATH}" \
+    LC_ALL=C.UTF-8
+
+# set final working directory to /data
+WORKDIR /data
+
+CMD pbptyper --help
+
+# new base for testing
+FROM app as test
+
+ARG PBPTYPER_VERSION
+
+RUN pbptyper --help && \
+    pbptyper --version
+
+# so that all test inputs & outputs are kept in /test
+WORKDIR /test
+
+# download test data from pbptyper repo
+RUN wget -q https://github.com/rpetit3/pbptyper/archive/refs/tags/v${PBPTYPER_VERSION}.tar.gz && \
+    tar -vxf v${PBPTYPER_VERSION}.tar.gz
+
+# shamelessly stolen and modified from https://github.com/rpetit3/pbptyper/blob/main/.github/workflows/test-pbptyper.yml (again)
+RUN cd pbptyper-${PBPTYPER_VERSION} && \
+    echo "ERR1065617" && \
+    pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/ERR1065617.fna.gz --prefix ERR1065617 && \
+    cat ERR1065617.tsv && \
+    head ERR1065617.tblastn.tsv && \
+    echo "SRR2912551" && \
+    pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/SRR2912551.fna.gz --prefix SRR2912551 && \
+    cat SRR2912551.tsv && \
+    head SRR2912551.tblastn.tsv && \
+    echo "SRR8654742" && \
+    pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/SRR8654742.fna --prefix SRR8654742 --outdir SRR8654742 && \
+    cat SRR8654742/SRR8654742.tsv && \
+    head SRR8654742/SRR8654742.tblastn.tsv && \
+    echo "S. pseudopneumoniae" && \
+    pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/spseudopneumoniae.fna.gz --prefix spseudopneumoniae --outdir spseudopneumoniae && \
+    cat spseudopneumoniae/spseudopneumoniae.tsv && \
+    head spseudopneumoniae/spseudopneumoniae.tblastn.tsv && \
+    echo "S. mitis" && \
+    pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/smitis.fna.gz --prefix smitis --outdir smitis && \
+    cat smitis/smitis.tsv && \
+    head smitis/smitis.tblastn.tsv && \
+    echo "S. suis" && \
+    pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/ssuis.fna.gz --prefix ssuis --outdir ssuis && \
+    cat ssuis/ssuis.tsv && \
+    head ssuis/ssuis.tblastn.tsv && \
+    echo "not-spn" && \
+    pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/not-spn.fna.gz --prefix not-spn && \
+    cat not-spn.tsv && \
+    head not-spn.tblastn.tsv && \
+    echo "not-a-fasta" && \
+    pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/not-a-fasta.fasta --prefix not-a-fasta && \
+    cat not-a-fasta.tsv && \
+    head not-a-fasta.tblastn.tsv && \
+    echo "poor" && \
+    pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/poor.fasta --prefix poor --outdir poor && \
+    cat poor/poor.tsv && \
+    head poor/poor.tblastn.tsv
+
+RUN cd pbptyper-${PBPTYPER_VERSION} && \
+    echo "ERR1065617 again" && \
+    pbptyper --input test/ERR1065617.fna.gz --prefix ERR1065617_2 && \
+    cat ERR1065617_2.tsv && \
+    head ERR1065617_2.tblastn.tsv

pbptyper/2.0.0/README.md

@@ -0,0 +1,31 @@
+# pbptyper container
+
+Main tool : [pbptyper](https://github.com/rpetit3/pbptyper)
+
+Full documentation: [https://github.com/rpetit3/pbptyper](https://github.com/rpetit3/pbptyper)
+
+In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies
+
+## Example Usage
+
+```bash
+# run pbptyper on an test S. pneumo assembly included with pbptyper 
+# WARNING: test data no longer included in docker image, visit here to get test data: https://github.com/rpetit3/pbptyper/tree/main/test
+$ pbptyper --input SRR2912551.fna.gz --prefix SRR2912551 --db /pbptyper-*/db/ --outdir /SRR2912551-pbptyper-test
+Running TBLASTN for 1A...
+TBLASTN results written to /SRR2912551-pbptyper-test/SRR2912551-1A.tblastn.tsv
+
+Running TBLASTN for 2B...
+TBLASTN results written to /SRR2912551-pbptyper-test/SRR2912551-2B.tblastn.tsv
+
+Running TBLASTN for 2X...
+TBLASTN results written to /SRR2912551-pbptyper-test/SRR2912551-2X.tblastn.tsv
+
+                                          Predicted PBP Type                                          
+┏━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━┓
+┃ sample     ┃ pbptype ┃ 1A_coverage ┃ 1A_pident ┃ 2B_coverage ┃ 2B_pident ┃ 2X_coverage ┃ 2X_pident ┃
+┡━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━┩
+│ SRR2912551 │ 23:0:2  │ 100         │ 100.000   │ 100         │ 100.000   │ 100         │ 100.000   │
+└────────────┴─────────┴─────────────┴───────────┴─────────────┴───────────┴─────────────┴───────────┘
+Predicted pbp type result written to /SRR2912551-pbptyper-test/SRR2912551.tsv
+```