Simplot-cl 1.0.3

Program_Licenses.md

@@ -202,6 +202,7 @@ The licenses of the open-source software that is contained in these Docker image
 | shigatyper | non-standard license see --> | https://github.com/CFSAN-Biostatistics/shigatyper/blob/master/LICENSE |
 | ShigEiFinder | GNU GPLv3 | https://github.com/LanLab/ShigEiFinder/blob/main/LICENSE |
 | Shovill | GNU GPLv3 | https://github.com/tseemann/shovill/blob/master/LICENSE |
+| simplot-cl | GNU GPLv3 | https://github.com/hodcroftlab/simplot-cl/blob/main/LICENSE.txt |
 | SISTR | Apache 2.0 | https://github.com/phac-nml/sistr_cmd/blob/master/LICENSE |
 | SKA | MIT | https://github.com/simonrharris/SKA/blob/master/LICENSE |
 | SKA2 | Apache 2.0 | https://github.com/bacpop/ska.rust/blob/master/LICENSE |

README.md

@@ -313,6 +313,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [ShigEiFinder](https://hub.docker.com/r/staphb/shigeifinder/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/shigeifinder)](https://hub.docker.com/r/staphb/shigeifinder) | <details><summary>Click to see all versions</summary> <ul><li>[1.3.2](./build-files/shigeifinder/1.3.2/)</li><li>[1.3.3](./build-files/shigeifinder/1.3.3/)</li><li>[1.3.5](./build-files/shigeifinder/1.3.5/)</li></ul> </details> | https://github.com/LanLab/ShigEiFinder |
 | [Shovill](https://hub.docker.com/r/staphb/shovill/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/shovill)](https://hub.docker.com/r/staphb/shovill) | <details><summary>Click to see all versions</summary> <ul><li>[1.0.4](./build-files/shovill/1.0.4/)</li><li>[1.1.0](./build-files/shovill/1.1.0/)</li><li>[1.4.2](./build-files/shovill/1.4.2/)</li></ul> </details> | https://github.com/tseemann/shovill |
 | [Shovill-se](https://hub.docker.com/r/staphb/shovill-se/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/shovill-se)](https://hub.docker.com/r/staphb/shovill-se) | <details><summary>Click to see all versions</summary> <ul><li>[1.1.0](./build-files/shovill-se/1.1.0/)</li></ul> </details> | https://github.com/rpetit3/shovill/tree/v1.1.0se |
+| [simplot-cl](https://hub.docker.com/r/staphb/simplot-cl/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/simplot-cl)](https://hub.docker.com/r/staphb/simplot-cl) | <details><summary>Click to see all versions</summary> <ul><li>[1.0.3](./build-files/simplot-cl/1.0.3/)</li></ul> </details> | https://github.com/hodcroftlab/simplot-cl |
 | [SISTR](https://hub.docker.com/r/staphb/sistr/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/sistr)](https://hub.docker.com/r/staphb/sistr) | <details><summary>Click to see all versions</summary> <ul><li>[1.0.2](./build-files/sistr/1.0.2/)</li><li>[1.1.1](./build-files/sistr/1.1.1/)</li><li>[1.1.2](./build-files/sistr/1.1.2/)</li><li>[1.1.3](./build-files/sistr/1.1.3/)</li></ul> </details> | https://github.com/phac-nml/sistr_cmd |
 | [SKA](https://hub.docker.com/r/staphb/ska/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ska)](https://hub.docker.com/r/staphb/ska) | <details><summary>Click to see all versions</summary> <ul><li>[1.0](./build-files/ska/1.0/)</li></ul> </details> | https://github.com/simonrharris/SKA |
 | [SKA2](https://hub.docker.com/r/staphb/ska2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ska2)](https://hub.docker.com/r/staphb/ska2) | <details><summary>Click to see all versions</summary> <ul><li>[0.3.6](./build-files/ska2/0.3.6/)</li><li>[0.3.7](./build-files/ska2/0.3.7/)</li><li>[0.3.10](./build-files/ska2/0.3.10/)</li><li>[0.4.0](./build-files/ska2/0.4.0/)</li><li>[0.4.1](./build-files/ska2/0.4.1/)</li><li>[0.5.0](./build-files/ska2/0.5.0/)</li><li>[0.5.1](./build-files/ska2/0.5.1/)</li></ul> </details> | https://github.com/bacpop/ska.rust |

build-files/simplot-cl/1.0.3/Dockerfile

@@ -0,0 +1,79 @@
+FROM mambaorg/micromamba:2.5.0-ubuntu24.04 AS app
+
+ARG SIMPLOT_CL_VER="1.0.3"
+
+USER root
+
+WORKDIR /
+
+LABEL base.image="mambaorg/micromamba:2.5.0-ubuntu24.04"
+LABEL dockerfile.version="1"
+LABEL software="simplot-cl"
+LABEL software.version="${SIMPLOT_CL_VER}"
+LABEL description="A Command-Line Similarity Plot Generator"
+LABEL website="https://github.com/hodcroftlab/simplot-cl/"
+LABEL license="https://github.com/hodcroftlab/simplot-cl/blob/main/LICENSE.txt"
+LABEL maintainer="Raheel Ahmed"
+LABEL maintainer.email="raheelsyedahmed@gmail.com"
+
+# Standard packages for downloading source code
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    procps && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# Decompress source code in /opt and llink /opt/simplot-cl-1.0.3 to /usr/local/bin for discovery in python path.
+WORKDIR /opt
+
+RUN wget -q https://github.com/hodcroftlab/simplot-cl/archive/refs/tags/v${SIMPLOT_CL_VER}.tar.gz && \
+    tar -xzf v${SIMPLOT_CL_VER}.tar.gz && \
+    rm v${SIMPLOT_CL_VER}.tar.gz && \
+    chmod +x /opt/simplot-cl-1.0.3/simplot.py && \
+    ln -s /opt/simplot-cl-${SIMPLOT_CL_VER}/simplot.py /usr/local/bin/simplot.py
+
+# Install from environment available in source code folder.
+RUN micromamba install --name base -f /opt/simplot-cl-${SIMPLOT_CL_VER}/environment.yml -y && \
+    micromamba clean -a -f -y && \
+    mkdir /data
+
+# Add micromamba packages to path and set locale.
+ENV PATH="/opt/conda/bin/:${PATH}" \
+    LC_ALL=C.UTF-8
+
+WORKDIR /data
+
+CMD [ "simplot.py", "-h" ]
+
+
+
+FROM app AS test
+
+ARG SIMPLOT_CL_VER="1.0.3"
+
+# List micromamba dependencies
+RUN micromamba list -n base
+
+WORKDIR /test
+
+
+# Run simplot help command
+RUN simplot.py -h
+
+# Generate simplots for queries listed through -q, using all other sequences in the supplied FASTA file as a reference.
+RUN simplot.py \
+    -s /opt/simplot-cl-${SIMPLOT_CL_VER}/demo_data/query_alignment.fasta \
+    -q OP137282.1 JX274981.1 \
+    -ws 150 \
+    -ss 50 \
+    -p simplots \
+    --no-align
+
+# Generate simplots for all sequences in the supplied FASTA file using all sequences in the reference FASTA as references.
+RUN simplot.py \
+    -s /opt/simplot-cl-${SIMPLOT_CL_VER}/demo_data/query_alignment.fasta \
+    -r /opt/simplot-cl-${SIMPLOT_CL_VER}/demo_data/reference_alignment.fasta \
+    -ws 200 \
+    -ss 100 \
+    -p simplots \
+    --no-align