Update to TOSTADAS v4.0.0 (replaces tbl2asn with table2asn in conda environment.yml file)

README.md

@@ -300,7 +300,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [sylph](https://hub.docker.com/r/staphb/sylph) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/sylph)](https://hub.docker.com/r/staphb/sylph) | <ul><li>[0.4.1](./sylph/0.4.1)</li><li>[0.5.1](./sylph/0.5.1)</li><li>[0.6.0](./sylph/0.6.0)</li><li>[0.6.1](./sylph/0.6.1)</li></ul> | https://github.com/bluenote-1577/sylph |
 | [TBProfiler](https://hub.docker.com/r/staphb/tbprofiler/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/tbprofiler)](https://hub.docker.com/r/staphb/tbprofiler) | <ul><li>[4.3.0](./tbprofiler/4.3.0/)</li><li>[4.4.0](./tbprofiler/4.4.0/)</li><li>[4.4.2](./tbprofiler/4.4.2/)</li><li>[5.0.1](tbprofiler/5.0.1/)</li><li>[6.2.0](tbprofiler/6.2.0/)</li><li>[6.2.1](tbprofiler/6.2.1/)</li><li>[6.3.0](tbprofiler/6.3.0/)</li><li>[6.4.0](tbprofiler/6.4.0/)</li></ul> | https://github.com/jodyphelan/TBProfiler |
 | [TipToft](https://hub.docker.com/r/staphb/tiptoft/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/tiptoft)](https://hub.docker.com/r/staphb/tiptoft) | <ul><li>1.0.0</li><li>1.0.2</li></ul> | https://github.com/andrewjpage/tiptoft |
-| [Tostadas](https://hub.docker.com/r/staphb/tostadas/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/tostadas)](https://hub.docker.com/r/staphb/tostadas) | <ul><li>[0.2.0-beta](./tostadas/0.2.0-beta/)</li><li>[3.1.0](./tostadas/3.1.0/)</li></ul> | https://github.com/CDCgov/tostadas |
+| [Tostadas](https://hub.docker.com/r/staphb/tostadas/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/tostadas)](https://hub.docker.com/r/staphb/tostadas) | <ul><li>[0.2.0-beta](./tostadas/0.2.0-beta/)</li><li>[3.1.0](./tostadas/3.1.0/)</li><li>[4.0.0](./tostadas/4.0.0/)</li></ul> | https://github.com/CDCgov/tostadas |
 | [Treemmer](https://hub.docker.com/r/staphb/treemmer/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/treemmer)](https://hub.docker.com/r/staphb/treemmer) | <ul><li>0.3</li></ul> | https://git.scicore.unibas.ch/TBRU/Treemmer (archived, moved to GitHub) </br> https://github.com/fmenardo/Treemmer |
 | [Trimmomatic](https://hub.docker.com/r/staphb/trimmomatic/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/trimmomatic)](https://hub.docker.com/r/staphb/trimmomatic) | <ul><li>0.38</li><li>0.39</li></ul> | http://www.usadellab.org/cms/?page=trimmomatic </br>https://github.com/usadellab/Trimmomatic |
 | [Trycycler](https://hub.docker.com/r/staphb/trycycler/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/trycycler)](https://hub.docker.com/r/staphb/trycycler) | <ul><li>[0.3.1](./trycycler/0.3.1/)</li><li>[0.3.2](./trycycler/0.3.2/)</li><li>[0.3.3](./trycycler/0.3.3/)</li><li>[0.5.0](./trycycler/0.5.0/)</li><li>[0.5.3](./trycycler/0.5.3/)</li><li>[0.5.4](./trycycler/0.5.4/)</li><li>[0.5.5](./trycycler/0.5.5/)</li></ul> | https://github.com/rrwick/Trycycler |

tostadas/4.0.0/Dockerfile

@@ -0,0 +1,58 @@
+FROM mambaorg/micromamba:1.5.8 as app
+
+ARG TOSTADAS_VER="4.0.0"
+
+USER root
+
+WORKDIR /
+
+LABEL authors="Jessica Rowell and Ankush Gupta"
+LABEL base.image="mambaorg/micromamba:1.5.8"
+LABEL dockerfile.version="3"
+LABEL software="tostadas"
+LABEL software.version=$TOSTADAS_VER
+LABEL description="Image for the TOSTADAS: Toolkit for Open Sequence Triage, Annotation and DAtabase Submission pipeline"
+LABEL website="https://github.com/CDCgov/tostadas"
+LABEL license="https://github.com/CDCgov/tostadas/LICENSE"
+LABEL maintainer="Jessica Rowell"
+LABEL maintainer.email="[email protected]"
+LABEL maintainer2="Kyle O'Connell"
+LABEL maintainer2.email="[email protected]"
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    procps && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# download tostadas repo, move to /tostadas, and create /data
+RUN wget https://github.com/CDCgov/tostadas/archive/refs/tags/v${TOSTADAS_VER}.tar.gz && \
+    tar -xvf v${TOSTADAS_VER}.tar.gz && \
+    rm v${TOSTADAS_VER}.tar.gz && \
+    mv tostadas-${TOSTADAS_VER} tostadas && \
+    mkdir /data
+
+# use mamba to install conda packages
+RUN micromamba env create -f tostadas/environment.yml && \
+    micromamba clean -a -y -f && \
+    echo "source activate tostadas" > ~/.bashrc && \
+    rm -rf /tostadas
+
+ENV PATH=/opt/conda/envs/tostadas/bin:/opt/conda/envs/env/bin:$PATH \
+    LC_ALL=C.UTF-8
+
+WORKDIR /data
+
+##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- #####
+###### Step 2. Set up the testing stage.                                 #####
+###### The docker image is built to the 'test' stage before merging, but #####
+###### the test stage (or any stage after 'app') will be lost.           #####
+###### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- #####
+
+# A second FROM instruction creates a new stage
+FROM app as test
+
+RUN liftoff --version && \
+    samtools --version && \
+    python --version && \
+    table2asn -help

tostadas/4.0.0/README.md

@@ -0,0 +1,42 @@
+# tostadas container
+
+Main tool : [tostadas](https://github.com/CDCgov/tostadas)
+Version: 4.0.0
+
+Additional tools installed via conda:
+  - pip
+  - libgcc-ng=12.1.0=h8d9b700_16
+  - libstdcxx-ng=12.1.0=ha89aaad_16
+  - liftoff=1.6.3=pyhdfd78af_0
+  - lxml=4.9.1=py39hb9d737c_0
+  - nameparser=1.0.5=py_0
+  - numpy=1.22.4=py39hc58783e_0
+  - packaging=21.3=pyhd3eb1b0_0
+  - pandas=1.4.2=py39h1832856_2
+  - paramiko=3.4.0=pyhd8ed1ab_0
+  - python-dateutil=2.8.2=pyhd8ed1ab_0
+  - python_abi=3.9=2_cp39
+  - pytz=2022.1=pyhd8ed1ab_0
+  - pyvcf3=1.0.3=pyhdfd78af_0
+  - pyyaml=6.0=py39hb9d737c_4
+  - readline=8.1=h46c0cb4_0
+  - requests=2.28.0=pyhd8ed1ab_1
+  - samtools=1.15.1=h1170115_0
+  - setuptools=62.3.2=py39hf3d152e_0
+  - simplejson=3.17.6=py39hb9d737c_1
+  - table2asn=1.28.1179=h48fe88c_0
+  - tbb=2021.5.0=h924138e_1
+  - tk=8.6.12=h27826a3_0
+  - tzdata=2022a=h191b570_0
+  - ujson=5.3.0=py39h5a03fae_0
+  - urllib3=1.26.9=pyhd8ed1ab_0
+  - wgs2ncbi=1.1.2=pl5262hdfd78af_1
+  - wheel=0.37.1=pyhd8ed1ab_0
+  - xz=5.2.5=h516909a_1
+  - yaml=0.2.5=h7f98852_2
+  - openpyxl=3.0.10
+  - xmltodict=0.13.0=pyhd8ed1ab_0
+
+Full documentation: https://github.com/CDCgov/tostadas
+
+[tostadas](https://github.com/CDCgov/tostadas) is a Nextflow workflow for annotation and submission of MonkeyPox Virus consensus sequences. The resultant container is not intended to run independently of the workflow.