update tostadas container to add table2asn and new environment.yml de…

…finition in README

tostadas/4.0.0/Dockerfile

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+FROM ubuntu:jammy as app
+
+ARG TOSTADAS_VER="4.0.0"
+ARG TABLE2ASN_RELEASE_DATE="2023-10-05"
+
+USER root
+
+WORKDIR /
+
+LABEL authors="Jessica Rowell and Ankush Gupta"
+LABEL base.image="ubuntu:focal"
+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-${TOSTADAS_VER} tostadas && \
+    mkdir /data
+
+# use mamba to install conda packages
+RUN micromamba env create -f tostadas/environment.yml && \
+    micromamba clean -a -y && \
+    echo "source activate tostadas" > ~/.bashrc && \
+    rm -rf /tostadas
+
+RUN wget -q https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/${TABLE2ASN_RELEASE_DATE}/by_program/table2asn/linux64.table2asn.gz && \
+    gunzip linux64.table2asn.gz && \
+    mv linux64.table2asn table2asn && \
+    chmod +x table2asn
+
+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 insruction creates a new stage
+FROM app as test
+ARG TABLE2ASN_RELEASE_DATE="2023-10-05"
+
+RUN liftoff --version && \
+    samtools --version && \
+    python --version && \
+    table2asn -help
+
+ARG FILES="table2asn_readme.txt \
+    SubmissionTemplate.sbt \
+    short.fsa"
+
+RUN for file in ${FILES}; do wget -q https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/${TABLE2ASN_RELEASE_DATE}/documentation/${file}; done && \
+    table2asn -t SubmissionTemplate.sbt -i short.fsa -o helicase.sqn

tostadas/4.0.0/README.md

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+# 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
+  - tbb=2021.5.0=h924138e_1
+  - tbl2asn=25.7=h9ee0642_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.