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Merge pull request StaPH-B#936 from jessicarowell/master
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update tostadas container to include additional py libraries required…
erinyoung authored Apr 3, 2024
2 parents 1043369 + 3bf9aaa commit 1c34e0a
Showing 3 changed files with 101 additions and 1 deletion.
2 changes: 1 addition & 1 deletion README.md
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| [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></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></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</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></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</li><li>0.3.2</li><li>0.3.3</li><li>0.5.0</li><li>0.5.3</li><li>0.5.4</li></ul> | https://github.com/rrwick/Trycycler |
59 changes: 59 additions & 0 deletions tostadas/3.1.0/Dockerfile
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FROM mambaorg/micromamba:1.5.8 as app

ARG TOSTADAS_VER="3.1.0"

USER root

WORKDIR /

LABEL authors="Cole and Ankush Gupta"
LABEL base.image="mambaorg/micromamba:1.5.8"
LABEL dockerfile.version="2"
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="Ankush Gupta"
LABEL maintainer.email="[email protected]"
LABEL maintainer2="Kyle O'Connell"
LABEL maintainer2.email="[email protected]"
LABEL maintainer3="Cole Tindall"
LABEL maintainer3.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

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

RUN liftoff --version && \
samtools --version && \
python --version
41 changes: 41 additions & 0 deletions tostadas/3.1.0/README.md
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# tostadas container

Main tool : [tostadas](https://github.com/CDCgov/tostadas)
Version: 3.1.0

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
- 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.

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