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Create unh dockerfile #21

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Merged
kyleoconnell-NIH merged 1 commit into from
Jun 6, 2025
Merged

Create unh dockerfile #21

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46 changes: 46 additions & 0 deletions dockerfiles/sagemaker-dockerfiles/unh
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FROM public.ecr.aws/sagemaker/sagemaker-distribution:latest-cpu

ARG NB_USER="sagemaker-user"
ARG NB_UID="1000"
ARG NB_GID="100"

ENV NB_USER=$NB_USER \
NB_UID=$NB_UID \
NB_GID=$NB_GID \
HOME=/home/$NB_USER

USER root

RUN apt-get update --yes && apt-get install -y bc

RUN conda install -y -c conda-forge mamb
RUN mamba install -y -c conda-forge -c bioconda \
nextflow=24.04.4 \
fastani=1.34 \
quast=5.2.0 \
busco=5.4.6 \
samtools=1.21 \
bwa=0.7.18 \
blobtools=1.1.1 \
spades=4.0.0 \
orthofinder=2.5.5 \
fastqc=0.12.1 \
bakta=1.9.4 \
pycirclize=1.7.1 \
upsetplot=0.9.0 \
fastp=0.23.4

RUN wget https://ftp-trace.ncbi.nlm.nih.gov/sr/sdk/3.1.1/sratoolkit.3.1.1-ubuntu64.tar.gz
RUN tar -xvzf sratoolkit.3.1.1-ubuntu.tar.gz -C /usr/local/bin --strip-components=2 \
sratoolkit.3.1.1-ubuntu64/bin/ && rm sratoolkit.3.1.1-ubuntu64.tar.gz

RUN python3 pip install --user seaborn --no-deps

WORKDIR $HOME
USER ${NB_UID}

CMD jupyter lab --ip 0.0.0.0 --port 8888 \
--ServerApp.base_url="/jupyterlab/default" \
--ServerApp.token='' \
--ServerApp.allow_origin='*'

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