diff --git a/dockerfiles/sagemaker-dockerfiles/unh b/dockerfiles/sagemaker-dockerfiles/unh new file mode 100644 index 0000000..70cd9b6 --- /dev/null +++ b/dockerfiles/sagemaker-dockerfiles/unh @@ -0,0 +1,46 @@ +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='*' +