singularity-container

问题 I have the following Singularity container recipe: #!/bin/bash Bootstrap: docker From: nipype/nipype:latest %labels Version v1.0 %post # Install nano apt-get update apt-get install nano # Set up Python environment CONDA_ENV=/opt/conda/bin export PATH=$CONDA_ENV:$PATH chmod -R 777 $CONDA_ENV # Activate conda environment conda activate neuro conda install seaborn pip install pybids and I build the container with Singularity as follows: sudo singularity build swish.simg Singularity.swish The

问题 I have the following Singularity container recipe: #!/bin/bash Bootstrap: docker From: nipype/nipype:latest %labels Version v1.0 %post # Install nano apt-get update apt-get install nano # Set up Python environment CONDA_ENV=/opt/conda/bin export PATH=$CONDA_ENV:$PATH chmod -R 777 $CONDA_ENV # Activate conda environment conda activate neuro conda install seaborn pip install pybids and I build the container with Singularity as follows: sudo singularity build swish.simg Singularity.swish The

问题 I have the following Singularity container recipe: #!/bin/bash Bootstrap: docker From: nipype/nipype:latest %labels Version v1.0 %post # Install nano apt-get update apt-get install nano # Set up Python environment CONDA_ENV=/opt/conda/bin export PATH=$CONDA_ENV:$PATH chmod -R 777 $CONDA_ENV # Activate conda environment conda activate neuro conda install seaborn pip install pybids and I build the container with Singularity as follows: sudo singularity build swish.simg Singularity.swish The

问题 I have the following Singularity container recipe: #!/bin/bash Bootstrap: docker From: nipype/nipype:latest %labels Version v1.0 %post # Install nano apt-get update apt-get install nano # Set up Python environment CONDA_ENV=/opt/conda/bin export PATH=$CONDA_ENV:$PATH chmod -R 777 $CONDA_ENV # Activate conda environment conda activate neuro conda install seaborn pip install pybids and I build the container with Singularity as follows: sudo singularity build swish.simg Singularity.swish The

问题 I have the following Singularity container recipe: #!/bin/bash Bootstrap: docker From: nipype/nipype:latest %labels Version v1.0 %post # Install nano apt-get update apt-get install nano # Set up Python environment CONDA_ENV=/opt/conda/bin export PATH=$CONDA_ENV:$PATH chmod -R 777 $CONDA_ENV # Activate conda environment conda activate neuro conda install seaborn pip install pybids and I build the container with Singularity as follows: sudo singularity build swish.simg Singularity.swish The

问题 I am trying to combine Snakemake with Singularity, and I noticed that a simple awk command no longer works when using singularity. The $1 in the last line gets replaced by bash instead of being used as the first field by awk . Here is a minimal working example ( Snakefile ): singularity: "docker://debian:stretch" rule all: input: "test.txt" rule test: output: "test.txt" shell: "cat /etc/passwd | awk -F':' '{{print $1}}' > {output}" When I run snakemake without singularity, the output test.txt

问题 I am trying to combine Snakemake with Singularity, and I noticed that a simple awk command no longer works when using singularity. The $1 in the last line gets replaced by bash instead of being used as the first field by awk . Here is a minimal working example ( Snakefile ): singularity: "docker://debian:stretch" rule all: input: "test.txt" rule test: output: "test.txt" shell: "cat /etc/passwd | awk -F':' '{{print $1}}' > {output}" When I run snakemake without singularity, the output test.txt

问题 I'm building a pipeline with snakemake and using conda and singularity environments to ensure reproducibility. I run into an error where the text on my plots is replaced by rectangles After experimenting with the pipeline on Linux and Mac systems and disabling the singularity container, it appears the issue stems from a missing font library as the text is drawn normally when I only run the pipeline using only conda ( --use-conda ) on my Mac. The singularity container is built from this

问题 I'm building a pipeline with snakemake and using conda and singularity environments to ensure reproducibility. I run into an error where the text on my plots is replaced by rectangles After experimenting with the pipeline on Linux and Mac systems and disabling the singularity container, it appears the issue stems from a missing font library as the text is drawn normally when I only run the pipeline using only conda ( --use-conda ) on my Mac. The singularity container is built from this

问题 I am trying to create a singularity image and recipe that will create an anaconda environment and then activate said environment so I can build the python wheel of a project in that environment so it's 100% installed and functional after the singularity build is completed. Bootstrap: docker From: nvidia/cuda:9.0-cudnn7-devel-ubuntu16.04 %environment # use bash as default shell SHELL=/bin/bash # add CUDA paths CPATH="/usr/local/cuda/include:$CPATH" PATH="/usr/local/cuda/bin:$PATH" LD_LIBRARY