nextflow-create-docker suggestions #31
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| @@ -98,7 +99,17 @@ In our example here, we will have you build your image using a `requirements.txt | |||
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| Our example will use the files in the [torch_cuda_test directory](https://github.com/uc-cdis/bio-nextflow/tree/master/nextflow_notebooks/containerized_gpu_workflows/torch_cuda_test) of the bio-nextflow repository. You can review the `readme` file in this directory for more information. It is a simple example that will build up from our base image by adding PyTorch. The Nextflow script will ultimately use a python script that checks the version of CUDA in the GPU instance and checks whether it is compatible with the version of PyTorch and CUDA available in the container. | |||
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| First, in the terminal, navigate to the directory where the downloaded Dockerfile and requirements.txt are located. | |||
| First, download the contents of the [torch_cuda_test directory](https://github.com/uc-cdis/bio-nextflow/tree/master/nextflow_notebooks/containerized_gpu_workflows/torch_cuda_test). If you have `git`, the easiest way is to clone the repository: | |||
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For this -- I put in the prerequisites that you should have already cloned the repo, so I would rather not put them here. I can add these steps up there, though
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gotcha, i still think "navigate to the directory where the downloaded Dockerfile and requirements.txt are located" is a bit out of the blue here, the prerequisite are a lot of text ago
maybe "from the directory where you cloned or downloaded the bio-nextflow repository as a prerequisite, navigate to the torch_cuda_test directory" and keep the cd command i added
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I updated this info to reflect your suggestions in a new PR
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| [https://quay.io/repository/cdis/containers?tab=tags&tag=latest](https://quay.io/repository/cdis/containers?tab=tags&tag=latest) | ||
| [https://quay.io/repository/cdis/containers?tab=tags](https://quay.io/repository/cdis/containers?tab=tags) |
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I accepted this change but in a new PR
| @@ -32,6 +32,7 @@ Some tools you may be using in your workflow can take advantage of GPU capacity | |||
| We have 2 images in our current selection that offer [CUDA](https://www.turing.com/kb/understanding-nvidia-cuda) support for running on GPUs -- these have "cuda" in the image name, followed by the CUDA version. When possible, please choose the latest version of CUDA compatible with your tools. | |||
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| > gen3-cuda-12.3-ubuntu22.04-openssl *(preferred)* | |||
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i accepted this change, but in a new PR
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closing this PR because I incorporated many of these in this PR - #32 |
Improvements