Merge pull request #57 from STRIDES/rework-readme-structure

README Reformatting
STRIDES · Mar 13, 2024 · 77afe0f · 77afe0f
2 parents e1d7f07 + 9af8b6c
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diff --git a/.markdown-link-check.json b/.markdown-link-check.json
@@ -19,8 +19,8 @@
       "replacement": "https://github.com/STRIDES/NIHCloudLabGCP/tree/main/docs"
     },
     {
-      "pattern": "^/tutorials",
-      "replacement": "https://github.com/STRIDES/NIHCloudLabGCP/tree/main/tutorials"
+      "pattern": "^/notebooks",
+      "replacement": "https://github.com/STRIDES/NIHCloudLabGCP/tree/main/notebooks"
     },
     {
       "pattern": "^/images",

diff --git a/README.md b/README.md
diff --git a/envs/environment.yaml b/envs/environment.yaml
diff --git a/...seq/ATACseq_Tutorial1_Preprocessing.ipynb → ...seq/ATACseq_Tutorial1_Preprocessing.ipynb b/...seq/ATACseq_Tutorial1_Preprocessing.ipynb → ...seq/ATACseq_Tutorial1_Preprocessing.ipynb
diff --git a/...seq/ATACseq_Tutorial2_PeakDetection.ipynb → ...seq/ATACseq_Tutorial2_PeakDetection.ipynb b/...seq/ATACseq_Tutorial2_PeakDetection.ipynb → ...seq/ATACseq_Tutorial2_PeakDetection.ipynb
diff --git a/...TACseq/ATACseq_Tutorial3_Downstream.ipynb → ...TACseq/ATACseq_Tutorial3_Downstream.ipynb b/...TACseq/ATACseq_Tutorial3_Downstream.ipynb → ...TACseq/ATACseq_Tutorial3_Downstream.ipynb
diff --git a/...DL-gwas-gcp-example/1-d10-run-first.ipynb → ...DL-gwas-gcp-example/1-d10-run-first.ipynb b/...DL-gwas-gcp-example/1-d10-run-first.ipynb → ...DL-gwas-gcp-example/1-d10-run-first.ipynb
diff --git a/...example/2-mse-run-second-in-jupyter.ipynb → ...example/2-mse-run-second-in-jupyter.ipynb b/...example/2-mse-run-second-in-jupyter.ipynb → ...example/2-mse-run-second-in-jupyter.ipynb
diff --git a/...s/notebooks/DL-gwas-gcp-example/README.md → notebooks/DL-gwas-gcp-example/README.md b/...s/notebooks/DL-gwas-gcp-example/README.md → notebooks/DL-gwas-gcp-example/README.md
diff --git a/...xample/assets/00-create-new-notebook1.png → ...xample/assets/00-create-new-notebook1.png b/...xample/assets/00-create-new-notebook1.png → ...xample/assets/00-create-new-notebook1.png
diff --git a/...as-gcp-example/assets/000-enable-apis.png → ...as-gcp-example/assets/000-enable-apis.png b/...as-gcp-example/assets/000-enable-apis.png → ...as-gcp-example/assets/000-enable-apis.png
diff --git a/...as-gcp-example/assets/001-marketplace.png → ...as-gcp-example/assets/001-marketplace.png b/...as-gcp-example/assets/001-marketplace.png → ...as-gcp-example/assets/001-marketplace.png
diff --git a/...as-gcp-example/assets/002-name-minikf.png → ...as-gcp-example/assets/002-name-minikf.png b/...as-gcp-example/assets/002-name-minikf.png → ...as-gcp-example/assets/002-name-minikf.png
diff --git a/...s-gcp-example/assets/003-pick-machine.png → ...s-gcp-example/assets/003-pick-machine.png b/...s-gcp-example/assets/003-pick-machine.png → ...s-gcp-example/assets/003-pick-machine.png
diff --git a/...-gwas-gcp-example/assets/004-notebook.png → ...-gwas-gcp-example/assets/004-notebook.png b/...-gwas-gcp-example/assets/004-notebook.png → ...-gwas-gcp-example/assets/004-notebook.png
diff --git a/...xample/assets/01-create-new-notebook2.png → ...xample/assets/01-create-new-notebook2.png b/...xample/assets/01-create-new-notebook2.png → ...xample/assets/01-create-new-notebook2.png
diff --git a/...ple/assets/01-r2-create-new-notebook2.png → ...ple/assets/01-r2-create-new-notebook2.png b/...ple/assets/01-r2-create-new-notebook2.png → ...ple/assets/01-r2-create-new-notebook2.png
diff --git a/...ple/assets/01-r3-create-new-notebook2.png → ...ple/assets/01-r3-create-new-notebook2.png b/...ple/assets/01-r3-create-new-notebook2.png → ...ple/assets/01-r3-create-new-notebook2.png
diff --git a/...xample/assets/02-create-new-notebook3.png → ...xample/assets/02-create-new-notebook3.png b/...xample/assets/02-create-new-notebook3.png → ...xample/assets/02-create-new-notebook3.png
diff --git a/...s-gcp-example/assets/03-open-notebook.png → ...s-gcp-example/assets/03-open-notebook.png b/...s-gcp-example/assets/03-open-notebook.png → ...s-gcp-example/assets/03-open-notebook.png
diff --git a/...le/assets/04-upload-notebook-and-data.png → ...le/assets/04-upload-notebook-and-data.png b/...le/assets/04-upload-notebook-and-data.png → ...le/assets/04-upload-notebook-and-data.png
diff --git a/...was-gcp-example/assets/05-enable-kale.png → ...was-gcp-example/assets/05-enable-kale.png b/...was-gcp-example/assets/05-enable-kale.png → ...was-gcp-example/assets/05-enable-kale.png
diff --git a/...example/assets/06-pipeline-parameters.png → ...example/assets/06-pipeline-parameters.png b/...example/assets/06-pipeline-parameters.png → ...example/assets/06-pipeline-parameters.png
diff --git a/...e/assets/07-pipeline-parameters-katib.png → ...e/assets/07-pipeline-parameters-katib.png b/...e/assets/07-pipeline-parameters-katib.png → ...e/assets/07-pipeline-parameters-katib.png
diff --git a/...s-gcp-example/assets/08-pipeline-step.png → ...s-gcp-example/assets/08-pipeline-step.png b/...s-gcp-example/assets/08-pipeline-step.png → ...s-gcp-example/assets/08-pipeline-step.png
diff --git a/...cp-example/assets/09-pipeline-metrics.png → ...cp-example/assets/09-pipeline-metrics.png b/...cp-example/assets/09-pipeline-metrics.png → ...cp-example/assets/09-pipeline-metrics.png
diff --git a/...was-gcp-example/assets/10-setup-katib.png → ...was-gcp-example/assets/10-setup-katib.png b/...was-gcp-example/assets/10-setup-katib.png → ...was-gcp-example/assets/10-setup-katib.png
diff --git a/...as-gcp-example/assets/11-r2-setup-job.png → ...as-gcp-example/assets/11-r2-setup-job.png b/...as-gcp-example/assets/11-r2-setup-job.png → ...as-gcp-example/assets/11-r2-setup-job.png
diff --git a/...-gwas-gcp-example/assets/11-setup-job.png → ...-gwas-gcp-example/assets/11-setup-job.png b/...-gwas-gcp-example/assets/11-setup-job.png → ...-gwas-gcp-example/assets/11-setup-job.png
diff --git a/...DL-gwas-gcp-example/assets/12-compare.png → ...DL-gwas-gcp-example/assets/12-compare.png b/...DL-gwas-gcp-example/assets/12-compare.png → ...DL-gwas-gcp-example/assets/12-compare.png
diff --git a/...gcp-example/assets/13-parallel-coords.png → ...gcp-example/assets/13-parallel-coords.png b/...gcp-example/assets/13-parallel-coords.png → ...gcp-example/assets/13-parallel-coords.png
diff --git a/...xample/assets/14-successful-katib-run.png → ...xample/assets/14-successful-katib-run.png b/...xample/assets/14-successful-katib-run.png → ...xample/assets/14-successful-katib-run.png
diff --git a/...cp-example/assets/click-set-cell-kind.png → ...cp-example/assets/click-set-cell-kind.png b/...cp-example/assets/click-set-cell-kind.png → ...cp-example/assets/click-set-cell-kind.png
diff --git a/...gcp-example/assets/dl-gwas-headline-1.png → ...gcp-example/assets/dl-gwas-headline-1.png b/...gcp-example/assets/dl-gwas-headline-1.png → ...gcp-example/assets/dl-gwas-headline-1.png
diff --git a/...gcp-example/assets/dl-gwas-headline-2.png → ...gcp-example/assets/dl-gwas-headline-2.png b/...gcp-example/assets/dl-gwas-headline-2.png → ...gcp-example/assets/dl-gwas-headline-2.png
diff --git a/...-example/assets/enable-compute-engine.png → ...-example/assets/enable-compute-engine.png b/...-example/assets/enable-compute-engine.png → ...-example/assets/enable-compute-engine.png
diff --git a/...mple/assets/enable-service-management.png → ...mple/assets/enable-service-management.png b/...mple/assets/enable-service-management.png → ...mple/assets/enable-service-management.png
diff --git a/...was-gcp-example/assets/n2-standard-16.png → ...was-gcp-example/assets/n2-standard-16.png b/...was-gcp-example/assets/n2-standard-16.png → ...was-gcp-example/assets/n2-standard-16.png
diff --git a/...cp-example/assets/old-11-r2-setup-job.png → ...cp-example/assets/old-11-r2-setup-job.png b/...cp-example/assets/old-11-r2-setup-job.png → ...cp-example/assets/old-11-r2-setup-job.png
diff --git a/...le/assets/old-x002-final-results-page.png → ...le/assets/old-x002-final-results-page.png b/...le/assets/old-x002-final-results-page.png → ...le/assets/old-x002-final-results-page.png
diff --git a/...gcp-example/assets/run-minikf-startup.png → ...gcp-example/assets/run-minikf-startup.png b/...gcp-example/assets/run-minikf-startup.png → ...gcp-example/assets/run-minikf-startup.png
diff --git a/...example/assets/service-management-api.png → ...example/assets/service-management-api.png b/...example/assets/service-management-api.png → ...example/assets/service-management-api.png
diff --git a/...-gcp-example/assets/service-usage-api.png → ...-gcp-example/assets/service-usage-api.png b/...-gcp-example/assets/service-usage-api.png → ...-gcp-example/assets/service-usage-api.png
diff --git a/...s/DL-gwas-gcp-example/assets/ssh-link.png → ...s/DL-gwas-gcp-example/assets/ssh-link.png b/...s/DL-gwas-gcp-example/assets/ssh-link.png → ...s/DL-gwas-gcp-example/assets/ssh-link.png
diff --git a/...gwas-gcp-example/assets/stop-instance.png → ...gwas-gcp-example/assets/stop-instance.png b/...gwas-gcp-example/assets/stop-instance.png → ...gwas-gcp-example/assets/stop-instance.png
diff --git a/...xample/assets/updated-pipeline-params.png → ...xample/assets/updated-pipeline-params.png b/...xample/assets/updated-pipeline-params.png → ...xample/assets/updated-pipeline-params.png
diff --git a/...-gcp-example/assets/x001-new-notebook.png → ...-gcp-example/assets/x001-new-notebook.png b/...-gcp-example/assets/x001-new-notebook.png → ...-gcp-example/assets/x001-new-notebook.png
diff --git a/...xample/assets/x002-final-results-page.png → ...xample/assets/x002-final-results-page.png b/...xample/assets/x002-final-results-page.png → ...xample/assets/x002-final-results-page.png
diff --git a/...was-gcp-example/assets/x003-git-clone.png → ...was-gcp-example/assets/x003-git-clone.png b/...was-gcp-example/assets/x003-git-clone.png → ...was-gcp-example/assets/x003-git-clone.png
diff --git a/...p-example/assets/x004-launch-terminal.png → ...p-example/assets/x004-launch-terminal.png b/...p-example/assets/x004-launch-terminal.png → ...p-example/assets/x004-launch-terminal.png
diff --git a/.../DL-gwas-gcp-example/assets/x006-skip.png → .../DL-gwas-gcp-example/assets/x006-skip.png b/.../DL-gwas-gcp-example/assets/x006-skip.png → .../DL-gwas-gcp-example/assets/x006-skip.png
diff --git a/.../DL-gwas-gcp-example/assets/x007-wait.png → .../DL-gwas-gcp-example/assets/x007-wait.png b/.../DL-gwas-gcp-example/assets/x007-wait.png → .../DL-gwas-gcp-example/assets/x007-wait.png
diff --git a/...as-gcp-example/assets/x008-restart-ok.png → ...as-gcp-example/assets/x008-restart-ok.png b/...as-gcp-example/assets/x008-restart-ok.png → ...as-gcp-example/assets/x008-restart-ok.png
diff --git a/...gcp-example/assets/x009-preprocessing.png → ...gcp-example/assets/x009-preprocessing.png b/...gcp-example/assets/x009-preprocessing.png → ...gcp-example/assets/x009-preprocessing.png
diff --git a/...gcp-example/assets/xx-0002-pick-a-run.png → ...gcp-example/assets/xx-0002-pick-a-run.png b/...gcp-example/assets/xx-0002-pick-a-run.png → ...gcp-example/assets/xx-0002-pick-a-run.png
diff --git a/.../assets/xx0001-navigate-to-experiment.png → .../assets/xx0001-navigate-to-experiment.png b/.../assets/xx0001-navigate-to-experiment.png → .../assets/xx0001-navigate-to-experiment.png
diff --git a/...mple/assets/xx0003-pick-pipeline-step.png → ...mple/assets/xx0003-pick-pipeline-step.png b/...mple/assets/xx0003-pick-pipeline-step.png → ...mple/assets/xx0003-pick-pipeline-step.png
diff --git a/...s-gcp-example/assets/xx0006-step-logs.png → ...s-gcp-example/assets/xx0006-step-logs.png b/...s-gcp-example/assets/xx0006-step-logs.png → ...s-gcp-example/assets/xx0006-step-logs.png
diff --git a/...was-gcp-example/assets/xx0007-step-io.png → ...was-gcp-example/assets/xx0007-step-io.png b/...was-gcp-example/assets/xx0007-step-io.png → ...was-gcp-example/assets/xx0007-step-io.png
diff --git a/...ple/nb_assets/x002-final-results-page.png → ...ple/nb_assets/x002-final-results-page.png b/...ple/nb_assets/x002-final-results-page.png → ...ple/nb_assets/x002-final-results-page.png
diff --git a/...books/GWASCoatColor/GWAS_coat_color.ipynb → ...books/GWASCoatColor/GWAS_coat_color.ipynb b/...books/GWASCoatColor/GWAS_coat_color.ipynb → ...books/GWASCoatColor/GWAS_coat_color.ipynb
diff --git a/...tebooks/GenAI/GCP_GenAI_Huggingface.ipynb → notebooks/GenAI/GCP_GenAI_Huggingface.ipynb b/...tebooks/GenAI/GCP_GenAI_Huggingface.ipynb → notebooks/GenAI/GCP_GenAI_Huggingface.ipynb
diff --git a/tutorials/notebooks/GenAI/Gemini_Intro.ipynb → notebooks/GenAI/Gemini_Intro.ipynb b/tutorials/notebooks/GenAI/Gemini_Intro.ipynb → notebooks/GenAI/Gemini_Intro.ipynb
diff --git a/.../notebooks/GenAI/GCP_Pubmed_chatbot.ipynb → notebooks/GenAI/Pubmed_RAG_chatbot.ipynb b/.../notebooks/GenAI/GCP_Pubmed_chatbot.ipynb → notebooks/GenAI/Pubmed_RAG_chatbot.ipynb
diff --git a/...s/notebooks/GenAI/VertexAIStudioGCP.ipynb → notebooks/GenAI/VertexAIStudioGCP.ipynb b/...s/notebooks/GenAI/VertexAIStudioGCP.ipynb → notebooks/GenAI/VertexAIStudioGCP.ipynb
diff --git a/...xample_langchain_chat_llama_2_zeroshot.py → ...xample_langchain_chat_llama_2_zeroshot.py b/...xample_langchain_chat_llama_2_zeroshot.py → ...xample_langchain_chat_llama_2_zeroshot.py
diff --git a/...ple_vectorsearch_chat_llama_2_zeroshot.py → ...ple_vectorsearch_chat_llama_2_zeroshot.py b/...ple_vectorsearch_chat_llama_2_zeroshot.py → ...ple_vectorsearch_chat_llama_2_zeroshot.py
diff --git a/...notebooks/GenAI/langchain_on_vertex.ipynb → notebooks/GenAI/langchain_on_vertex.ipynb b/...notebooks/GenAI/langchain_on_vertex.ipynb → notebooks/GenAI/langchain_on_vertex.ipynb
diff --git a/tutorials/notebooks/GoogleBatch/.gitkeep → notebooks/GoogleBatch/.gitkeep b/tutorials/notebooks/GoogleBatch/.gitkeep → notebooks/GoogleBatch/.gitkeep
diff --git a/...atch/nextflow/Part1_GBatch_Nextflow.ipynb → ...atch/nextflow/Part1_GBatch_Nextflow.ipynb b/...atch/nextflow/Part1_GBatch_Nextflow.ipynb → ...atch/nextflow/Part1_GBatch_Nextflow.ipynb
diff --git a/...atch/nextflow/Part2_GBatch_Nextflow.ipynb → ...atch/nextflow/Part2_GBatch_Nextflow.ipynb b/...atch/nextflow/Part2_GBatch_Nextflow.ipynb → ...atch/nextflow/Part2_GBatch_Nextflow.ipynb
diff --git a/...sAPI/nextflow/Part1_LS_API_Nextflow.ipynb → ...sAPI/nextflow/Part1_LS_API_Nextflow.ipynb b/...sAPI/nextflow/Part1_LS_API_Nextflow.ipynb → ...sAPI/nextflow/Part1_LS_API_Nextflow.ipynb
diff --git a/...sAPI/nextflow/Part2_LS_API_Nextflow.ipynb → ...sAPI/nextflow/Part2_LS_API_Nextflow.ipynb b/...sAPI/nextflow/Part2_LS_API_Nextflow.ipynb → ...sAPI/nextflow/Part2_LS_API_Nextflow.ipynb
diff --git a/...encesAPI/snakemake/LS_API_Snakemake.ipynb → ...encesAPI/snakemake/LS_API_Snakemake.ipynb b/...encesAPI/snakemake/LS_API_Snakemake.ipynb → ...encesAPI/snakemake/LS_API_Snakemake.ipynb
diff --git a/.../notebooks/SRADownload/SRA-Download.ipynb → notebooks/SRADownload/SRA-Download.ipynb b/.../notebooks/SRADownload/SRA-Download.ipynb → notebooks/SRADownload/SRA-Download.ipynb
diff --git a/...tebooks/SpleenLiverSegmentation/README.md → notebooks/SpleenLiverSegmentation/README.md b/...tebooks/SpleenLiverSegmentation/README.md → notebooks/SpleenLiverSegmentation/README.md
diff --git a/...mentation/SpleenSeg_Pretrained-4_27.ipynb → ...mentation/SpleenSeg_Pretrained-4_27.ipynb b/...mentation/SpleenSeg_Pretrained-4_27.ipynb → ...mentation/SpleenSeg_Pretrained-4_27.ipynb
diff --git a/...a/Spleen_best_metric_model_pretrained.pth → ...a/Spleen_best_metric_model_pretrained.pth b/...a/Spleen_best_metric_model_pretrained.pth → ...a/Spleen_best_metric_model_pretrained.pth
diff --git a/...ooks/elasticBLAST/run_elastic_blast.ipynb → ...ooks/elasticBLAST/run_elastic_blast.ipynb b/...ooks/elasticBLAST/run_elastic_blast.ipynb → ...ooks/elasticBLAST/run_elastic_blast.ipynb
diff --git a/...ks/ncbi-stat-tutorial/STAT-tutorial.ipynb → ...ks/ncbi-stat-tutorial/STAT-tutorial.ipynb b/...ks/ncbi-stat-tutorial/STAT-tutorial.ipynb → ...ks/ncbi-stat-tutorial/STAT-tutorial.ipynb
diff --git a/...otebooks/pangolin/pangolin_pipeline.ipynb → notebooks/pangolin/pangolin_pipeline.ipynb b/...otebooks/pangolin/pangolin_pipeline.ipynb → notebooks/pangolin/pangolin_pipeline.ipynb
diff --git a/tutorials/README.md b/tutorials/README.md