diff --git a/_compdemos/Apptainer.md b/_compdemos/Apptainer.md index f0f84a14..3634b0e8 100644 --- a/_compdemos/Apptainer.md +++ b/_compdemos/Apptainer.md @@ -1,6 +1,5 @@ --- title: Using Apptainer Containers -last_modified_at: 2021-07-30 main_author: Michael Gutteridge primary_reviewers: bmcgough, atombaby --- diff --git a/_compdemos/Docker.md b/_compdemos/Docker.md index 5d5c6645..b1ee2354 100644 --- a/_compdemos/Docker.md +++ b/_compdemos/Docker.md @@ -1,6 +1,5 @@ --- title: Using Docker at Fred Hutch -last_modified_at: 2026-01-27 main_author: Taylor Firman, Emma Bishop original_author: Dirk Petersen primary_reviewers: dtenenba, dirkpetersen, tefirman diff --git a/_compdemos/alphafold3.md b/_compdemos/alphafold3.md index 9b37956f..010c00e3 100644 --- a/_compdemos/alphafold3.md +++ b/_compdemos/alphafold3.md @@ -1,6 +1,5 @@ --- title: AlphaFold-3 -last_modified_at: 2024-12-19 main_author: John Dey primary_reviewers: --- diff --git a/_compdemos/aspera-on-nx.md b/_compdemos/aspera-on-nx.md index 05f173ec..d59147ae 100644 --- a/_compdemos/aspera-on-nx.md +++ b/_compdemos/aspera-on-nx.md @@ -1,6 +1,5 @@ --- title: Managing Aspera Connect on NoMachine -last_modified_at: 2021-05-25 main_author: Michael Gutteridge primary_reviewers: atombaby --- diff --git a/_compdemos/managing-module-versions.md b/_compdemos/managing-module-versions.md index 1b92a56c..50bdc458 100644 --- a/_compdemos/managing-module-versions.md +++ b/_compdemos/managing-module-versions.md @@ -1,6 +1,5 @@ --- title: Managing Module Versions -last_modified_at: 2023-05-24 main_author: Michael Gutteridge primary_reviewers: atombaby --- diff --git a/_compdemos/microbiome_tools.md b/_compdemos/microbiome_tools.md index 151a814e..06d511dc 100644 --- a/_compdemos/microbiome_tools.md +++ b/_compdemos/microbiome_tools.md @@ -1,6 +1,5 @@ --- title: Bioinformatics Tools for Microbiome Analysis -last_modified_at: 2020-03-25 primary_reviewers: sminot --- diff --git a/_compdemos/motuz.md b/_compdemos/motuz.md index eef6509c..2724fc74 100644 --- a/_compdemos/motuz.md +++ b/_compdemos/motuz.md @@ -1,6 +1,5 @@ --- title: Using Motuz to Move Large Data -last_modified_at: 2019-08-22 main_author: Dan Tenenbaum primary_reviewers: dtenenba --- diff --git a/_compdemos/mydb.md b/_compdemos/mydb.md index f8f3a98c..0d809b95 100644 --- a/_compdemos/mydb.md +++ b/_compdemos/mydb.md @@ -1,6 +1,5 @@ --- title: Configuring Databases on MyDB -last_modified_at: 2023-02-02 primary_reviewers: fizwit, atombaby --- diff --git a/_compdemos/nextflow.md b/_compdemos/nextflow.md index 9236c155..e18bd01e 100644 --- a/_compdemos/nextflow.md +++ b/_compdemos/nextflow.md @@ -1,6 +1,5 @@ --- title: Nextflow - an Emerging Service for Workflow Management -last_modified_at: 2021-04-14 primary_reviewers: sminot --- diff --git a/_compdemos/snapshots.md b/_compdemos/snapshots.md index f6c515ba..b193d745 100644 --- a/_compdemos/snapshots.md +++ b/_compdemos/snapshots.md @@ -1,6 +1,5 @@ --- title: Snapshots -last_modified_at: 2018-12-10 main_author: Ben McGough primary_reviewers: --- diff --git a/_compdemos/store_job_local.md b/_compdemos/store_job_local.md index 03419dca..65a247c8 100644 --- a/_compdemos/store_job_local.md +++ b/_compdemos/store_job_local.md @@ -1,6 +1,5 @@ --- title: Job Local Storage -last_modified_at: 2023-04-28 main_author: Michael Gutteridge primary_reviewers: atombaby --- diff --git a/_compdemos/toolbox.md b/_compdemos/toolbox.md index a89e7385..06040263 100644 --- a/_compdemos/toolbox.md +++ b/_compdemos/toolbox.md @@ -1,6 +1,5 @@ --- title: Using Toolbox to Get Hutch Master Data -last_modified_at: 2019-01-13 main_author: Dirk Petersen primary_reviewers: mrg, dirkpetersen --- diff --git a/_compdemos/vscode_markdown_howto.md b/_compdemos/vscode_markdown_howto.md index aafb4c89..ef124557 100644 --- a/_compdemos/vscode_markdown_howto.md +++ b/_compdemos/vscode_markdown_howto.md @@ -1,6 +1,5 @@ --- title: Using Markdown with Visual Studio Code -last_modified_at: 2018-06-07 main_author: Robert McDermott --- diff --git a/_contributors/STTR.md b/_contributors/STTR.md index 78998498..6309d0ae 100644 --- a/_contributors/STTR.md +++ b/_contributors/STTR.md @@ -1,6 +1,5 @@ --- title: STTR Group -last_modified_at: 2018-09-06 --- ## Affiliation diff --git a/_contributors/kmcclosk.md b/_contributors/kmcclosk.md index 73a59854..352461dc 100644 --- a/_contributors/kmcclosk.md +++ b/_contributors/kmcclosk.md @@ -1,6 +1,5 @@ --- title: Kylie McCloskey -last_modified_at: 2018-09-06 --- ## Affiliation diff --git a/_contributors/ptvan.md b/_contributors/ptvan.md index 7fa0a862..ce633933 100644 --- a/_contributors/ptvan.md +++ b/_contributors/ptvan.md @@ -1,6 +1,5 @@ --- title: Phu T. Van -last_modified_at: 2018-06-06 --- ## Affiliation Vaccine & Infectious Disease Division diff --git a/_datademos/cbio_examples_of_using_cbio.md b/_datademos/cbio_examples_of_using_cbio.md index 34493cfa..bd62af4a 100644 --- a/_datademos/cbio_examples_of_using_cbio.md +++ b/_datademos/cbio_examples_of_using_cbio.md @@ -1,6 +1,5 @@ --- title: How you can use cBioPortal -last_modified_at: 2025-04-18 main_authors: sitapriyamoorthi primary_reviewers: tfirman, laderast --- diff --git a/_datademos/cbio_how_to_prepare_files.md b/_datademos/cbio_how_to_prepare_files.md index 38ef39c3..341ba9a6 100644 --- a/_datademos/cbio_how_to_prepare_files.md +++ b/_datademos/cbio_how_to_prepare_files.md @@ -1,6 +1,5 @@ --- title: Helpful tips on how to prepare files for cBioPortal -last_modified_at: 2025-04-18 main_authors: sitapriyamoorthi primary_reviewers: tfirman, laderast --- diff --git a/_datademos/cbio_how_to_upload_data_to_cbio_s3.md b/_datademos/cbio_how_to_upload_data_to_cbio_s3.md index 0fddd52e..fae3b6ab 100644 --- a/_datademos/cbio_how_to_upload_data_to_cbio_s3.md +++ b/_datademos/cbio_how_to_upload_data_to_cbio_s3.md @@ -1,6 +1,5 @@ --- title: Uploading your study into `fh-dasl-cbio` S3 bucket -last_modified_at: 2025-04-18 main_authors: sitapriyamoorthi primary_reviewers: tfirman, laderast --- diff --git a/_datademos/cbio_test_access_to_cbio_s3_bucket.md b/_datademos/cbio_test_access_to_cbio_s3_bucket.md index 6cfb898f..67a5bbdd 100644 --- a/_datademos/cbio_test_access_to_cbio_s3_bucket.md +++ b/_datademos/cbio_test_access_to_cbio_s3_bucket.md @@ -1,6 +1,5 @@ --- title: Testing access to Fred Hutch cBioPortal S3 bucket -last_modified_at: 2025-04-18 main_authors: sitapriyamoorthi primary_reviewers: tfirman, laderast --- diff --git a/_datademos/tidy-data.md b/_datademos/tidy-data.md index ca9cfc81..3e680c31 100644 --- a/_datademos/tidy-data.md +++ b/_datademos/tidy-data.md @@ -1,6 +1,5 @@ --- title: Guidance for Making "Tidy" Data -last_modified_at: 2019-11-06 main_author: primary_reviewers: ptvan --- diff --git a/_datascience/wdl_execution_engines.md b/_datascience/wdl_execution_engines.md index 57b27e43..ad4dba57 100644 --- a/_datascience/wdl_execution_engines.md +++ b/_datascience/wdl_execution_engines.md @@ -1,6 +1,5 @@ --- title: WDL Execution Engines -last_modified_at: 2025-11-11 --- ## What is an Execution Engine? diff --git a/_pathways/path-cbio-fh-instance.md b/_pathways/path-cbio-fh-instance.md index f0b8bbff..f8ff915a 100644 --- a/_pathways/path-cbio-fh-instance.md +++ b/_pathways/path-cbio-fh-instance.md @@ -1,6 +1,5 @@ --- title: How to upload your study into the Fred Hutch instance of cBioPortal -last_modified_at: 2025-04-18 main_authors: sitapriyamoorthi primary_reviewers: tfirman, laderast --- diff --git a/_pathways/path-interactive.md b/_pathways/path-interactive.md index 4d4311da..b8130a34 100644 --- a/_pathways/path-interactive.md +++ b/_pathways/path-interactive.md @@ -1,6 +1,5 @@ --- title: Getting and Using Interactive Sessions -last_modified_at: 2024-05-29 primary_reviewers: atombaby --- diff --git a/_scicomputing/access_overview.md b/_scicomputing/access_overview.md index 00cd47f0..914b0232 100644 --- a/_scicomputing/access_overview.md +++ b/_scicomputing/access_overview.md @@ -1,6 +1,5 @@ --- title: Computing Access Overview -last_modified_at: 2019-09-05 primary_reviewers: vortexing --- This overview describes what types of credentials are needed for [various Fred Hutch computing resources](/compdemos/) and provides instructions for accessing those supported computing resources. diff --git a/_scicomputing/access_permissions.md b/_scicomputing/access_permissions.md index 7b37c0d0..6e07c867 100644 --- a/_scicomputing/access_permissions.md +++ b/_scicomputing/access_permissions.md @@ -1,6 +1,5 @@ --- title: Permissions -last_modified_at: 2019-09-05 primary_reviewers: --- diff --git a/_scicomputing/comp_index.md b/_scicomputing/comp_index.md index fbd7c5f0..ebedf806 100644 --- a/_scicomputing/comp_index.md +++ b/_scicomputing/comp_index.md @@ -1,6 +1,5 @@ --- title: Overview of Scientific Computing at Fred Hutch -last_modified_at: 2019-05-30 primary_reviewers: vortexing --- Various groups support computational capacity at the Hutch. Center IT supports general computing tasks, such as email and desktop computer software; further information can be found on the Center IT pages in Centernet. This section of the Wiki represents information relating to research and scientific computing, which generally require additional software, hardware, and skills. If you have questions that aren't answered here, please email `SciComp` or ask a public question on [The Fred Hutch Data Community Slack Workspace](https://fhdata.slack.com) in the `question-and-answer` channel. diff --git a/_scicomputing/compute_accounts.md b/_scicomputing/compute_accounts.md index e61723ac..5d1a6be3 100644 --- a/_scicomputing/compute_accounts.md +++ b/_scicomputing/compute_accounts.md @@ -1,6 +1,5 @@ --- title: Cluster Accounts -last_modified_at: 2021-02-09 primary_reviewer: atombaby --- diff --git a/_scicomputing/compute_environments.md b/_scicomputing/compute_environments.md index 06b2e9be..ff79dfc4 100644 --- a/_scicomputing/compute_environments.md +++ b/_scicomputing/compute_environments.md @@ -1,6 +1,5 @@ --- title: Computing Environments and Containers -last_modified_at: 2025-11-11 primary_reviewers: bmcgough --- diff --git a/_scicomputing/compute_gpu.md b/_scicomputing/compute_gpu.md index 114df80b..e4755131 100644 --- a/_scicomputing/compute_gpu.md +++ b/_scicomputing/compute_gpu.md @@ -1,6 +1,5 @@ --- title: Computing with GPUs -last_modified_at: 2023-03-31 primary_reviewer: atombaby --- @@ -66,4 +65,4 @@ When submitting jobs make sure that your current environment does not have modul ## Using GPUs -When your job is assigned a GPU, Slurm sets the environment variable CUDA_VISIBLE_DEVICES. This environment variable indicates the assigned GPU- most CUDA tools (e.g. tensorflow) use this to restrict execution to that device. \ No newline at end of file +When your job is assigned a GPU, Slurm sets the environment variable CUDA_VISIBLE_DEVICES. This environment variable indicates the assigned GPU- most CUDA tools (e.g. tensorflow) use this to restrict execution to that device. diff --git a/_scicomputing/compute_job_scheduling.md b/_scicomputing/compute_job_scheduling.md index 712f83a3..05557e23 100644 --- a/_scicomputing/compute_job_scheduling.md +++ b/_scicomputing/compute_job_scheduling.md @@ -1,6 +1,5 @@ --- title: Gizmo Job Scheduling -last_modified_at: 2021-02-09 primary_reviewer: atombaby --- diff --git a/_scicomputing/compute_parallel.md b/_scicomputing/compute_parallel.md index 40a9aed0..7ca546d2 100644 --- a/_scicomputing/compute_parallel.md +++ b/_scicomputing/compute_parallel.md @@ -1,6 +1,5 @@ --- title: Parallel Computing on Slurm Clusters -last_modified_at: 2019-05-02 primary_reviewer: atombaby --- diff --git a/_scicomputing/hutchgo_guest_collection.md b/_scicomputing/hutchgo_guest_collection.md index c4bb3204..077569f6 100644 --- a/_scicomputing/hutchgo_guest_collection.md +++ b/_scicomputing/hutchgo_guest_collection.md @@ -1,6 +1,5 @@ --- title: Creating Guest Collections in HutchGO -last_modified_at: 2024-07-01 primary_reviewers: atombaby --- diff --git a/_scicomputing/hutchgo_overview.md b/_scicomputing/hutchgo_overview.md index e8937504..05e14f8e 100644 --- a/_scicomputing/hutchgo_overview.md +++ b/_scicomputing/hutchgo_overview.md @@ -1,6 +1,5 @@ --- title: Hutch Globus Online - HutchGO -last_modified_at: 2024-08-16 primary_reviewers: atombaby --- diff --git a/_scicomputing/reference_training.md b/_scicomputing/reference_training.md index dc8f591b..dd8dc247 100644 --- a/_scicomputing/reference_training.md +++ b/_scicomputing/reference_training.md @@ -1,6 +1,5 @@ --- title: Training, Community and Finding Help -last_modified_at: 2020-06-02 primary_reviewers: k8hertweck, vortexing --- There are a variety of resources for training on various aspects of bioinformatics, analytics and data skills available at the Fred Hutch, in the Seattle area and on the web. diff --git a/_scicomputing/store_databases.md b/_scicomputing/store_databases.md index 90bc426e..ccfb01c7 100644 --- a/_scicomputing/store_databases.md +++ b/_scicomputing/store_databases.md @@ -1,6 +1,5 @@ --- title: Data Storage in Databases -last_modified_at: 2018-04-01 primary_reviewers: vortexing --- diff --git a/_scicomputing/store_overview.md b/_scicomputing/store_overview.md index f3964b4e..c360cdb1 100644 --- a/_scicomputing/store_overview.md +++ b/_scicomputing/store_overview.md @@ -1,6 +1,5 @@ --- title: Overview of Data Storage at Fred Hutch -last_modified_at: 2023-03-24 primary_reviewers: --- diff --git a/contributorTemplate.md b/contributorTemplate.md index 84acaef1..f6b9734b 100644 --- a/contributorTemplate.md +++ b/contributorTemplate.md @@ -1,6 +1,5 @@ --- title: Your Name -last_modified_at: 2018-06-06 --- ## Affiliation Clinical Research Division