{"id":21674209,"url":"https://github.com/aehrc/tribes","last_synced_at":"2025-04-12T04:24:10.252Z","repository":{"id":67767091,"uuid":"181599736","full_name":"aehrc/TRIBES","owner":"aehrc","description":"Finding cryptic relationships to boost disease gene detection","archived":false,"fork":false,"pushed_at":"2023-05-31T16:47:48.000Z","size":29098,"stargazers_count":12,"open_issues_count":6,"forks_count":5,"subscribers_count":6,"default_branch":"branch-0.2","last_synced_at":"2025-03-25T23:51:26.809Z","etag":null,"topics":["estimate-relationships","ibd-segments","pipeline","vcf"],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/aehrc.png","metadata":{"files":{"readme":"README-CSIRO.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2019-04-16T02:29:19.000Z","updated_at":"2024-06-21T23:03:34.000Z","dependencies_parsed_at":null,"dependency_job_id":"73d67009-ab75-4c84-b8b5-a50b8202dd64","html_url":"https://github.com/aehrc/TRIBES","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aehrc%2FTRIBES","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aehrc%2FTRIBES/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aehrc%2FTRIBES/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aehrc%2FTRIBES/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/aehrc","download_url":"https://codeload.github.com/aehrc/TRIBES/tar.gz/refs/heads/branch-0.2","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248514951,"owners_count":21117073,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["estimate-relationships","ibd-segments","pipeline","vcf"],"created_at":"2024-11-25T13:43:28.070Z","updated_at":"2025-04-12T04:24:10.232Z","avatar_url":"https://github.com/aehrc.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"TRIBES\n======\n\nThis section is specific to setting up and running TRIBES in CSIRO HPC cluster pearcey.\nIt can be used as reference for runnign tribes in other cluster environments.\n\n\nCSIRO HPC cluster is running 20CPU 128GB nodes with `slurm` as scheduler and `env modulules` to support versioning of tools and applications. \n\n## Running with Singularity\n\n\n\tsnakemake --profile cluster --use-singularity -d /scratch1/szu004/tribes/TFCeu estimate_degree_vs_true\n\n\n## Setting up on pearcey \n\nThis is CSIRO internal setup, but in the futre will be extened to support \nnon CSIRO environments.\n\nPerform the following installation setps.\n\n* install snakemake\u003e=5.4 with in python 3.6.1 \n* install tribes.tools R package from sources in R/3.5.0\n\nE.g:\n\n\tmodule load python/3.6.1\n\tpip install --user --upgrade 'snakemake\u003e=5.4'\n\n\n\tmodule load R/3.5.0\n\tR --no-save\n\n\t\u003e\u003e in R shell type\n\n\tinstall.packages('R/tribes.tools', repos=NULL, type='source')\n\n\t\u003e\u003e then agree to create a user library\n\nConfigure tribes:\n\n\tcp setup/pearcey/tribesrc ~/.tribesrc\n\tmkdir -p ~/.config/snakemake/cluster\n\tcp setup/pearcey/cluster.config.yaml ~/.config/snakemake/cluster/config.yaml\n\n## Running examples on pearcey\n\nssh to one of the pearcey interactive nodes e.g. `pearcey-i1.hpc.csiro.au`.\n\nSelect working directory for the sample dataset e.g. `/flush3/$USER/TFCeu`\n\nCopy the example dataset with configuration from `/flush2/projects/HB_TB_Share/TRIBES/samples/TFCeu` to your working dir.\n\n\tcp -r /flush2/projects/HB_TB_Share/TRIBES/samples/TFCeu /flush3/$USER/TFCeu\n\nTo run TRIBES (estimate relatedness) locally using 4 CPU cores:\n\n\t./tribes -d /flush3/$USER/TFCeu --cores 4 estimate_degree\n\nTo run TRIBES using slurm:\n\n\t./tribes -d /flush3/$USER/TFCeu --profile cluster estimate_degree\n\nTo generate report comparing the estimated relatendess against the reported relations:\n\n\t./tribes -d /flush3/$USER/TFCeu --profile cluster estimate_degree_vs_true\n\n\nThe results are in the working dir `/flush3/$USER/TFCeu`:\n\n- `TF-CEU-15-2_BiSnp_EurAF:0.01_LD_GRM-allchr_IBD.csv` - estimated IBD0 and EstimatedDegree\n- `TF-CEU-15-2_BiSnp_EurAF:0.01_LD_GRM-allchr_IBD_RVT.html` - comparision agains reported relatedness\n\n\n\n\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faehrc%2Ftribes","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Faehrc%2Ftribes","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faehrc%2Ftribes/lists"}