{"id":22295378,"url":"https://github.com/alkc/parallel-structure","last_synced_at":"2025-10-13T22:31:19.332Z","repository":{"id":52871238,"uuid":"125206866","full_name":"alkc/parallel-structure","owner":"alkc","description":"A probably over-engineered bash-script for starting parallel runs of structure for different population sizes and numbers of replicates.","archived":false,"fork":false,"pushed_at":"2021-04-26T12:22:17.000Z","size":31,"stargazers_count":3,"open_issues_count":0,"forks_count":2,"subscribers_count":2,"default_branch":"master","last_synced_at":"2024-12-03T17:52:06.733Z","etag":null,"topics":["parallel","population-genetics","structure"],"latest_commit_sha":null,"homepage":"","language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/alkc.png","metadata":{"files":{"readme":"README.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}},"created_at":"2018-03-14T12:10:00.000Z","updated_at":"2024-05-11T13:46:02.000Z","dependencies_parsed_at":"2022-08-23T03:20:33.617Z","dependency_job_id":null,"html_url":"https://github.com/alkc/parallel-structure","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alkc%2Fparallel-structure","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alkc%2Fparallel-structure/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alkc%2Fparallel-structure/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alkc%2Fparallel-structure/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/alkc","download_url":"https://codeload.github.com/alkc/parallel-structure/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":236414733,"owners_count":19145076,"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":["parallel","population-genetics","structure"],"created_at":"2024-12-03T17:41:56.190Z","updated_at":"2025-10-13T22:31:14.013Z","avatar_url":"https://github.com/alkc.png","language":"Shell","readme":"# parallel-structure\n\nGlued-together bash script for running parallel runs \"Structure\" for population genetics inference for different values of `K` and reps.\n\nYou will need both `parallel` and structure installed — an easy task with conda:\n\n```\nconda install -c bioconda parallel structure\n```\n\n## Example\n\nTo check if the script works, please use the included example data set. More info about the sample data can be found at: https://web.stanford.edu/group/pritchardlab/software/structure-data_v.2.3.1.html (testdata1)\n\nPlease run the following command from the script directory:\n\n```\nbash parallel-structure.sh example-data/mainparams example-data/extraparams example-data/testdata1 output_dir 1 3 5 8\n```\n\nIn the last four digits of the above command you are able to set, in the following order: minimum K, maximum K, number of repetitions and number of parallel jobs. \n\nThe command starts 8 parallel jobs for K=1 to K=3 with 5 replicates for each tested value K.\n\nAll  output is saved to `output_dir/`\n\n## Citation\n\n[![DOI](https://zenodo.org/badge/125206866.svg)](https://zenodo.org/badge/latestdoi/125206866)\n\nIf this script has been useful to you and you think more researchers would benefit from knowing about it, then feel free to cite it at as follows: \n\n* Alexander Koc. (2021, April 16). alkc/parallel-structure: (Version v0.6.1). Zenodo. http://doi.org/10.5281/zenodo.4697229\n\nMore importantly, you should probably cite both structure and parallel on which this script relies.\n\nFor more info about how to cite Structure please refer to page 37 of the official [Structure 3.4 manual (PDF)](https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/structure_doc.pdf)\n\nFor more info about how to cite GNU parallel, please look here https://doi.org/10.5281/zenodo.1146014 (or run `parallel --citation` in the bash prompt!).\n\n## CHANGELOG\n\n## version 0.6.1\n\n* Prepare for release on Zenodo\n* UPDATED README with better description\n\n##  version 0.6 \u003c2021-04-13\u003e\n\n* FIXED bug where replicate runs started with the same seed, which defeated the purpose of reps.\n* ADDED Ability to set min K, max K, number of reps and number of parallel jobs from the command line\n* ADDED More informative error messages if files missing at specified paths  \n\n## TODO:\n\n* Add installation instructions?\n* Add long named parameters (probably requires moving away from using bash?)\n* Add some parameter validation (e.g. exit with informative error if input files do not exist)\n* Make nbr parallel jobs parameter optional (default to nproc - 1?)\n \n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falkc%2Fparallel-structure","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falkc%2Fparallel-structure","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falkc%2Fparallel-structure/lists"}