{"id":19243835,"url":"https://github.com/brocbyte/bioinformatics","last_synced_at":"2025-02-23T15:13:53.215Z","repository":{"id":61902572,"uuid":"555781336","full_name":"brocbyte/bioinformatics","owner":"brocbyte","description":null,"archived":false,"fork":false,"pushed_at":"2022-11-04T06:44:33.000Z","size":62143,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"trunk","last_synced_at":"2025-01-05T03:49:06.214Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/brocbyte.png","metadata":{"files":{"readme":"README.txt","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2022-10-22T10:09:23.000Z","updated_at":"2022-10-22T11:46:51.000Z","dependencies_parsed_at":"2023-01-21T12:17:40.164Z","dependency_job_id":null,"html_url":"https://github.com/brocbyte/bioinformatics","commit_stats":null,"previous_names":["brocbyte/bioinformatics"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brocbyte%2Fbioinformatics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brocbyte%2Fbioinformatics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brocbyte%2Fbioinformatics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brocbyte%2Fbioinformatics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/brocbyte","download_url":"https://codeload.github.com/brocbyte/bioinformatics/tar.gz/refs/heads/trunk","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240331362,"owners_count":19784646,"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":[],"created_at":"2024-11-09T17:20:29.941Z","updated_at":"2025-02-23T15:13:53.193Z","avatar_url":"https://github.com/brocbyte.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Assignment 4\r\n\r\n1. Escherichia coli: https://www.ncbi.nlm.nih.gov/sra/SRX9196450\r\n\r\n2. bash-script: run.sh\r\n\r\n3. samtools flagstat res: samtools-results/GCF_000005845.2_ASM584v2_genomic_SRR12717711.txt\r\n\r\n4. python parser script: parser.py\r\n\r\n5. all temporary files in *-results/ folders\r\n\r\n6.\r\n## Snakemake Setup\r\n\r\nto install \u0026 run:\r\n1) install python3\r\n2) install pip3\r\n3) pip3 install snakemake\r\n4) write your Snakemake file according to https://snakemake.readthedocs.io/en/stable/tutorial/basics.html\r\n5) python3 -m snakemake -c1 {your_goal}\r\n\r\n## Snakemake Run\r\n\r\ncd snakemake-files\r\n./runit.sh\r\n\r\n7. snakemake-files/Snakemake\r\n8. Report generated with pipeline: GCF_000005845.2_ASM584v2_genomic_SRR12717711_report.txt (obsolete, now in console)\r\n\r\n10. snakemake-files/Snakemake\r\n11. Report generated with pipeline: GCF_000005845.2_ASM584v2_genomic_SRR12717711_report.txt (obsolete, now in console)\r\n12. snakemake-files/.snakemake/log (pick latest one)\r\n\r\n13. full_dag.svg, qc_report_dag.svg\r\n\r\n14. command for generating those file can be found in ./snakemake-files/runit.sh\r\n\r\nfull_dag.svg differs slightly from one in Assignment 4, cause \"if-statement\" is implemented by hand:\r\nparse_flagstat_result rule calls ./parse.py, which will log parsed result and, if it is \u003e 90%, will\r\nwrite special file *.ok. This file is a dependency for samtools_sort rule. If parsed results was \u003c 90%,\r\nsamtools_sort won't be executed.\r\n\r\nalso QC-report generation is fully separated and can be use as a standalone goal (see ./snakemake-files/runit.sh)\r\n\r\n\r\n\r\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrocbyte%2Fbioinformatics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbrocbyte%2Fbioinformatics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrocbyte%2Fbioinformatics/lists"}