{"id":21882271,"url":"https://github.com/bfssi-bioinformatics-lab/centreseq","last_synced_at":"2025-03-22T01:14:59.164Z","repository":{"id":62561353,"uuid":"189637842","full_name":"BFSSI-Bioinformatics-Lab/centreseq","owner":"BFSSI-Bioinformatics-Lab","description":"Easily establish a core genome among bacterial strains","archived":false,"fork":false,"pushed_at":"2022-06-14T17:19:41.000Z","size":467,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-02-23T12:41:01.254Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","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/BFSSI-Bioinformatics-Lab.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":"2019-05-31T18:06:29.000Z","updated_at":"2022-06-14T17:19:45.000Z","dependencies_parsed_at":"2022-11-03T15:15:27.354Z","dependency_job_id":null,"html_url":"https://github.com/BFSSI-Bioinformatics-Lab/centreseq","commit_stats":null,"previous_names":["bfssi-forest-dussault/centreseq"],"tags_count":20,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BFSSI-Bioinformatics-Lab%2Fcentreseq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BFSSI-Bioinformatics-Lab%2Fcentreseq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BFSSI-Bioinformatics-Lab%2Fcentreseq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BFSSI-Bioinformatics-Lab%2Fcentreseq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BFSSI-Bioinformatics-Lab","download_url":"https://codeload.github.com/BFSSI-Bioinformatics-Lab/centreseq/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244890097,"owners_count":20527035,"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":"2024-11-28T09:28:04.114Z","updated_at":"2025-03-22T01:14:59.143Z","avatar_url":"https://github.com/BFSSI-Bioinformatics-Lab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/centreseq/README.html)\n[![Documentation Status](https://readthedocs.org/projects/centreseq/badge/?version=latest)](https://centreseq.readthedocs.io/en/latest/?badge=latest)\n\nThe most recent documentation can be found at the following URL: https://centreseq.readthedocs.io/en/latest/\n\n### Quick installation in a Conda environment\nDue to some strange Conda/Bioconda issues with both centreseq and Prokka, \nthe installation process is convoluted to get everything working. The following incantation should work: \n```text\nconda config --add channels defaults\nconda config --add channels bioconda\nconda config --add channels conda-forge\n\nconda create -n centreseq python=3.7\nconda activate centreseq\nconda install centreseq -c bioconda\nconda uninstall prokka\nconda install -c conda-forge -c bioconda -c defaults prokka\nconda install centreseq -c bioconda\n```\n\n\n### Developer notes/Known issues\n- Version of mmseqs2 has been pinned at 9-d36de in meta.yaml due to 10-6d92c containing a bug which causes the functional test to \nhang indefinitely on some systems.\n- Prokka's installation appears to be broken in some cases when just running `conda install prokka -c bioconda`, \nthe solution is to downgrade Perl with `conda install perl=5.22.0`","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbfssi-bioinformatics-lab%2Fcentreseq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbfssi-bioinformatics-lab%2Fcentreseq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbfssi-bioinformatics-lab%2Fcentreseq/lists"}