{"id":26450410,"url":"https://github.com/ibchgenomic/hpc-apptainer","last_synced_at":"2025-06-19T03:39:16.136Z","repository":{"id":258485087,"uuid":"865613767","full_name":"IBCHgenomic/HPC-apptainer","owner":"IBCHgenomic","description":"apptainer for HPC genome, phylogenomics and evolutionary analysis","archived":false,"fork":false,"pushed_at":"2025-02-25T20:16:51.000Z","size":26,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-04-28T07:45:36.144Z","etag":null,"topics":["apptainer","apptainer-container","devops","devops-platform","devops-team","high-performance-computing","phylogenomics","phylogenomics-bioinformatics"],"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/IBCHgenomic.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-09-30T20:26:28.000Z","updated_at":"2025-02-25T20:47:43.000Z","dependencies_parsed_at":"2025-03-11T23:15:37.380Z","dependency_job_id":"19ce074e-3fdb-45c6-a895-6ed32772b9c4","html_url":"https://github.com/IBCHgenomic/HPC-apptainer","commit_stats":null,"previous_names":["codecreatede/phylogenomics-apptainer","applicativesystem/phylogenomics-apptainer","sciencegenome/phylogenomics-apptainer","ibchgenomic/hpc-apptainer","sciencegenome/hpc-apptainer"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/IBCHgenomic/HPC-apptainer","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IBCHgenomic%2FHPC-apptainer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IBCHgenomic%2FHPC-apptainer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IBCHgenomic%2FHPC-apptainer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IBCHgenomic%2FHPC-apptainer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/IBCHgenomic","download_url":"https://codeload.github.com/IBCHgenomic/HPC-apptainer/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IBCHgenomic%2FHPC-apptainer/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":260682474,"owners_count":23046058,"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":["apptainer","apptainer-container","devops","devops-platform","devops-team","high-performance-computing","phylogenomics","phylogenomics-bioinformatics"],"created_at":"2025-03-18T15:25:53.466Z","updated_at":"2025-06-19T03:39:11.121Z","avatar_url":"https://github.com/IBCHgenomic.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# HPC-apptainer\n\n## Multiple apptainer images for HPC computing. \n\n- a apptainer for the phylogenomics. it contains all the applications combined in a single container for the phylogenomics. it incldues orthofinder, astral, trimal, alignmentGO, raxml and clipkit. all the applications required for the genome analysis and genome or gene based phylogenomics.  \n```\napptainer exec phylogenomics.def\nGiven an folder of the fasta file you can invoke the apptainer as\napptainer run phylogenomics.sif orthofinder PATH-FASTA-FOLDER\napptainer run phylogenomics.sif astral -h\napptainer run phylogenomics.sif trimal -h\napptainer run phylogenomics.sif alignmentGO -h\napptainer run clipkit -h\n```\n- post genome assembly apptainer. genome completeness, phylogenomic profiling search. protein-genome alignment for genome annotation inclduing the hint search. \n```\napptainer build genomeannotate.sif genomeannotate.def\n```\n- apptainer for the genome assembly coming from the pacbiohifi reads. it includes two genome assembler and one is hifiasm and the other is verkko. The benchmark for the assembly for these assemblers are located at my another repository [genomeasembly-pacbiohifi](https://github.com/sciencegenome/genomeassembly-pacbiohifi)\n- to invoke the hifiasm apptainer \n```\nmodule load singularity\napptainer run hifiasm.sif hifiasm\n```\n- to build and invoke the verkko conda based apptainer. I wrote the verkko yaml so that you can directly import and run with in the apptainer. \n```\nmodule load singularity \napptainer build verkko.sif verkko.def \necho \".opt/conda/etc/profile.d/conda.sh\" \u003e\u003e $ENV_PATH\n```\n- inspect the images after the build \n```\nfor i in *.sif; do apptainer inspect ${i}; done\n```\n- apptainer images for the cpat you can directly call this from the sanbox repositories. \n```\napptainer build cpat.sif apptainer.def\n```\n- to inspect the image\n```\napptainer inspect cpat.sif\n```\n- to run the apptainer image \n```\napptainer exec cpat.sif cpat \n```\n- to run on the computing cluster with the singularity installed\n```\nmodule load singularity\n```\n- to install the apptainer on the new ubuntu version.\n```\nsh apptainer-install.sh \n```\n\nGaurav Sablok\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fibchgenomic%2Fhpc-apptainer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fibchgenomic%2Fhpc-apptainer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fibchgenomic%2Fhpc-apptainer/lists"}