{"id":29224619,"url":"https://github.com/sing-group/compi-blast-example","last_synced_at":"2026-02-03T13:06:49.529Z","repository":{"id":88302650,"uuid":"362006337","full_name":"sing-group/compi-blast-example","owner":"sing-group","description":"A Compi pipeline based on the Nextflow blast-example: https://github.com/nextflow-io/blast-example","archived":false,"fork":false,"pushed_at":"2021-04-27T06:38:29.000Z","size":3,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":4,"default_branch":"master","last_synced_at":"2026-01-15T05:04:18.364Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Dockerfile","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/sing-group.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,"zenodo":null}},"created_at":"2021-04-27T06:35:21.000Z","updated_at":"2021-04-27T06:38:32.000Z","dependencies_parsed_at":null,"dependency_job_id":"c676f7ce-a062-47bc-b2b9-e45a271d270a","html_url":"https://github.com/sing-group/compi-blast-example","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/sing-group/compi-blast-example","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fcompi-blast-example","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fcompi-blast-example/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fcompi-blast-example/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fcompi-blast-example/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sing-group","download_url":"https://codeload.github.com/sing-group/compi-blast-example/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fcompi-blast-example/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29046503,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-03T10:09:22.136Z","status":"ssl_error","status_checked_at":"2026-02-03T10:09:16.814Z","response_time":96,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":"2025-07-03T06:07:26.884Z","updated_at":"2026-02-03T13:06:49.506Z","avatar_url":"https://github.com/sing-group.png","language":"Dockerfile","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Compi pipeline blast example\nThis is a Compi example which ports to Compi a [Nextflow example pipeline](https://github.com/nextflow-io/blast-example) using BLAST.\n\n## Prerequisites\n\n- [Compi Development Kit (Compi-DK)](https://sing-group.org/compi/#downloads)\n- [Docker](https://www.docker.com/)\n\n## Building the pipeline\n\nMove to the directory of the cloned respository of this pipeline and run `compi-dk build` inside it.\n\n```bash\ncompi-dk build\n```\n\n## Running the pipeline with sample data\n\nThe Nextflow example contains some sample data:\n\n- A fasta file, located at `/data/fasta.fa` inside the Docker image.\n- A Blast database, located at `/blast-db/pdb/tiny` inside the Docker image.\n\n\nIn order to run the pipeline with the same sample data as Nextflow example, you have to run:\n\n```bash\ndocker run -v /tmp:/result sing-group/compi-blast-example -o -- --chunkSize 2\n```\n\nA `results.txt` file will be created inside `/tmp` (see `-v /tmp:/result`).\n\n## Running the pipeline with custom data\n\nYou can specify the `query` and `database` parameters of the pipeline. You will have to mount your data directory when running the Docker image. For example, `my-data-dir` could be a directory in your host machine containing both the fasta files and the BLAST database.\n\n- `my-data-dir`\n    - `myfasta.fa`\n    - `/blast-db/mydatabase`\n\nNext, you have to mount the data directory inside the Docker image when running it (see `-v my-data-dir:/data`) and pass the `query` and `database` parameters.\n\n```bash\ndocker run -v /tmp:/result -v my-data-dir:/data sing-group/compi-blast-example -o -- --chunkSize 2 --query /data/myfasta.fa --database /data/blast-db/mydatabase\n```\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsing-group%2Fcompi-blast-example","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsing-group%2Fcompi-blast-example","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsing-group%2Fcompi-blast-example/lists"}