{"id":16314359,"url":"https://github.com/stolarczyk/saarpipeline","last_synced_at":"2026-05-18T15:31:24.417Z","repository":{"id":126809377,"uuid":"121327431","full_name":"stolarczyk/SAARpipeline","owner":"stolarczyk","description":"Origin mechanisms of SAARs – use case of L-SAARs in signal peptides among higher Eukaryotes","archived":false,"fork":false,"pushed_at":"2018-11-10T18:21:53.000Z","size":148237,"stargazers_count":0,"open_issues_count":4,"forks_count":0,"subscribers_count":0,"default_branch":"master","last_synced_at":"2025-08-01T05:19:44.256Z","etag":null,"topics":["evolution","l-saars","low-complexity-regions","perl","signal-peptides","snakemake-workflows"],"latest_commit_sha":null,"homepage":"","language":"R","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/stolarczyk.png","metadata":{"files":{"readme":"README.md","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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-02-13T02:06:45.000Z","updated_at":"2018-11-10T18:21:56.000Z","dependencies_parsed_at":"2023-06-18T04:02:28.993Z","dependency_job_id":null,"html_url":"https://github.com/stolarczyk/SAARpipeline","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/stolarczyk/SAARpipeline","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stolarczyk%2FSAARpipeline","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stolarczyk%2FSAARpipeline/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stolarczyk%2FSAARpipeline/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stolarczyk%2FSAARpipeline/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/stolarczyk","download_url":"https://codeload.github.com/stolarczyk/SAARpipeline/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stolarczyk%2FSAARpipeline/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33182701,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-18T09:27:30.708Z","status":"ssl_error","status_checked_at":"2026-05-18T09:27:28.300Z","response_time":71,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 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":["evolution","l-saars","low-complexity-regions","perl","signal-peptides","snakemake-workflows"],"created_at":"2024-10-10T21:53:48.377Z","updated_at":"2026-05-18T15:31:24.395Z","avatar_url":"https://github.com/stolarczyk.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Single amino acid repeats (SAAR) evolutionary analysis pipeline\r\n\r\nThis repository consists of a suite of R and Perl scripts performing the evolutionary SAAR analysis. The workflow is automatized and maintained by [Snakemake](https://snakemake.readthedocs.io/en/stable/) software.\r\n\r\nFor the convenience of the portability and ease of use it is also distributed as a [Docker](https://www.docker.com/) container, which can be accessed at [DockerHub repository](https://hub.docker.com/r/mstolarczyk/saarpipeline/).\r\n\r\n## Usage\r\n**1. Install the Docker software**\r\n  \r\n  The Docker installation guide can be found [here](https://docs.docker.com/install/)\r\n\r\n**2. Downolad the container with the pipeline setup and all dependencies installed**\r\n\r\n`(sudo) docker pull mstolarczyk/saarpipeline`\r\n\r\n**3. Make sure the image is available**\r\n\r\n`(sudo) docker images`\r\n\r\nThe line above should output similar to the one presented below\r\n\r\n```\r\nREPOSITORY                         TAG                 IMAGE ID            CREATED             SIZE\r\nmstolarczyk/saarpipeline           latest              1142d796e7ad        3 minutes ago       6.27GB\r\n```\r\n\r\n**4. Run the image**\r\n\r\n`(sudo) docker run -it mstolarczyk/saarpipeline `\r\n\r\n**5. Perform the analysis**\r\n\r\nThe commands that will run the analysis are `Snakemake` commands:\r\n\r\n`snakemake \u003ctarget file\u003e`\r\n\r\nTo test the part of workflow to be executed run\r\n\r\n`snakemake -np \u003ctarget file\u003e`\r\n\r\nThe line above will show the execution plan instead of actually perform the steps. The `-p` flag instructs Snakemake to also print the resulting shell command for illustration\r\n\r\n_More details regarding the usage will be provided soon_\r\n\r\nAfter completion of the analysis exit the container\r\n\r\n`exit`\r\n\r\n**6. Save the docker container state and copy the results**\r\n\r\nIn order to pick up when you have left save the state of the container\r\n\r\n`(sudo) docker commit \u003ccontainer ID\u003e \u003ctag\u003e`\r\n\r\ne.g. `sudo docker commit 1bf3b5f36b94 mstolarczyk/saarpipeline_changed`\r\n`(sudo)`\r\n\r\nTo copy the results of the analysis use the Docker `docker cp` command, for more details see the [website](https://docs.docker.com/engine/reference/commandline/cp/#description)\r\n\r\n```\r\ndocker cp [OPTIONS] CONTAINER:SRC_PATH DEST_PATH|-\r\ndocker cp [OPTIONS] SRC_PATH|- CONTAINER:DEST_PATH\r\n```\r\n\r\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstolarczyk%2Fsaarpipeline","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fstolarczyk%2Fsaarpipeline","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstolarczyk%2Fsaarpipeline/lists"}