{"id":19749526,"url":"https://github.com/mskcc/roslin-variant","last_synced_at":"2025-07-19T19:35:17.475Z","repository":{"id":49530370,"uuid":"84960936","full_name":"mskcc/roslin-variant","owner":"mskcc","description":"Roslin is a reproducible and reusable workflow for Cancer Genomic Sequencing Analysis","archived":false,"fork":false,"pushed_at":"2021-06-15T21:49:48.000Z","size":831610,"stargazers_count":15,"open_issues_count":11,"forks_count":7,"subscribers_count":31,"default_branch":"2.6.x","last_synced_at":"2023-10-20T21:55:37.062Z","etag":null,"topics":["pipeline","prism"],"latest_commit_sha":null,"homepage":"","language":"Python","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/mskcc.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}},"created_at":"2017-03-14T14:49:44.000Z","updated_at":"2021-06-15T21:48:23.000Z","dependencies_parsed_at":"2022-09-21T07:54:29.694Z","dependency_job_id":null,"html_url":"https://github.com/mskcc/roslin-variant","commit_stats":null,"previous_names":[],"tags_count":24,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Froslin-variant","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Froslin-variant/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Froslin-variant/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Froslin-variant/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mskcc","download_url":"https://codeload.github.com/mskcc/roslin-variant/tar.gz/refs/heads/2.6.x","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224204890,"owners_count":17273209,"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":["pipeline","prism"],"created_at":"2024-11-12T02:27:05.580Z","updated_at":"2024-11-12T02:27:06.278Z","avatar_url":"https://github.com/mskcc.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Roslin-variant\n\nRoslin-variant is a reproducible and reusable workflow for Cancer Genomic Sequencing Analysis\n\n## Prerequisites\n\nTo build, deploy, and use Roslin, you will need:\n\n- [Python 3](https://packages.ubuntu.com/bionic/python3)\n- [Python3-dev](https://packages.ubuntu.com/bionic/python3-dev)\n- [Singularity 3.3.0+](https://sylabs.io/guides/3.0/user-guide/installation.html#distribution-packages-of-singularity)\n- [MongoDB 3.0.15+](https://docs.openstack.org/project-install-guide/meter/newton/database/environment-nosql-database-rdo.html) (optional)\n\nMost testing of Roslin has been done with the specific versions above on hosts running CentOS 7.6. If you run into problems, search through [the issues](../../issues) for related solutions. If you cannot solve the problem without our help, then please create a [new issue](../../issues/new) with detailed information on how to reproduce your problem.\n\n## Installation\n\nClone the repo, switch to the current branch, init and update submodules:\n```\ngit clone --branch 2.6.x --recurse-submodules https://github.com/mskcc/roslin-variant.git\n```\n\nEnter the repo and edit the configuration files as appropriate for your host/environment. At minimum, enter your MongoDB admin user/password in `core/config.core.yaml`:\n```\ncd roslin-variant\nvi core/config.core.yaml\nvi config.variant.yaml\n```\n\nUsers of the Juno cluster at MSKCC, can simply copy [sample-juno-config.yaml](sample-juno-config.yaml) instead:\n```\ncp sample-juno-config.yaml config.variant.yaml\n```\n\n1. Add the root with the path where you want to install the pipeline\n2. Modify `TOIL_LSF_ARGS` within both root and test env's as appropriate\n\nYou can use `TOIL_LSF_ARGS` to run all your jobs under a SLA or increase walltime. For example:\n```\nTOIL_LSF_ARGS: '-sla jvSC -W 168:00'\n```\n\nHere is a table containing the description of important keys in `core/config.core.yaml`:\n\n| Key       | Description       |\n| :------------- |:-------------|\n| root      | The path to install roslin core, or an existing installation of roslin core |\n| mongo      | All the information needed to connect to the mongo database |\n\nHere is a table containing the description of important keys in `config.variant.yaml`:\n\n| Key       | Description       |\n| :------------- |:-------------|\n| root      | The path to install roslin pipeline |\n| binding.extra      | All the paths in the host system that needs to be mounted |\n| env      | Envirornment variables to set before running the pipeline |\n| dependencies.singularity      | Location of singularity binary files |\n| build.installCore     | Option to either install core or use an existing installation |\n| test.tempDir     | Path to test tempdir |\n| test.runArgs     | Path to test run arguments |\n\nHere is how to use the `source` key under `dependencies` in `config.variant.yaml`:\n\n| Type       | Example       | Description |  Dependency Supported |\n| :------------- |:-------------| :-------------| :-------------|\n| path      | path:/usr/local/bin/singularity | Path to binary or source files | singularity, cmo, toil\n| module      | module:singularity | Module name with the version key representing the module version | singularity\n| github      | github:https://github.com/dataBiosphere/toil | Github repo with the version key representing the branch/tag | toil, cmo\n\nFor installation, simply run this script. Make sure it has internet access:\n```\n./build-pipeline.sh\n```\n\nAfter installation is completed you should see a message like this:\n```\n ______     ______     ______     __         __     __   __\n/\\  == \\   /\\  __ \\   /\\  ___\\   /\\ \\       /\\ \\   /\\ \"-.\\ \\\n\\ \\  __\u003c   \\ \\ \\/\\ \\  \\ \\___  \\  \\ \\ \\____  \\ \\ \\  \\ \\ \\-.  \\\n \\ \\_\\ \\_\\  \\ \\_____\\  \\/\\_____\\  \\ \\_____\\  \\ \\_\\  \\ \\_\\\\\"\\_\\\n  \\/_/ /_/   \\/_____/   \\/_____/   \\/_____/   \\/_/   \\/_/ \\/_/\n ______   __     ______   ______     __         __     __   __     ______\n/\\  == \\ /\\ \\   /\\  == \\ /\\  ___\\   /\\ \\       /\\ \\   /\\ \"-.\\ \\   /\\  ___\\\n\\ \\  _-/ \\ \\ \\  \\ \\  _-/ \\ \\  __\\   \\ \\ \\____  \\ \\ \\  \\ \\ \\-.  \\  \\ \\  __\\\n \\ \\_\\    \\ \\_\\  \\ \\_\\    \\ \\_____\\  \\ \\_____\\  \\ \\_\\  \\ \\_\\\\\"\\_\\  \\ \\_____\\\n  \\/_/     \\/_/   \\/_/     \\/_____/   \\/_____/   \\/_/   \\/_/ \\/_/   \\/_____/\n\nRoslin Pipeline\n\nYour workspace: /home/vagrant/roslin-pipelines/variant/2.6.0/workspace/vagrant-3.10\n\nAdd the following line to your .profile or .bashrc if not already added:\n\nsource /home/vagrant/roslin-core/2.1.2/config/settings.sh\n```\n\nThis message has two important pieces of information:\n1. The location of your workspace in the pipeline\n2. The settings.sh file that sets your env to operate the pipeline\n\nMake sure to source the `settings.sh` in your `~/.bashrc` or some other appropriate startup dotfile.\n\n## Test an example\n\nSource the `settings.sh`, enter a folder with sample data, and run the bash wrapper around `roslin_request_to_yaml.py` and `roslin_submit.py`:\n```\nsource [your settings.sh file path]\ncd [your workspace path]/examples/SampleWorkflow\n./run-example.sh\n```\n\n## Add a user\n\nIf another user wants to run your deployment of Roslin, they can setup their own workspace by running:\n```\nsource [your settings.sh file path]\nroslin_workspace_init.py --name [your pipeline name] --version [your pipeline version]\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Froslin-variant","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmskcc%2Froslin-variant","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Froslin-variant/lists"}