{"id":19749527,"url":"https://github.com/mskcc/igo-qc","last_synced_at":"2026-01-27T08:03:34.049Z","repository":{"id":37896182,"uuid":"45417066","full_name":"mskcc/igo-qc","owner":"mskcc","description":null,"archived":false,"fork":false,"pushed_at":"2023-04-16T20:27:07.000Z","size":17511,"stargazers_count":3,"open_issues_count":16,"forks_count":0,"subscribers_count":32,"default_branch":"master","last_synced_at":"2025-07-08T21:48:43.360Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"HTML","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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2015-11-02T19:32:28.000Z","updated_at":"2023-04-20T13:38:13.000Z","dependencies_parsed_at":"2025-01-17T05:31:22.855Z","dependency_job_id":null,"html_url":"https://github.com/mskcc/igo-qc","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/mskcc/igo-qc","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Figo-qc","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Figo-qc/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Figo-qc/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Figo-qc/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mskcc","download_url":"https://codeload.github.com/mskcc/igo-qc/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Figo-qc/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28809337,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-27T07:41:26.337Z","status":"ssl_error","status_checked_at":"2026-01-27T07:41:08.776Z","response_time":168,"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":"2024-11-12T02:27:05.581Z","updated_at":"2026-01-27T08:03:34.034Z","avatar_url":"https://github.com/mskcc.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# igo-qc\n\n## Contents\n* [Description](#description)\n* [Development Steps](#development-notes)\n* [Deployment Steps](#deployment-steps)\n\n## Description\nSite displaying run statistics of sequencing projects (E.g. GATK Picard, Cell Ranger, etc.). \n\n### Features\n* Pulls data from LIMS and ngs-stats to visualize in grid and graphs\n* Allows users to reset qc-status of runs\n\n## Development Notes\nAfter setting up `Mongo`, `Backend`, \u0026 `Frontend` (in that order), the igo-qc app should be available at `localhost:3000`\n\n### Mongo\n```\nWRITE_DATA_HERE=...\nmongod --dbpath=${WRITE_DATA_HERE}\n```\n\n### Backend\n1. Update `lims_user_config_prod` with what is available on dev/prod. We need the values for `username`, `password`, \u0026 `secret_key`. Note - This is copied into `lims_user_config` on `make run-prod`. On the host, see `/srv/www/new-igo-qc/app/lims_user_config`. \n\n    ```\n    scp igo.mskcc.org:/srv/www/new-igo-qc/app/lims_user_config lims_user_config_prod\n    ```\n\n2. Install virtual environment\n\n    *Python 2*\n    ```\n    # pip install virtualenv\t# If not already installed\n    $ virtualenv venv\n    ```\n    *Python 3*\n    ```\n    # pip3 install virtualenv\t# If not already installed\n    python3 -m venv venv\n    ```\n\n3. Install Dependencies\n    ```\n    $ source venv/bin/activate\n    (venv) $ pip install -r requirements.txt\n    (venv) $ make run\n    ```\n\n    Note - `make run-prod` is a `Makefile` command. If there are issues w/ this step, please review the `run-prod` step of the [Makefile](https://github.com/mskcc/igo-qc/blob/master/Makefile) \n    \n### Frontend\n```\ncd static/seq-qc/\nnpm install \u0026\u0026 npm run start\n```\n\n### Troubleshooting\n#### Mongo\n* Is mongo running? i.e. The `mongo` command allows you to connect to your mongo instance. If mongo is running, you should see something like below -\n```\n$ ps -ef | grep mongo\n1774903000 39995 39879   0 12:40PM ttys001    0:00.75 /Users/streidd/data/mongodb-macos-x86_64-4.2.1/bin/mongod --dbpath=/Users/streidd/data/db\n```\n\n* Do you have write access to the directory specified in `--dbpath=`?\n```\n$ ls -ltr /Users/streidd/data | grep db\ndrwxr-xr-x     73 streidd  MSKCC\\Domain Users      2336 Oct 25 12:40 db\n```\n\n## Deployment Steps\n```\nHOST=igo.mskcc.org  # Production\n# HOST=dlviigoweb1  # Development\nmake HOST=${HOST} deploy\n```\n\nNotes:\n* This *DELETES* the existing application on the `HOST` specified. It then copies the packaged application created locally to the new location.\n* This creates and copies a `dist` directory to the `deployments` directory in your home on the `HOST` specified. Make sure your `~/deployments` exists on that `HOST`!\n* `make deploy` is a `Makefile` command. If there are issues w/ this step, please review the `deploy` step of the [Makefile](https://github.com/mskcc/igo-qc/blob/master/Makefile)\n* Expect to enter your password four times - once to `scp` the packaged application, once to remotely send the install command, and twice to run `dzdo` remotely (`dzdo` allows for root access on our VM's and is needed so you can re-deploy if another user was the last to deploy) \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Figo-qc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmskcc%2Figo-qc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Figo-qc/lists"}