{"id":16948790,"url":"https://github.com/tiagoantao/congen-docker","last_synced_at":"2026-05-16T13:36:32.517Z","repository":{"id":147146280,"uuid":"66028851","full_name":"tiagoantao/congen-docker","owner":"tiagoantao","description":"A Docker repository for a course on analysis of genomic data","archived":false,"fork":false,"pushed_at":"2017-09-25T21:07:17.000Z","size":387,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-03-21T09:48:11.848Z","etag":null,"topics":["bioinformatics","conservation-genetics","data-science","docker","population-genetics"],"latest_commit_sha":null,"homepage":null,"language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"agpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/tiagoantao.png","metadata":{"files":{"readme":"README.rst","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":"2016-08-18T20:34:46.000Z","updated_at":"2017-09-24T15:03:12.000Z","dependencies_parsed_at":"2023-04-18T05:33:08.403Z","dependency_job_id":null,"html_url":"https://github.com/tiagoantao/congen-docker","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/tiagoantao/congen-docker","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tiagoantao%2Fcongen-docker","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tiagoantao%2Fcongen-docker/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tiagoantao%2Fcongen-docker/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tiagoantao%2Fcongen-docker/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tiagoantao","download_url":"https://codeload.github.com/tiagoantao/congen-docker/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tiagoantao%2Fcongen-docker/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33104708,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-16T04:41:52.686Z","status":"ssl_error","status_checked_at":"2026-05-16T04:41:52.009Z","response_time":115,"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":["bioinformatics","conservation-genetics","data-science","docker","population-genetics"],"created_at":"2024-10-13T21:52:24.320Z","updated_at":"2026-05-16T13:36:32.502Z","avatar_url":"https://github.com/tiagoantao.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"A docker machine for data analysis of genomics data\n===================================================\n\n\nThis machine is used for a course in conservation genetics at the\nUniversity of Montana\n\nHow to run it\n-------------\n\n**Requirements**\n\nYou should have a zip file with data (provided by the course).\n\n**Initial note (for more advanced users)**\n\nThe docker container runs a VNC and SSH server. If you have a VNC client\ninstalled you do not need to use the browser interface as it is slower.\nJust point your VNC server to port 5901.\n\nYou can also connect directly via ssh. User root, password congen17.\n\nYou will have root access and that is fine. There will be no special user.\n\n\n**If you are on Windows or Mac (see below for Linux)**\n\n- Install Kitematic_ (Docker Toolbox).\n\n- Start it\n\n- Pull tiagoantao/congen-docker (using the search box)\n\n- Make the congen container is running (UI - see below)\n\n- Map your data volume (see below, the purple arrow)\n\n.. image:: Docker_screenshot_volumes.png\n\n- Restart the machine (look for the button on top)\n\n- Go to settings (see image below)\n\n.. image:: Docker_screenshot.png\n\n- Click on the 6080 port (see below)\n\n.. image:: Docker_screenshot_portsetttings.png\n\n- This should start a browser\n\n- Password is `congen17`\n\n**If you get no connection to server on noVNC here is an alternative path**\n\n- Stop the container\n\n- On the Windows/Mac desktop click the \"Docker Quickstart terminal\"\n\n- On the terminal type ``docker run -p 5901:5901 -p 6080:6080 -v /path/to/data:/data tiagoantao/congen-docker``\n\n- If you get a error like ``port is already allocated`` make sure you stopped the container\n\n- Now, use the IP from the **screenshot** above with the port 6080, in this case:\n``http://192.168.99.100:6080/``\n\n- Password is ``congen17``\n\n\n\n\n**What to do if your base operating system is Linux**\n\n- Install docker\n\n- Make sure the docker server is running\n\n- Your user has to be on the docker group\n\n- ``docker pull tiagoantao/congen-docker``\n\n- ``docker run -p 5901:5901 -p 6080:6080 -v /path_to_your_data:/data -t tiagoantao/congen-docker``\n\n- Change `path_to_your_data` with the path to your data.\n\n- Start a browser pointing to the address ``http://127.0.0.1:6080``\n\n- Password is ``congen17``\n\n- If you try to restart the machine, make sure the previous one is killed:\n``docker ps; docker rm -f your_image``\n\n\n.. _Kitematic: https://kitematic.com/\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftiagoantao%2Fcongen-docker","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftiagoantao%2Fcongen-docker","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftiagoantao%2Fcongen-docker/lists"}