{"id":24360496,"url":"https://github.com/simonsfoundation/jp_gene_viz","last_synced_at":"2025-04-10T08:54:33.101Z","repository":{"id":87271815,"uuid":"42265874","full_name":"simonsfoundation/jp_gene_viz","owner":"simonsfoundation","description":"A collection of visualizations for genomics related information for use with Jupyter notebooks.","archived":false,"fork":false,"pushed_at":"2022-02-28T18:03:09.000Z","size":37877,"stargazers_count":10,"open_issues_count":6,"forks_count":9,"subscribers_count":13,"default_branch":"master","last_synced_at":"2025-03-24T08:11:13.658Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/simonsfoundation.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":"2015-09-10T19:26:17.000Z","updated_at":"2022-02-28T18:03:13.000Z","dependencies_parsed_at":"2023-05-18T21:15:29.749Z","dependency_job_id":null,"html_url":"https://github.com/simonsfoundation/jp_gene_viz","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simonsfoundation%2Fjp_gene_viz","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simonsfoundation%2Fjp_gene_viz/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simonsfoundation%2Fjp_gene_viz/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/simonsfoundation%2Fjp_gene_viz/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/simonsfoundation","download_url":"https://codeload.github.com/simonsfoundation/jp_gene_viz/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248190407,"owners_count":21062277,"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":[],"created_at":"2025-01-18T21:30:17.934Z","updated_at":"2025-04-10T08:54:33.090Z","avatar_url":"https://github.com/simonsfoundation.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# jp_gene_viz\n\nA collection of visualizations for genomics related information for use with Jupyter notebooks.\n\n# NOTE: THIS REPOSITORY IS DEPRECATED\n\nThis repository is deprecated because the Jupyter project no longer supports Python 2.\nComponents of the repository use libraries which only work correctly in Python 2.\n\nAs far as I know at this writing you can still install these components into a legacy Python 2 kernel\nand everything will still work in classic Jupyter notebooks, but it may stop working at some future Jupyter release.\n\nSome useful functionality from this repository has been ported to run in Python 3 with Jupyter using the\n\u003ca href=\"https://github.com/AaronWatters/jp_doodle\"\u003ejp_doodle Jupyter widget infrastructure\u003c/a\u003e.\nPlease post an issue if you would like to see other features ported.\n\n# The package\n\nPlease see the [index.ipynb](index.ipynb) IPython notebook for\na guide to the package content.\n\nTo launch a container to run the package in the Binder service, please\nclick the image link below:\n\n[![Binder](http://mybinder.org/badge.svg)](http://mybinder.org/repo/simonsfoundation/jp_gene_viz)\n\n# Installation\n\nThe installation requires the Python module `jp_gene_viz` to be installed with its\ndependencies and for the wigdets extension to be enabled in Jupyter/IPython.\n\nFor example the following sequence completes a first time complete installation\n\n### install prerequisites\n\nYou will need Python 2.7 and some other libraries for the installation\nto succeed.  I recommend installing \n[Anaconda for python 2.7](https://www.continuum.io/downloads) to get all\nneeded prerequisite dependencies.\n\n### Linux only:\n\nOn Debian Linux without using Anaconda I needed to add the following system\nlibraries\n\n```\nsudo apt-get install python-pip\nsudo apt-get install python-dev\nsudo apt-get install -y libigraph0-dev \nsudo apt-get install libxml2-dev\nsudo apt-get install zlib1g-dev\nsudo apt-get install libblas-dev liblapack-dev libatlas-base-dev gfortran\n```\n\n### clone the repository and change directory into the repository folder\n\n```\ngit clone https://github.com/simonsfoundation/jp_gene_viz.git\ncd jp_gene_viz\n```\n\n### Linux and Mac: install the requirements and the module\n```\npip install -r requirements.txt\npython setup.py install\n```\n\n### Mac notes\n\nFor some Macs the `pip` install of requirements fails to install `python-igraph`.\nIf this happens use [homebrew](https://brew.sh/) to install the `igraph` library\n```\nbrew install igraph\n```\nand then run the `pip` install again.\n\n### Windows install\n\nTo install for windows the `python-igraph` package must be installed in a separate step.\nto to [http://www.lfd.uci.edu/~gohlke/pythonlibs/#python-igraph](http://www.lfd.uci.edu/~gohlke/pythonlibs/#python-igraph) to get\n`python_igraph‑0.7.1.post6‑cp27‑cp27m‑win_amd64.whl` and then install using a command\nsimilar to\n\n```\npython -m pip install Downloads\\python_igraph-0.7.1.post6-cp27-cp27m-win_amd64.whl\n```\n\nThen install the remaining components\n\n```\npip install -r windows_requirements.txt \npython setup.py install\n```\n\n### enable the widgets extension (just in case it isn't already enabled)\n```\njupyter nbextension enable --py --sys-prefix widgetsnbextension\n```\n\nNote: We are upgrading the repository to work with the latest ipywidgets and iPython\nreleases.  If you have problems installing the package please post an issue at\n[https://github.com/simonsfoundation/jp_gene_viz](https://github.com/simonsfoundation/jp_gene_viz).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsimonsfoundation%2Fjp_gene_viz","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsimonsfoundation%2Fjp_gene_viz","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsimonsfoundation%2Fjp_gene_viz/lists"}