{"id":37671357,"url":"https://github.com/dicaso/genairics","last_synced_at":"2026-01-16T12:04:44.155Z","repository":{"id":57433467,"uuid":"113557252","full_name":"dicaso/genairics","owner":"dicaso","description":"GENeric AIRtight omICS pipelines","archived":false,"fork":false,"pushed_at":"2020-12-16T13:04:11.000Z","size":1266,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-09-13T05:34:01.292Z","etag":null,"topics":["bioinformatics","omics","pipelines"],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dicaso.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2017-12-08T09:32:01.000Z","updated_at":"2020-12-16T13:04:13.000Z","dependencies_parsed_at":"2022-08-28T04:40:51.938Z","dependency_job_id":null,"html_url":"https://github.com/dicaso/genairics","commit_stats":null,"previous_names":["beukueb/genairics"],"tags_count":11,"template":false,"template_full_name":null,"purl":"pkg:github/dicaso/genairics","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dicaso%2Fgenairics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dicaso%2Fgenairics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dicaso%2Fgenairics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dicaso%2Fgenairics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dicaso","download_url":"https://codeload.github.com/dicaso/genairics/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dicaso%2Fgenairics/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28478429,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T11:59:17.896Z","status":"ssl_error","status_checked_at":"2026-01-16T11:55:55.838Z","response_time":107,"last_error":"SSL_read: 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","omics","pipelines"],"created_at":"2026-01-16T12:04:43.553Z","updated_at":"2026-01-16T12:04:44.142Z","avatar_url":"https://github.com/dicaso.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Latest Version](https://img.shields.io/pypi/v/genairics.svg)](https://pypi.python.org/pypi/genairics/)\n[![Docker](https://img.shields.io/docker/automated/beukueb/genairics.svg)](https://hub.docker.com/r/beukueb/genairics/)\n[![License](https://img.shields.io/pypi/l/genairics.svg)](https://pypi.python.org/pypi/genairics/)\n\n# GENeric AIRtight omICS pipelines\n\u003cimg title=\"genairics logo\" src=\"gax_logo.svg\" width=\"500\"\u003e\n\n## Design goals\n\n### generic pipelines\n\nThe pipelines here available are mainly developed for my specific\nbioinformatics needs and that of my collaborators. They are build up\nin a generic way, and some of the functionality in the main genairics\npackage file might help or inspire you to build your own\npipelines. The core of the pipelines is build with\n[luigi](https://luigi.readthedocs.io) and extensions are provided in\nthis package's initialization file.\n\n### airtight pipelines\n\nThe pipelines are build so they can be started with a single,\nfool-proof command.  This should allow collaborators, or scientists\nwanting to replicate my results, to easily do so. A docker container\nis provided with the package so the processing can be started up on\nany platform.\n\n### omics pipelines\n\nThe pipelines grow organically, as my research needs expand. I aim to\nprocess any kind of data. If you want to use my set of pipelines, but\ndesire an expansion to make it more omics-like, contact me and we can\nsee if there are opportunities to collaborate. More generally,\neveryone is welcome to leave suggestions in the [issues\nsection](https://github.com/beukueb/genairics/issues) of the\nrepository.\n\n## Installation\n\n### genairics package\n\n#### Dependencies\n\nPython 3 has to be installed: see https://www.python.org/downloads/ for instructions.\n\n#### Prepare virtualenvwrapper [optional]\n\n     sudo pip3 install virtualenvwrapper\n     echo \"export WORKON_HOME=~/Envs\" \u003e\u003e ~/.bashrc\n     echo \"export VIRTUALENVWRAPPER_PYTHON=$(which python3)\" \u003e\u003e ~/.bashrc\n     . ~/.bashrc\n     mkdir -p $WORKON_HOME\n     . /usr/local/bin/virtualenvwrapper.sh\n     mkvirtualenv -a ~/genairics -i ipython\n\n#### Install\n\n     workon genairics #only when working in virtualenv\n     # For stable version:\n     pip3 install genairics\n     # For latest development version:\n     # pip3 install git+https://github.com/dicaso/genairics.git\n\nStart up console with `genairics console` and execute the following line:\n\n    InstallDependencies()\n\n### Get your BASESPACE_API_TOKEN accessToken\n\nFollow the steps 1-5 from this link:\nhttps://help.basespace.illumina.com/articles/tutorials/using-the-python-run-downloader/\n\n\temacs ~/.BASESPACE_API #Store your accessToke here, instead of emacs use any editor you like\n\tchmod 600 ~/.BASESPACE_API #For security, only rw access for your user\n\n### Prepare your HPC account [for UGent collaborators]\n\nGo to https://www.ugent.be/hpc/en/access/faq/access to apply for access to the HPC.\n\n#### add to your HPC ~/.bashrc =\u003e\n\n    export GAX_RESOURCES=$VSC_DATA_VO/resources\n    export GAX_DATADIR=$VSC_DATA_VO_USER/data\n    export GAX_RESULTSDIR=$VSC_DATA_VO_USER/results\n    export BASESPACE_API_TOKEN= #Set this to your basespace api token\n    export PATH=$VSC_DATA_VO/resources/bin:$PATH:~/.local/bin\n    if [[ -v SET_LUIGI_FRIENDLY ]]; then module load pandas; unset SET_LUIGI_FRIENDLY; fi\n    if [[ -v R_MODULE ]]; then module purge; module load R-bundle-Bioconductor; unset R_MODULE; fi\n\n#### Execute the following commands\n\n    module load pandas\n    pip3 install --user --upgrade genairics\n    mkdir $VSC_DATA_VO_USER/{data,results}\n\nRerun the first two of these lines whenever you need to upgrade your genairics version.\n\n## Example run\n\n### Docker\n\n    docker run -v ~/resources:/resources -v ~/data:/data -v ~/results:/results \\\n\t       --env-file ~/.BASESPACE_API beukueb/genairics RNAseq \\\n\t       NSQ_Run240 --genome saccharomyces_cerevisiae\n\n### qsub job\n\n    genairics --job-launcher qsub RNAseq NSQ_Run240\n\n## Epilogue\n\nThere comes a point in time when any human just has to develop their\nown, fully-fledged computational genomics platform. This is not that\ntime for me, but it is good to set it as an aim: aiming for the stars,\nlanding somewhere on the moon. Of course, with help I should be able\ncover more distance, so if you like this project and want to help out,\ncontact me.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdicaso%2Fgenairics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdicaso%2Fgenairics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdicaso%2Fgenairics/lists"}