{"id":23535180,"url":"https://github.com/warelab/sciapps","last_synced_at":"2025-07-03T17:32:46.701Z","repository":{"id":71605855,"uuid":"42608784","full_name":"warelab/sciapps","owner":"warelab","description":"SciApps: a cloud-based platform for reproducible bioinformatics workflows","archived":false,"fork":false,"pushed_at":"2020-10-06T14:28:12.000Z","size":9669,"stargazers_count":2,"open_issues_count":4,"forks_count":1,"subscribers_count":16,"default_branch":"master","last_synced_at":"2025-05-14T20:44:15.109Z","etag":null,"topics":["agave","cyverse","workflow"],"latest_commit_sha":null,"homepage":"https://www.sciapps.org","language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/warelab.png","metadata":{"files":{"readme":"README.md","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,"zenodo":null}},"created_at":"2015-09-16T19:30:43.000Z","updated_at":"2020-10-06T14:28:16.000Z","dependencies_parsed_at":"2023-03-11T10:51:07.983Z","dependency_job_id":null,"html_url":"https://github.com/warelab/sciapps","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/warelab/sciapps","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/warelab%2Fsciapps","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/warelab%2Fsciapps/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/warelab%2Fsciapps/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/warelab%2Fsciapps/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/warelab","download_url":"https://codeload.github.com/warelab/sciapps/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/warelab%2Fsciapps/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263369632,"owners_count":23456334,"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":["agave","cyverse","workflow"],"created_at":"2024-12-26T01:15:23.858Z","updated_at":"2025-07-03T17:32:46.687Z","avatar_url":"https://github.com/warelab.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# SciApps: a cloud-based platform for reproducible bioinformatics workflows\n## Introduction\nSciApps is a bioinformatics workflow package developed to leverage local clusters or TACC/XSEDE resources for computing and CyVerse Data Store for storage. SciApps is built on top of the Agave API that can also virtualize commercial resources, e.g., Amazon EC2/S3 for computing and storage. Both GUI and RESTful API are available for interactive or batch processing of NGS data.\n\n## Installation of SciApps\n    git clone https://github.com/warelab/sciapps.git\n    cd sciapps/agavedancer\n    sudo npm install -g grunt-cli\n    npm install\n    grunt package\n    sudo /usr/sbin/apachectl graceful  \n\n## Providing CyVerse credentials\nUpdate defaultUser to \"XXX\" in agavedancer/environments/production.yml (or development.yml), and create the following file.\n\n    cd sciapps/agavedancer\n    touch .agave\n      .agave content:\n          {\"username\":\"XXX\",\"password\":\"YYY\"}\n\n## Setting up iRODS (for accessing CyVerse Data Store)\n    wget ftp://ftp.renci.org/pub/irods/releases/4.1.10/centos7/irods-icommands-4.1.10-centos7-x86_64.rpm\n    sudo yum install fuse fuse-libs\n    sudo rpm -i irods-icommands-4.1.10-centos7-x86_64.rpm \n    cd /usr/share/httpd\n    sudo touch irodsEnv\n    sudo chmod 664 irodsEnv\n    sudo chown apache:apache irodsEnv\n      irodsEnv content:\n        {\n          \"irods_host\": \"data.iplantcollaborative.org\",\n          \"irods_user_name\": \"XXX\",\n          \"irods_port\": 1247,\n          \"irods_zone_name\": \"iplant\",\n          \"irods_authentication_file\": \"/usr/share/httpd/irodsA\"\n        }\n    sudo touch irodsA\n    sudo chmod 664 irodsA\n    sudo chown apache:apache irodsA\n    sudo -u apache /bin/bash\n    export IRODS_ENVIRONMENT_FILE=/usr/share/httpd/irodsEnv\n    iinit\n\n## Integrating new Apps/Tools\nFollow this instruction for developing new Agave apps. And put the app json file in the following assets folder (e.g., Bismark-0.14.4.json).\n\n    cd agavedancer/public/assets\n    touch agaveAppsList.json\n    agaveAppsList.json content\n       {\n          \"tags\": [\"Methylation\"],\n          \"id\": \"Bismark-0.14.4\",\n          \"label\": \"Bismark\",\n          \"name\": \"Bismark\",\n          \"version\": \"0.14.4\"\n       },\n       {\n         ...\n       }\n\n## Configuring web server\nSciApps.org can be configured with an Apache server using the following demo configuration file. The sciapps.conf file should be placed under /etc/httpd/conf.d/ (Centos 7) or /usr/local/apache2/conf/ (Centos 6). Note that SSL certificate is needed to be able to authenticate to the cloud systems.\n\n    \u003cVirtualHost 143.48.220.100:443\u003e\n        SSLEngine on\n        SSLCertificateFile /etc/letsencrypt/live/www.sciapps.org/fullchain.pem\n        SSLCertificateKeyFile /etc/letsencrypt/live/www.sciapps.org/privkey.pem\n        SSLCertificateChainFile /etc/letsencrypt/live/www.sciapps.org/chain.pem\n        ServerName       www.sciapps.org\n        ServerAlias      sciapps.org\n        DocumentRoot     /home/YOURUSERNAME/sciapps/agavedancer/public\n        RewriteEngine on\n        RewriteRule ^/app_id/(.*)      https://www.sciapps.org/?app_id=$1 [L]\n        RewriteRule ^/page/(.*)     https://www.sciapps.org/?page_id=$1 [L]\n        RewriteRule ^/data/(.*)     https://www.sciapps.org/?page_id=dataWorkflows\u0026data_item=$1 [L]\n\n        SetEnv DANCER_ENVIRONMENT \"production\"\n        \u003cDirectory \"/home/YOURUSERNAME/sciapps/agavedancer/public\"\u003e\n            AllowOverride none\n            Require all granted\n            DirectoryIndex index.html index.php\n        \u003c/Directory\u003e\n        \u003cLocation /\u003e\n            SetHandler perl-script\n            PerlResponseHandler Plack::Handler::Apache2\n            PerlSetVar psgi_app /home/YOURUSERNAME/sciapps/agavedancer/bin/app.pl\n        \u003c/Location\u003e\n    \u003c/VirtualHost\u003e\n\n## Citation\nWang, L., Lu, Z., Van Buren, P., \u0026 Ware, D. (2018). SciApps: a cloud-based platform for reproducible bioinformatics workflows. Bioinformatics, 34(22), 3917-3920. [Link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6223375/)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwarelab%2Fsciapps","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fwarelab%2Fsciapps","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwarelab%2Fsciapps/lists"}