https://github.com/warelab/sciapps

SciApps: a cloud-based platform for reproducible bioinformatics workflows
https://github.com/warelab/sciapps

agave cyverse workflow

Last synced: 12 months ago
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SciApps: a cloud-based platform for reproducible bioinformatics workflows

• Host: GitHub
• URL: https://github.com/warelab/sciapps
• Owner: warelab
• License: apache-2.0
• Created: 2015-09-16T19:30:43.000Z (almost 11 years ago)
• Default Branch: master
• Last Pushed: 2020-10-06T14:28:12.000Z (over 5 years ago)
• Last Synced: 2025-05-14T20:44:15.109Z (about 1 year ago)
• Topics: agave, cyverse, workflow
• Language: JavaScript
• Homepage: https://www.sciapps.org
• Size: 9.22 MB
• Stars: 2
• Watchers: 16
• Forks: 1
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# SciApps: a cloud-based platform for reproducible bioinformatics workflows

## Introduction

SciApps 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.

## Installation of SciApps

    git clone https://github.com/warelab/sciapps.git

    cd sciapps/agavedancer

    sudo npm install -g grunt-cli

    npm install

    grunt package

    sudo /usr/sbin/apachectl graceful  

## Providing CyVerse credentials

Update defaultUser to "XXX" in agavedancer/environments/production.yml (or development.yml), and create the following file.

    cd sciapps/agavedancer

    touch .agave

      .agave content:

          {"username":"XXX","password":"YYY"}

## Setting up iRODS (for accessing CyVerse Data Store)

    wget ftp://ftp.renci.org/pub/irods/releases/4.1.10/centos7/irods-icommands-4.1.10-centos7-x86_64.rpm

    sudo yum install fuse fuse-libs

    sudo rpm -i irods-icommands-4.1.10-centos7-x86_64.rpm 

    cd /usr/share/httpd

    sudo touch irodsEnv

    sudo chmod 664 irodsEnv

    sudo chown apache:apache irodsEnv

      irodsEnv content:

        {

          "irods_host": "data.iplantcollaborative.org",

          "irods_user_name": "XXX",

          "irods_port": 1247,

          "irods_zone_name": "iplant",

          "irods_authentication_file": "/usr/share/httpd/irodsA"

        }

    sudo touch irodsA

    sudo chmod 664 irodsA

    sudo chown apache:apache irodsA

    sudo -u apache /bin/bash

    export IRODS_ENVIRONMENT_FILE=/usr/share/httpd/irodsEnv

    iinit

## Integrating new Apps/Tools

Follow 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).

    cd agavedancer/public/assets

    touch agaveAppsList.json

    agaveAppsList.json content

       {

          "tags": ["Methylation"],

          "id": "Bismark-0.14.4",

          "label": "Bismark",

          "name": "Bismark",

          "version": "0.14.4"

       },

       {

         ...

       }

## Configuring web server

SciApps.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.

    

        SSLEngine on

        SSLCertificateFile /etc/letsencrypt/live/www.sciapps.org/fullchain.pem

        SSLCertificateKeyFile /etc/letsencrypt/live/www.sciapps.org/privkey.pem

        SSLCertificateChainFile /etc/letsencrypt/live/www.sciapps.org/chain.pem

        ServerName       www.sciapps.org

        ServerAlias      sciapps.org

        DocumentRoot     /home/YOURUSERNAME/sciapps/agavedancer/public

        RewriteEngine on

        RewriteRule ^/app_id/(.*)      https://www.sciapps.org/?app_id=$1 [L]

        RewriteRule ^/page/(.*)     https://www.sciapps.org/?page_id=$1 [L]

        RewriteRule ^/data/(.*)     https://www.sciapps.org/?page_id=dataWorkflows&data_item=$1 [L]

        SetEnv DANCER_ENVIRONMENT "production"

        

            AllowOverride none

            Require all granted

            DirectoryIndex index.html index.php

        

        

            SetHandler perl-script

            PerlResponseHandler Plack::Handler::Apache2

            PerlSetVar psgi_app /home/YOURUSERNAME/sciapps/agavedancer/bin/app.pl

        

    

## Citation

Wang, L., Lu, Z., Van Buren, P., & 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/)