Free public satellite can be used for educational purposes. The data and samples will be deleted periodically. Do not use private data. We are not responsible for data safety. Public satellite is limited by memory and cpu power.
To start using public satellite go to profiles settings.
How it works details can be found at https://scidap.com/tutorials/installation/howitworks.
In order to run the analysis scidap.com needs access to a private scidap-satellite installation. SciDAP provides a limited
and authorized access to the scidap-satellite installation. There are two types of scidap-satellite installation: per laboratory and corporate.
For corporate installation please contact us
All laboratory members can add the analysis and view the results. Do not invite strangers to the laboratory.
Latest installation manuals available at https://scidap.com/tutorials.
Datirium provides scidap-satellite bundle to simplify setup process. Otherwise
all the components must be installed and configured manually. scidap-satellite includes pre configured open-source software:
- CWL-Airflow - python3 pipeline manager
- aria2c - download manager
- MongoDB 4.2.x - NoSQL database
- BioWardrobe-NG - micro-service to proxy commands from scidap.com to CWL-Airflow
- pm2.io - process management https://github.com/Unitech/pm2
The analysis runs on your hardware (where scidap-satellite is installed - desktop/server/cluster or cloud).
Some of our pipelines require at least 24GB of memory. We recommend at least 32GB per processing unit.
scidap.com can start a pipeline from any place with the Internet. However, to access all the results a direct connection
to the satellite is required.
Limited information is transferred between a scidap-satellite installation and scidap.com:
- Sample's metadata
- Sample's CWL file (CWL files can be checked at https://github.com/datirium/workflows)
- Sample's status like running, failed, finished
- Sample's mapping statistics for basic analysis
OSX must be version 10.15 or newer: i.e. Catalina (10.15) or Big Sur (11.2.1). Mac hardware must be a 2013 or a newer model with at least 32GB of RAM. We recommend 2018 Mac mini with 6-core i7 CPU and 32GB or 64GB memory.
Download and install Docker and scidap-satellite (current version)
Change the default preferences for Docker (docs)
- CPUs number - 2 or more
- Memory - 24GB or more (leave about 6GB to OSX)
Once the software is installed and launched you can go back to scidap.com satellite settings add available genomes and start the analysis.
Follow instructions for each required package:
- Docker
- CWL-Airflow - python3 pipeline manager
- aria2c - download manager
- MongoDB 4.2.x - NoSQL database
- BioWardrobe-NG - micro-service to proxy commands from scidap.com to CWL-Airflow
- pm2.io - process management https://github.com/Unitech/pm2
Please contact us for installation instructions