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README.md

myFAIR

Dependencies
Installation Instructions
Install myFAIR
Install SEEK
Galaxy
Run myFAIR with B2DROP
Create a new study
Create a new assay
Upload fies to SEEK
Run myFAIR with SEEK
See results
Store your history
Run the analysis again

For this testcase we are using variant selection by GEMINI analysis using genome in the bottle data. Specifically, we will be using Ashkenazim Father-Mother-Son trio data from the Personal Genome Project. You can download the down sampled version of the dataset created by the GEMINI team from a GIAB trio dataset. The vcf file can be found here and the ped file can be found here.

Dependencies

  • Python 3.6 or higher
  • Django 2.1.2 or higher
  • Bioblend 0.11.0 or higer
  • rdflib 4.2.2 or higher
  • lftp 4.8.1 or higher
  • python-magic 0.4.15 or higher
  • plotly 3.3.0 or higher
  • sparqlwrapper 1.8.2 or higher
  • EDAM browser
  • An account on a local or external Galaxy server with the following tools available:
    1. GEMINI (load, autosomal recessive/dominant, de novo, comp hets)
    2. Add Column, Strip Header and File Concatenate (all can be found under the name file_manipulation in the Galaxy tool shed)
    3. The Galaxy server should allow an FTP to send data files larger than 2GB.
  • An account to an external SEEK server or a local SEEK server.

Installation Instructions

Install myFAIR

To install myFAIR on your existing Virtual Machine follow these steps:

Install dependencies

sudo apt update
sudo apt upgrade
sudo apt install python3 python3-pip lftp
pip3 install django bioblend rdflib plotly python-magic sparqlwrapper

Get myFAIR

git clone https://github.com/ErasmusMC-Bioinformatics/myFAIR

Run the server

Run the following command to run the myFAIR server.

python3 myFAIR/manage.py runserver 0.0.0.0:8080

Set permissions

If manage.py does not have the right permissions run the following command:

chmod +x myFAIR/manage.py

Get and run EDAM browser

git clone https://github.com/IFB-ElixirFr/edam-browser
cd edam-browser
python start_edam_stand_alone_browser.py

Test the server

Go to 127.0.0.1:8080 (or other chosen port) and check if the myFAIR login page is visible.

Install SEEK

You can download the latest version of SEEK here. For more information on installing SEEK click here.

Follow these instructions to install the Virtuoso triple store and connect the triple store to your SEEK server.

Galaxy

Go to usegalaxy and create an account or log in with an existing account to see if it is still working.

Importing the GEMINI workflow

Import the GEMINI workflow using this url: https://usegalaxy.eu/u/rickjansen/w/geminivcfanalysis.

ISA structure

Create a new study

Follow these steps to create a new study on the SEEK server you entered when logging in.

  1. Logon to the myFAIR webpage with your Galaxy and SEEK credentials.
  2. Got to the Upload to SEEK page.
  3. Enter your full name (same as registered in SEEK)
  4. Select the project from the dropdown menu.
  5. Select the investigation from the dropdown menu.
  6. Select the create new study? option.
  7. Enter a name, title and description for the new study. Click Create new study

Create a new assay

Follow these steps to create a new assay on the SEEK server you entered when logging in. This option only works when you have the right permissions to the SEEK study.

  1. Logon to the myFAIR webpage with your Galaxy and SEEK credentials.
  2. Got to the Upload to SEEK page.
  3. Enter your full name (same as registered in SEEK)
  4. Select the project from the dropdown menu.
  5. Select the investigation from the dropdown menu.
  6. Select the study from the dropdown menu.
  7. Select the create new assay? option.
  8. Enter a name, title and description for the new assay.
  9. Select assay type from the dropdown menu.
  10. Select technology type from the dropdown menu.
  11. Click on the Create new assay button.

Upload files to SEEK

Follow these steps to upload a data file to an assay on the SEEK server. This option only works when you have the right permissions to the SEEK assay.

  1. Logon to the myFAIR webpage with your Galaxy and SEEK credentials.
  2. Got to the Upload to SEEK page.
  3. Enter your full name (same as registered in SEEK)
  4. Select the project from the dropdown menu.
  5. Select the investigation from the dropdown menu.
  6. Select the study from the dropdown menu.
  7. Select the assay from the dropdown menu.
  8. Enter a data file title and description.
  9. Select the file to upload.
  10. Tag the data file with a diseas by entering a disease in the DisGeNET textbox and click the Search button. Select the disease from the dropdown menu after the search is finished.
  11. tag the data file with an EDAM operation by selecting the type of operation from the EDAM browser. Click the Select this ontology button to add this ontology.

Run myFAIR with SEEK

To run myFAIR with SEEK data you need to follow the Upload files to SEEK steps first or make sure data is already uploaded using the SEEK GUI instead. After uploading the data files you can search the data from the homepage.

You can search the SEEK data based on the investigation, study or assay. You can search in on of the three available textboxes.

Follow the next steps to search for data files linked to an investigation, study or assay:

  1. Enter the investigation name in the first textbox or a study name in the second textbox or an assay name in the third textbox to search for the data linked to an investigation, study or assay.
  2. Click the Search button to show the results.
  3. Select the data you want to send to Galaxy and select the "Send datafile only" option.
  4. Select the filetype and database.
  5. Enter a history name and click the send to Galaxy button.

Results will be automaticallyuploaded to the SEEK server. A new assay will be created with the studyname + result + a unique ID. This is done to make it an easier process to find assays that are results instead of the regular assays created by the user.

See results

The following steps can be used to view the results of your analysis.

  1. Enter the study name that you want to get the results from.
  2. Click on the Search >> button to start searching for all results based on that study.
  3. Select the results you want to view.
  4. Click on the Show results button.
  5. A new page will open with the input and output files and the analysis details.
  6. Click on the view icon to view the SEEK data in the SEEK GUI or click on the download icon to download that file to your computer.

Store your history

myFAIR will not upload your results to Owncloud or B2DROP when there was no workflow used. To send your results to Owncloud or B2DROP and make them searchable, please follow these steps:

  1. Choose an investigation folder in the dropdown menu (top level folder).
  2. Click the "Get studies" button to find all studies in the investigation.
  3. Select the history you want to store in the Owncloud folder.
  4. Select the study you want to store the results in (sub folder in the investigation folder).
  5. Click on the Send history to Owncloud button.
  6. A new page will appear telling you the results are stored and are now searchable in myFAIR.
  7. Follow the See results steps to view your results.

Run the analysis again

Follow these steps to run the analysis shown in the result page again:

  1. In the results page click on the Run again button.
  2. A cat will appear to show that the analysis is running.
  3. After the files are send to Galaxy a checkmark will appear and you will be redirected the result page.
  4. Visit the Galaxy page to see the analysis.

The results generated from rerunning the analysis will not be stored in SEEK or ownCloud. To store a new result please run a new analysis with the same data and same workflow. Click on the Erasmus MC logo to go back to the homepage and search for another result or do run another analysis.

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