FAQs
PhenoMeNal is comprehensive and standardised e-infrastructure that supports the data processing and analysis pipelines for molecular phenotype data generated by metabolomics applications. You can deploy your own instance of PhenoMeNal with a few clicks. More information can be found here.
The PhenoMeNal Gateway, also known as the PhenoMeNal portal, is the entry point to the PhenoMeNal e-infrastructure where you can find metabolomics data analysis tools and workflows. You can create your own Cloud Research Environment (CRE) through the PhenoMeNal Portal on a cloud provider of your choice. Your new CRE will be identical to the public instance, but will only be accessible by you and will run on your preferred cloud computers (rather than our machines).
The App library is the service catalogue of freely available Metabolomic tools available within the PhenoMeNal Cloud Research Environment.
The CRE can be started via the PhenoMeNal portal, which can guide you through the deployment. Alternatively, the PhenoNeNal CRE can also be started through the command-line on Amazon, Google Cloud, Microsoft Azure or in a public or private OpenStack environment. For more information go to our help section.
The PhenoMeNal Galaxy Instance is a public PhenoMeNal instance hosting a Galaxy environment to let you test drive a CRE. Use it to see how you like PhenoMeNal. However, remember that it is a shared space: you will be sharing the Galaxy instance with other users and hardware resources are limited so you won’t be able to process very large datasets.
The public instance is a shared space. The time taken to process your requests depends on overall user load. Also, though we do our best, we cannot guarantee that no one else will be able to see your data. On the other hand, deployment on a cloud provider of your choice (including your private cloud) is private to you. It will be less likely to suffer downtime. With the proper care, it can also be made completely isolated and suitable to process sensitive data.
We do not guarantee either the security or persistence of your data in public instance CRE. This shared installation is only intended to provide a way to test the e-infrastructure services freely before deciding to commit to their own deployment.
There are two ways to do that: 1) you can follow the instructions on our wiki on how to make your software available through PhenoMeNal; 2) you can manually deploy the infrastructure and add the tools directly. More information on how to manually deploy PhenoMeNal can be found also on our wiki at: QuickStart Installation for Local PhenoMeNal Workflow. This page also explains the preferred way to test your software locally before making it available through PhenoMeNal.
Nothing! All our software is freely available on GitHub, and access to the portal is of course also free). However, you may have to pay for cloud computing services to deploy your own CRE.
As easy as clicking Contact Us. You can reach the same for through our website. Enter a description and click Submit Ticket to send your feedback directly to our help desk.
We can only help with operational aspects of the PhenoMeNal infrastructure and the cloud deployment mechanisms available though the PhenoMeNal CRE Portal. For questions about the usage of any tools available in the PhenoMeNal infrastructure we advise users to directly contact the respective tool developers. An overview of the tools and the relevant contact information can be found in the App Library.
We can only help with operational aspects of the PhenoMeNal infrastructure and the cloud deployment mechanisms available though the PhenoMeNal CRE Portal. Queries such as these can be posted on relevant discussion forums, such as http://www.metabolomics-forum.com/. If you’d like to see additional infrastructure functionality or have queries related to adding new tools to PhenoMeNal, please contact us and we will do our best to accommodate your request.
Check the logs and scroll a little higher. You should see a more informative error message starting with the text Error applying plan.
The free GCP account doesn't offer sufficient resources to run PhenoMeNal. If you try deploying you'll get an error like
Error applying plan:
2 error(s) occurred:
* module.edge.google_compute_instance.instance[0]: 1 error(s) occurred:
* google_compute_instance.instance.0: Quota 'CPUS' exceeded. Limit: 8.0 in region europe-west1.
* module.glusternode.google_compute_disk.extra_standard_disk: 1 error(s) occurred:
* google_compute_disk.extra_standard_disk: Error creating Disk: googleapi: Error 403: Quota 'SSD_TOTAL_GB' exceeded. Limit: 100.0 in region euro
The full error message should be something like
Your TSI portal account has obsolete Application Repositories called "Phenomenal VRE".
You need to delete these directly from the TSI portal.
Perhaps you were a tested early versions of PhenoMeNal (before Dalcotidine). These older versions of PhenoMeNal left an incompatible application repository in your account on the TSI portal which need to be deleted for the portal to work properly. Follow these instructions:
- Go to the TSI portal: https://portal.tsi.ebi.ac.uk
- Log in using the same account you use for the PhenoMeNal portal.
- Click on the menu button on the upper left (three little horizontal dashes on top of each other).
- Select "Application Repository".
- You should now see a card that says "Phenomenal VRE". Click on it.
- Click on the garbage can on the top right.
Now your account on the PhenoMeNal portal should work again.
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Funded by the EC Horizon 2020 programme, grant agreement number 654241 |  |
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