This is a recording of our Orientation Webinar. We received several questions during our Question & Answer session. We've provided the transcribed questions and answers here for ease of use.
GENERAL GENOMESPACE QUESTIONS:
Q: Can you unzip/compress within GenomeSpace?
A: Yes, GenomeSpace will allow you to zip/unzip on the server, as well as a few other compression formats such as .tar and .tar.gz.
Q: Will GenomeSpace provide any training workshops in the future?
A: The GenomeSpace team will continue to host both orientation and recipe-focused webinars. We will continue to provide these kinds of webinars in the future, and we host workshops at different conferences such as ISMB. If you would like to invite the GenomeSpace team to travel to your location and conduct a workshop, please send us an email at firstname.lastname@example.org.
Q: What do the Dropbox and Google Drive integration look like in GenomeSpace? Is there a specific location in GenomeSpace where this integration occurs?
A: The integration of cloud storage creates a new folder in your GenomeSpace account. For example, if the user 'RecipeUser' adds their private Google Drive account to GenomeSpace, they will have a new folder, "googledrive:email@example.com" added to their GenomeSpace account. This will be a public folder, separated from the other folders in this user's private Google Drive account. The other files and folders on the user's private Google Drive account will NOT be integrated.
Q: Is the search capability only search on filenames and tags? What’s the search engine behind GenomeSpace?
A: You can search the entire GenomeSpace.org website on the main page using any terminology you desire. Within the GenomeSpace User Interface, we currently only support search for file names and file tags.
Q: Does GenomeSpace has an offline version?
A: GenomeSpace itself is an online tool, however you can create your own server and instance to run. However, this feature is provided mostly for tool developers, and is not necessarily useful to the average GenomeSpace user.
Q: Is there plan to have Recipes include something like Common Workflow Language (CWL) so one can programmatically execute a recipe with some JSON input pointing at data input sources?
A: Currently, there is no plan to have CWL integrated, although we do have plans in the works for more interactive recipes which may support that feature. We will not be supporting CWL at this time since most tools in GenomeSpace do not support this capability, but we are working on integrating GenomeSpace with Jupyter, which would allow some tools to be driven programmatically.
Q: For tools with multiple variants (e.g. Galaxy), can we specify somewhere in GenomeSpace which galaxy instance we want to use?
A: Yes. The Galaxy icon launches the main Galaxy instance; however, you can connect additional instances of Galaxy, or your own private server, by adding it as a private tool into GenomeSpace. Find more information in the User Guide documentation.
Q: How can I load NCBI GEO data into GenomeSpace?
A: There are many ways to obtain GEO data and load it into GenomeSpace. You can use a module, "GEOImporter" in GenePattern. You can also use a resource or other database tool, such as InSilicoDB.
Q: Has anyone implemented the recent aligner/mapper hisat/hisat2 in GenomeSpace?
A: Currently there is no implementation of these aligners and mappers in GenomeSpace-enabled tools. However, these aligners may be added into tools such as Galaxy in the future, if the Galaxy development team adds the tool.
Q: How do I use own data by some recipes?
A: To use your own data on a recipe, you can just read through a recipe and substitute your own data where we would normally provide the Recipe Resource example data. We describe file formats and provide information about the type of input files a recipe takes, so as long as your own data matches that format, you can substitute it easily.
Q: How do F1000 publications work? How do I submit my recipe?
A: First, submit the recipe to the Recipe Resource. Once you've submitted a recipe, please email the GenomeSpace team at firstname.lastname@example.org, and we will coordinate with you to publish your recipe as an F1000 paper.
Q: Can you direct the output of a recipe or a tool to a particular folder of the file browser, e.g. directly into a Dropbox or Google Drive account, instead of your main GenomeSpace account.
A: You can direct the output of different tools to different folders within your GenomeSpace account. If you have added a Google Drive account or Dropbox account, you will be able save from it from any of the supported tools.