I am new to Qiime 2 platform. I am using Amazon Web Services.
I was trying to import my data. My FASTQ file and metadata is in my local computer as shown below (Under OneDrive -Personal folder under R).
First, I want to know how to import my data to the directory that I created above, and I also want to know how to create URL in order to follow below commands.
There are lots of ways to move files between computers. Here's what I recommend
Get files from your local computer into a linux machine:
I like using the Remote Explorer in VS Code. This tutorials show how to set up VS Code Remote Explorer for AWS. This works great on AWS, and Azure, and local supercomputers at your university!
I also like VS Code as text editor, and it's free, get it here
Once you get VS Code set up and Remote Explorer connected to your AWS VM, you can drag and drop you files from your desktop to your remote machine.
From inside VS Code, type >remote and add a new SSH Host with your username and IP address of your AWS machine. So in your case, this would be root and 172.31.1.88
Thank you for your response! I tried the steps for VirtualBox, but for me, the button they require me to click was inactivated on my end. Please see below image and help me! Thank you
Yes, I uninstalled and reinstalled the virtualbox. Then, I imported the qiime2 OVF, but still having the same problem. I also removed the qiime2 in the VM and reimported the qiime2, but having the same error message. What can I do? Please help me with this
I'm at a bit of a loss here, as I've never seen this error when using Virtualbox. I found that troubleshooting tutorial using this google search. There may be better results on that list.
What do you think we should try next to diagnose this problem? Have you been able to get any other VMs working with Virtualbox? Would you like to pivot back to using AWS and VS Code to move files there?
The Remote Explorer uses SSH, so try the SSH client tab shown on that Amazon AWS screenshot.
To start, let's see if we can get a basic SSH session running between your computer and your EC2 instance.
That's the right command! See if that SSH client tab gives other advice about connecting to your instance.
Thanks for sticking with it while we figure this out. I apologize for the scatter-shot approach. There's a bunch of ways to set up this software and connect to remote machines.
You mentioned that you were new to Qiime2, but also you are using AWS and Docker which is well beyond many traditional microbiologists. What kinds of unix software have you used before? Maybe we can use that as a starting point for qiime2.
I have never used any types of software before. That is why I am struggling a lot. I think I completely messed up with my computer because it doesn't allow me to open docker or uninstall it. I previously downloaded the docker and I uninstalled and deleted the program in the (C:) folder, but it now seems that some folders are still there because it did not allow me to delete it. Can you help me with this..?
Thanks for telling me more. Let's see if we can get Qiime2 installed using Windows Subsystem for Linux, as that's probably the easiest way forward.
(Before we start, you can restart your computer and try uninstalling both docker and VirtualBox, and deleting the VirtualBox image to save some space.)
As you can see it is formatted with excel sheet, and I know I have to convert excel to biom format. Can you help me how to create biom format? I have tried biom convert from other forum questions, but it did not work. Can you walk me through the process in detail as I am savvy to these software or programming?
Please help me with this
)! Thank you so much for your help.
