Yes!! pip install . in the portal_client folder worked successfully and the client seems to be fully downloaded after some processing in the terminal! We are so close. I'm going to continue to test out the commands to download the files and I'll let you know if I run into any difficulty.
Thank you so much for all your help.
Hello Colin!
I'm back again with another question for you. You have been a huge help so far and I'm so grateful that I've been able to progress further.
Now that portal_client is installed, I'm now in the process of running commands to import the iHMP manifest file. I dragged the manifest file into the portal_client directory to run the commands but I seem to be running into trouble with the URLs. I used the following command as you mentioned in an earlier post:
This was the command that popped up when I tried to import the manifest file:
This is what I found on GitHub that probably is the solution is to the problem:
which ascp, nothing pops up. What do you recommend I do to install ASCP in order to download the data that is from Aspera? Additionally, what would I use as my username?
Thank you!
-Hasti
Hello again,
Looks like Aspera isn't open source software, but you can download it for free from here:
https://downloads.asperasoft.com/connect2/
Once you get it installed, check if which ascp works, and try some of those commands again.
Not sure what the username is either... this might be a good time to reach out to the DACC and let them know their platform is harder to use than intended...
Let me go do that!
Colin
I just got this feedback from the portal_client GitHub:
Hi! If you want to use aspera sever to download the data you should ask for credentials here: NIH Human Microbiome Project - Download Instructions. The link is below the "Transferring Files To/From the Aspera Server:" paragraph.
Does that help?
Hi Colin!
Interesting. I downloaded Aspera from the link that you provided yet the which ascp command isn't popping up anything. This is harder than intended like you said... I also asked for credentials from the HMP site that you linked and I was granted access! I tried to run some of the commands and use the user option from that but the terminal was still telling me that I need to download the ASCP binary.
Nevertheless, I was somehow able to download another manifest file from iHMP that had a different kind of URL (hmp.dacc) instead of Aspera. I'm gonna continue to dive deeper with this data (taken from prediabetes) and see what I come up with.
I will continue to keep you updated!
OK great!
I'm glad you are making progress.
Are you running this on a Mac or Linux system? I can try getting Aspera set up on a matching machine and see if that process works for you.
Colin
Thank you! I couldn't have made it this far without your help.
I'm running this on a Linux system! I wouldn't want to take your time but if you do end up doing so, that will be nice to find out.
-Hasti
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