How to determine Function with MMseqs2 or humann2 for now? #60
Comments
|
Hi there,
No problem. So, for (1) – if you want to use HUMAnN2, you can always install it still by following the instructions here: https://huttenhower.sph.harvard.edu/humann2/. There has been a HUMAnN3 version out for a while though (https://huttenhower.sph.harvard.edu/humann) – I haven’t personally tested out the difference between the two versions, but I would assume that the performance of HUMAnN3 will be better (although I know it takes longer to run, and potentially has larger computational requirements).
For (3) – are you unable to download from Dropbox because you can’t do that from your end, or did you try recently and got an error? We have been having some issues with the Dropbox reaching exceeding its bandwidth but these seem to be OK at the moment so if it’s not an issue on your end then you could try downloading again. The database is the largest part of the tutorial data (22GB out of 30GB to download, more once unzipped), so I don’t think it will be very helpful for me to upload only the database somewhere. I have attached a zipped folder containing all of the functional scripts, though.
Thanks,
Robyn
From: Wang ***@***.***>
Date: Thursday, January 5, 2023 at 10:40 AM
To: LangilleLab/microbiome_helper ***@***.***>
Cc: Subscribed ***@***.***>
Subject: [LangilleLab/microbiome_helper] How to determine Function with MMseqs2 or humann2 for now? (Issue #60)
CAUTION: The Sender of this email is not from within Dalhousie.
Sorry to bother you.
I am an old user of Microbiome helper, and deeply love since it is easy to use. Recently, it is hard to get into google group in China, even with VPN, so I do not read your answer on my other problems. My problem is mainly on MMseq2, since
1. humann2 in old version was no longer in microbiome helper (I am using conda version (https://anaconda.org/hcc/microbiome-helper)
2. VirtualBox version can not be used in my server.
3. The script for MMseq2 can not found (for the sample season of internet problem, I can not download the tutorial in dropbox and extract the script）
My questions:
In https://github.com/LangilleLab/microbiome_helper/wiki/Metagenomics-Standard-Operating-Procedure-v3
where can we download
the database /home/dhwani/databases/mmseqsUniref90DB
the scripts, such as /home/dhwani/MyGit/MH2_test/run_TaxonomyFunctionSearchMegan.pl
/home/dhwani/MyGit/MH2_test/pick_uniref_top_hit.py
Thank you for your attention!
—
Reply to this email directly, view it on GitHub<#60>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AEAYQDT3HXHFFUZFX4XTP6LWQ3MOJANCNFSM6AAAAAATSA3DVU>.
You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>
|
|
Thank you for your timely reply. According to your description, I believe the dropbox tutorial is necessary. I asked my friend to download it, however, he said its link has been dated. Might the dropbox link I saved is dated, and I forgot this link existed on which page in wiki. Could you kindly suggest the microbiome helper wiki page which the dropbox link existed? |
|
If you are referring to the dropbox link to get the data, you can get it using the following command:
I am downloding it at the moment. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Sorry to bother you.
I am an old user of Microbiome helper, and deeply love since it is easy to use. Recently, it is hard to get into google group in China, even with VPN, so I do not read your answer on my other problems. My problem is mainly on MMseq2, since
My questions:
In https://github.com/LangilleLab/microbiome_helper/wiki/Metagenomics-Standard-Operating-Procedure-v3
where can we download
the database /home/dhwani/databases/mmseqsUniref90DB
the scripts, such as /home/dhwani/MyGit/MH2_test/run_TaxonomyFunctionSearchMegan.pl
/home/dhwani/MyGit/MH2_test/pick_uniref_top_hit.py
Thank you for your attention!
The text was updated successfully, but these errors were encountered: