VM box on website download link issue

[S. Kose]

Hi all, 

I wanted to see if the VM Box OVA is still available for Microbiome Helper?

The website isn't allowing downloads.

Thanks

S.K

[Andre Comeau]

Are you referring to the link for the amplicon-only 12 Gb linked on this page:https://github.com/LangilleLab/microbiome_helper/wiki/Microbiome-Helper-Virtual-Box

This points to a file on our server Kronos and the link is downloading for me from home, meaning to problem for off-campus/external downloads. However, some modern browsers (mine included so I had to bypass) will complain about the download being from an HTTP instead of HTTPS and will cancel it, but there is an option in your Downloads list of the browser to "accept the risk" and continue (at least for me on FireFox).

	ANDRÉ M. COMEAU, PhD Manager • Integrated Microbiome Resource (IMR) T: 902.494.2684 | E: andre....@dal.ca	​Address for deliveries: Dept. of Pharmacology Tupper Med. Bldg., room 5D Dalhousie University 5850 College St. Halifax NS B3H 4R2
​	Research Associate (Lab Manager) Morgan Langille Lab • Dept. of Pharmacology ResearchGate Profile • GoogleScholar Publications
"Without fantasy, there is no science. Without fact, there is no art." - Nabokov "The good thing about science is that it's true whether or not you believe in it." - Neil deGrasse Tyson

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From: microbio...@googlegroups.com <microbio...@googlegroups.com> on behalf of S. Kose <sureyy...@gmail.com>
Sent: May 10, 2024 12:16 PM
To: Microbiome Helper <microbio...@googlegroups.com>
Subject: [microbiome-helper] VM box on website download link issue

 

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[S. Kose]

Thank you Andre, much appreciated!

I can download the amplicon only - which I am assuming is to process amplicon data with picrust2 etc. I have tried to download the full VM Box for metagenome data

but it auto-links to the amplicon or 0.4 ova image. Is that VM no longer available in your Kronos server? 

Thanks Su

[Andre Comeau]

Hmm...the link just below that for the MGS OVA on Kronos is also still working for me when I click on it and it is downloading the right file (http://kronos.pharmacology.dal.ca/public_files/MH/Microbiome_Helper_Vbox/MicrobiomeHelper_v2.3.0.ova).

	ANDRÉ M. COMEAU, PhD Manager • Integrated Microbiome Resource (IMR) T: 902.494.2684 | E: andre....@dal.ca	​Address for deliveries: Dept. of Pharmacology Tupper Med. Bldg., room 5D Dalhousie University 5850 College St. Halifax NS B3H 4R2
​	Research Associate (Lab Manager) Morgan Langille Lab • Dept. of Pharmacology ResearchGate Profile • GoogleScholar Publications
"Without fantasy, there is no science. Without fact, there is no art." - Nabokov "The good thing about science is that it's true whether or not you believe in it." - Neil deGrasse Tyson

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From: microbio...@googlegroups.com <microbio...@googlegroups.com> on behalf of S. Kose <sureyy...@gmail.com>

Sent: May 10, 2024 4:29 PM
To: Microbiome Helper <microbio...@googlegroups.com>
Subject: Re: [microbiome-helper] VM box on website download link issue

 

To view this discussion on the web visit https://groups.google.com/d/msgid/microbiome-helper/1b533aba-3eed-4c88-9149-4f0e66f2d732n%40googlegroups.com.

[S. Kose]

Thanks Andre,

I clicked on the link you pasted and that started working, so perhaps a browser issue on my end with Chrome auto shuting down the d/l instead of giving a warning. 

Thanks for helping me sort it out! 

Best wishes,

Su

[S. Kose]

Hi Andre,

That's all working now, thank you. I also wanted to ask about the picrust2 workflow, in the metagenome workflow we can map KOs/ECs to MyC pathways and show which taxa is associated with which pathway. In the amplicon workflow this isn't apparent, is there a way to place taxanomic information in to the unstrat/strat files produced? Or at least to the file with pathway information?

Thanks,

Su

[Andre Comeau]

Hmm...I don't have that answer off the top of my head. Since it is related to PICRUSt2 and not MicrobiomeHelper directly per se, could you follow the PICRUSt Wiki directions for questions:

"For other general questions and comments about PICRUSt2 please search the PICRUSt google group. If the question has not been previously answered then please make a new thread."

	ANDRÉ M. COMEAU, PhD Manager • Integrated Microbiome Resource (IMR) T: 902.494.2684 | E: andre....@dal.ca	​Address for deliveries: Dept. of Pharmacology Tupper Med. Bldg., room 5D Dalhousie University 5850 College St. Halifax NS B3H 4R2
​	Research Associate (Lab Manager) Morgan Langille Lab • Dept. of Pharmacology ResearchGate Profile • GoogleScholar Publications
"Without fantasy, there is no science. Without fact, there is no art." - Nabokov "The good thing about science is that it's true whether or not you believe in it." - Neil deGrasse Tyson

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From: microbio...@googlegroups.com <microbio...@googlegroups.com> on behalf of S. Kose <sureyy...@gmail.com>

Sent: May 13, 2024 10:42 AM

To view this discussion on the web visit https://groups.google.com/d/msgid/microbiome-helper/c8552a85-30a6-46f9-819f-697ffd44ac24n%40googlegroups.com.