Mac Local Install

[Andrew Brooks]

Hi,

I am a microbial evolutionary geneticist with quite a few datasets I am analyzing. Came across Phinch and yelled across my lab in excitement. 

Couple questions:

I could not get my biom files to load on the web version (many are very large so that makes sense). Even small ones are not working however (~500kb) so I wondered if it might be on my end in chrome?

Downloaded the local version from Github and am trying to get it up and running. Are there any changes to chrome I need to make such as allowing developer tools? The install is not to descriptive so I was wondering about dependencies: I may be missing a proper PHP client. May be lack of knowledge but I am opening the folder in google chrome and navigating to the config file but it is opening as the PHP code itself and not actually running. 

I am good with the command line and local tools, but have no experience with local web programs or PHP itself so I apologize if I sound foolish. Any help would be greatly appreciated!

Thank you in advance, the program looks incredible,

Andy

[Holly Bik]

Hi Andy,

At this point we don't have an option for a "local install" - our Github repo is just so people have access to the source code. The implementation of the code on http://phinch.org is actually using your local machine - the .biom files get processed and indexed using Chrome's libraries and nothing is uploaded over the internet.

Do your .biom files have both taxonomy and sample metadata added in? Phinch won't be able to parse the files without this information - instructions on how to add this in are in the "Help" tab in the upper righthand corner of the website.

If Phinch still isn't working after adding in taxonomy and metadata, can you give me more information about what is happening? Are you seeing an error message? We'll try to get your files working ASAP!

Holly

[Andrew Brooks]

Hi Holly,

Once I filled in my entire meta-data from my mapping files (foolish of me) and ran it on the web version it works incredibly, so much faster and beautiful than running each Qiime command. Thank you so much for the prompt and succinct response, I saw my mistakes as soon as I read it. 

Keep up the great work, it is very appreciated!

Andy 

 

For future reference if anyone reads this - make sure you do this command with a QIIME formatted mapping file:

biom add-metadata -i my_table.biom -m my_map.txt -o my_table_w_metadata.biom