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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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microbio_me_qiime() #509

Closed mendessoares closed 9 years ago

mendessoares commented 9 years ago

Hi. I have tried repeatedly to download files from the qitta using the above command and was never able to establish a connection with the server. I was wondering if I am the problem ( I may be missing something) or the server is the problem? Here's the info:

GlobalPatterns = microbio_me_qiime(721) #or 722 trying URL 'ftp://thebeast.colorado.edu/pub/QIIME_DB_Public_Studies/study_721_split_library_seqs_and_mapping.zip' downloaded 0 bytes

Error in download.file(zipftp, zipfile, ...) : Couldn't connect to server

And here is the system information: platform x86_64-apple-darwin13.4.0
arch x86_64
os darwin13.4.0
system x86_64, darwin13.4.0
status
major 3
minor 2.1
year 2015
month 06
day 18
svn rev 68531
language R
version.string R version 3.2.1 (2015-06-18) nickname World-Famous Astronaut

Thanks.

joey711 commented 9 years ago

FYI, this is basically a duplicate issue to a previous question regarding the "Restroom Biogeography" tutorial

https://github.com/joey711/phyloseq/issues/491

Short answer: There is no Qiita API yet, at least not that I'm aware of. The QIIME-DB server based at University of Colorado Boulder is permanently down. In this sense, the microbio_me_qiime function should be considered deprecated.

However, a user can manually download files from Qiita in biom format, and then import them into phyloseq.

Please post further comments on the earlier issue.

Thanks!

mendessoares commented 9 years ago

Awesome! Thanks!

On Tue, Aug 4, 2015 at 11:40 AM, Paul J. McMurdie notifications@github.com wrote:

FYI, this is basically a duplicate issue to a previous question regarding the "Restroom Biogeography" tutorial

491 https://github.com/joey711/phyloseq/issues/491

Short answer: There is no Qiita API yet, at least not that I'm aware of. The QIIME-DB server based at University of Colorado Boulder is permanently down. In this sense, the microbio_me_qiime function should be considered deprecated.

However, a user can manually download files from Qiita in biom format, and then import them into phyloseq.

Please post further comments on the earlier issue.

Thanks!

— Reply to this email directly or view it on GitHub https://github.com/joey711/phyloseq/issues/509#issuecomment-127668849.