Regarding QIIME upgradation

[roy1234...@gmail.com]

Hi every body

1. I want to upgrade my QIIME version from 1.8.0 to 1.9.1. but i am not able to upgrade because it gives errors.

2. How can i label taxas to tree tips. i am running the command convert_tree_tips_to_taxa.py

but the result displayed was command not found. However i think that i am using QIIME 1.8.0 may be it may not be having the feasibility for this command.

However i was reading for an alternative like GraPhLan. But i donot know how to use it. and do i need to install it in qiime. if so please let me know how to install GraPhLan and with what file i have to start analysis.

Best wishes   

[TonyWalters]

Hello,

For 1., you're probably going to need to post the specific error you're getting. I'd recommend using the miniconda approach outlined here in any case:http://qiime.org/install/install.html

2. This is a custom script, not specifically part of the QIIME package. It specifically comes from here: https://gist.github.com/walterst/17d9e777e6b8cadb9546
You'd have to download or find the script on your system, and put it in your $PATH environment to run it.

I haven't used GraPhLan, but you can probably install it and use it from here: https://huttenhower.sph.harvard.edu/graphlan
There is also iTOL for colorizing/labeling phylogenetic trees that you might find useful: https://itol.embl.de/

[roy1234...@gmail.com]

Thanks Tony,

i got through iTOL but i am not able to understand it properly. and secondly is there any tutorial of iTOL

Does i have to install GraPhLan in qiime. if so please mention the full command.

[TonyWalters]

Both ITOL and GraPhLan are independent software packages from QIIME, so our support of these will be limited. For iTOL, see their help page: https://itol.embl.de/video_tutorial.cgi

You wouldn't install GraPhLan in qiime (I'm not quite sure what it means to install it in qiime in any case), since it's a separate package. I won't be able to tell you the "full command"-but the installation guide from their site should provide some insight.

[roy1234...@gmail.com]

Thanks Tony

 i downloaded the custom script from  https://gist.github.com/walterst/17d9e777e6b8cadb9546  and i got a zip folder after extracting it i got a file convert_tree_tips_to_taxa.py.

But what hurts me that i am not able to run it. because being new to qiime and Linux as well i am not able to do it. Please will you guide me over here how to run it.

[TonyWalters]

Did you try the -h option that is mentioned in the text of the file:
# USAGE: See help text with python convert_tree_tips_to_taxa.py -h

[divyapr...@gmail.com]

Hi Tony 

While running the command python convert_tree_tips_to_taxa.py -h this is the error that i got

Traceback (most recent call last):

  File "convert_tree_tips_to_taxa.py", line 18, in <module>

    from biom import load_table

ImportError: cannot import name load_table

[TonyWalters]

Hello,

That means that you do not have the QIIME 1.9 environment set up on the system.

Also, I thought I was talking to "roy". Please use a single user name.

-Tony