for *.py such as join_paired_ends.py Command not found in conda environment?

omomo · September 30, 2019, 1:30pm

Version of QIIME 2 you are running, and how it is installed (e.g. Virtualbox, conda, etc.)

I used conda to install qiime2-2019.7 and also tried the old version qiime2-2019.4.
'qiime --help' worked well

But *.py scripts can not work. command not found.

And scrpts which qiime2 websites metioned are not in the /anaconda2/envs/qiime2-2019.4/bin

Other tools works well such as 'qiime tools import'

jwdebelius · September 30, 2019, 1:52pm

Hi @omomo,

join_paired_ends.py is a QIIME 1 script, and the scripts you referenced are QIIME 1 scripts. You may want to look at the QIIME2 for Experienced Reserachers documentation as a starting place.

Best,
Justine

omomo · September 30, 2019, 2:20pm

Hi @jwdebelius,
thanks very much!
It means that there are no longer scripts I mentioned in qiime2 right?

Best,
omomo

jwdebelius · September 30, 2019, 2:23pm

Hi @omomo,

The same functionality to do things like joined paired ends, cluster (or denoise!) etc is in QIIME 2, it just has slightly different names. I think that if you look through the tutorials, you'll find most of what you're looking for from QIIME 1.

Best,
Justine

omomo · October 1, 2019, 4:48am

Hi @jwdebelius

Thanks a lot for your reply~~!!

Best,
omomo