I tried to update qiime2-2017.5 to qiime2-2017.6 in AWS. I followed the instructions as below
Amazon AWS
In a shell on the remote AWS machine, run the following command:
sudo env "PATH=$PATH" conda update conda
sudo env "PATH=$PATH" conda install --file https://data.qiime2.org/distro/core/qiime2-2017.6-conda-linux-64.txt`
How can I set the "PATH=$PATH here for the AWS QIIME update? Below is the errors I got:
[ec2-user@ip-172-31-27-120 ~]$ sudo env "PATH=$PATH" conda update conda
Traceback (most recent call last):
File "/home/ec2-user/miniconda3/bin/conda", line 4, in <module>
import conda.cli
ImportError: No module named 'conda'
[ec2-user@ip-172-31-27-120 ~]$ sudo env "/home/ec2-user/miniconda3/bin" conda update conda
env: /home/ec2-user/miniconda3/bin: Permission denied
Hi @Bing, are you running an official QIIME 2 AWS image? Those instructions are specific to the custom image that we are providing, and likely won’t work if you have set up your own AWS EC2 instance. I suspect you are running your own image, because the user account in your post (ec2-user) is not the user account that we set up in the official images (user qiime2). Assuming you are running your own image, you should use the native linux instructions:
conda update conda
# If you named your conda environment something else when you initially installed QIIME 2, use that name here.
source activate qiime2-2017.6
conda install --file https://data.qiime2.org/distro/core/qiime2-2017.6-conda-linux-64.txt
As well, I have created an issue to update the text in those documents to make it more clear that the AWS upgrade instructions posted there are specific to the official QIIME 2 image.
