How to give file path in qiime2 virtualbox installs

Hi!
I wonder if you could help me to use the following command in Qiime2 virtualbox machine.
How would be the command style?
Why on the earth command formats are differing between qiime2 native install and virtualbox and docker?

qiime tools export
feature-table.qza
–output-dir exported-feature-table

imagine i have my table.qza file in my shared file at the address: /media/sf_QIIME, then how can i use that address at the above mentioned command?
best wishes

Hi @sajjad.sarikhan!

The formatting of the commands will be the same whether you’re using a native install, VirtualBox, or the AWS AMI; each of those environments provide a terminal emulator where you can run commands on the command line.

For example, the following command can be run in a native install, VirtualBox, or AWS:

qiime info

Now, the file paths you use in the commands will need to be adapted, as the file paths you choose will be specific to your analyses, and those files could exist anywhere on your file system. QIIME 2 does not require that your data files exist in any particular location, nor does it place restrictions on what file names you choose. Thus, the commands provided in the QIIME 2 tutorials (and elsewhere) can be used in any of the installation/deployment environments I listed above, but you’ll need to adapt the commands to suit your own data files.

The QIIME 2 Docker image requires some modifications to the commands you’ll run – this is just a requirement of Docker because it is a container-based VM, and it’s not something we control (we don’t develop Docker). See the QIIME 2 Docker install guide for an example of how to format those commands (each command must be prefixed with docker run and some options).

It looks like you’re following along with the exporting tutorial. The command you pasted from the tutorial assumes you have a file called feature-table.qza in your current working directory. If you’re following along with the tutorial, the feature-table.qza file will have been previously downloaded to your current working directory – this is why the command works without any modifications (we intentionally design the tutorials this way to make them easy to follow along with, i.e. copy-and-paste).

As mentioned above, you’ll need to adapt this command to work with your own data. If your feature table file is located at /media/sf_QIIME/table.qza, you would provide that file path in your export command:

qiime tools export /media/sf_QIIME/table.qza --output-dir exported-feature-table

Note that /media/sf_QIIME/table.qza is an absolute path, and exported-feature-table is a relative path, so if you run this command, a directory called exported-feature-table will be created in your current working directory.

If you’re not familiar with the terms current working directory, absolute path, and relative path, I recommend following along with some Linux/macOS command line tutorials online, as they’ll teach you these general concepts (and much more!) that apply to any work you’ll do from the command line (i.e. it’s not just applicable to QIIME 2 commands). The time you invest in learning the command line interface will definitely pay off in the long run!

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Hi @ jairideout

Thank you for your helpful comments. That solved my issue.
With the best
Sajjad

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