How to transfer my seq files from win7 local drive to a docker containter

Hello and thanks a lot for developing such this informative forum for qiime2 users!
I am a beginner in using docker. I have installed docker toolbox and also pulled qiime2/core 2017.10 and checked it. I use docker in my win7 OS. But now i am very confused with so many docker commands and detailed explanations which i read in forums. My main questions are as following:
1- I have downloaded my fastq files from ftp link and i have them now in a windows local address. So, the question is that how can i address this local folder in docker commands or how to transfer my data to a docker folder or container to be used in the analyses? Is it necessary to create a new container or just the qiime2 container in enough?

2- I followed the guide at this url ""
to make a container and after finishing the process i run “docker ps -a” and got the result as follows:
44461f7b943f b7c2f7ef1a74 “/usr/bin/tini – …” About an hour
ago Exited (0) About an hour ago elastic_noyce
4be7ed1d5b5e qiime2/core:2017.10 “/usr/bin/tini – …” 3 hours ago
Exited (2) 40 minutes ago flamboyant_yalow
08f8d919a671 hello-world “/hello” 2 days ago
Exited (0) 2 days ago fervent_shaw
fa15d8541544 qiime2/core:2017.10 “/usr/bin/tini – …” 2 days ago
Exited (0) 2 days ago optimistic_wing
96ee4f3c8ce5 qiime2/core:2017.10 “/usr/bin/tini – …” 2 days ago
Exited (0) 2 days ago inspiring_shannon
557769860fe7 hello-world “/hello” 2 days ago
Exited (0) 2 days ago hopeful_borg

Would you please explain why i have 3 qiime containers and also please let me know how can i remove extra containers?

3- is there an simple way to transfer data to docker folders? (like direct copy and paste of files from win7 local driver to docker folders)

4- As, being confused with so many instructions regarding using docker for qiime2 commands would you mind just listing the main steps according to which a beginner like me can handle qiime2 commands through docker?

Thanks in advance

Hi @sajjad.sarikhan! Thanks for writing! I noticed you are using docker toolbox on Windows 7 — in my opinion you would be better off using the QIIME 2 VirtualBox image. I suggest that, because unlike docker on Windows 10, the docker toolbox actually runs a virtual machine in order to run docker inside of it. If you aren’t already familiar with docker, this most likely will represent a pretty significant barrier to entry, as well as a noticeable waste on resources.

Try out our VirtualBox image and let us know how it goes! :t_rex:

Hi Matthew
Thank you for your kindly comments for using virtualbox instead of docker, But as far as i see about the future plans for Qiime2, it seems that you are going to lay away qiime Virtualbox and Amazon in near future and just keep going ahead with docker? If so, then what is the best choice for me?
Best wishes

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Thanks @sajjad.sarikhan! I would recommend using the Virtualbox for now. We aren’t sure how much longer we will continue to provide Virtualbox builds, but, there will be ample warning if we decide to discontinue it. This will get you moving quickly on your analyses. In the meantime, I suggest you read up on Docker, that way if we ever do get around to ending VirtualBox support, you can help out here on the forum when people start getting interested in Docker! :wink: Thanks! :t_rex:

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Hello Sajjad,

As you can see in this blog post, Qiime 2 will continue to support virtualboxes and Amazon.

I agree with Matt and think that Virtualbox is a fast and easy way to deploy and run Qiime 2.


@colinbrislawn, that is outdated information - please see this post for reference.


Whoops! Thank you for the correction.

I like the plan to make Qiime easy to deploy anywhere and encourage cross platform usage.

What’s the best place to get news and announcements about Qiime 2? The Announcements section on the forums or the Qiime blog?

Hi Matthew ! thanks again for quick reply!

Hi again,
Would you please tell me the differences between QIIME 2 VirtualBox image and the virtual box located within the docker? May i use Kitematic alpha in docker toolbox instead of QIIME 2 VirtualBox image? Or you suggest using the latter one?

thanks in advance

Please see my post from above:

My recommendation is to use the official QIIME 2 VirtualBox Image (linked to in the post above). We are unable to provide support for third-party tools like Kitematic. Thanks!

I will do that! Thank you for prompt reply!

The QIIME 1 blog will be discontinued. Like you noted, the QIIME 2 Forum Announcements category is a good place to follow, as well as the qiime2 Twitter account.

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