Re: Anvio

A. Murat Eren

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Jul 3, 2020, 12:40:32 PM7/3/20

to Podar, Mircea, Anvi'o, Peter Podar

Dear Mircea,

Great to hear from you!

I'm sorry you're dealing with installation issues. I know solving the environment step can take ages. This is a problem related to conda and there is nothing anvi'o developers can do about it at this point :( It is very frustrating, but I'm sure it will be resolved one way or another.

Meanwhile I will send you a workaround implemented by Blake Sanders, a student at the University of Chicago, and will ask you to try it. The work around I'm sending you will essentially replace these steps in the installation manual:

conda create -y --name anvio-6.2 python=3.6
conda activate anvio-6.2
conda install -y -c conda-forge -c bioconda anvio==6.2

Everything else in the installation document will remain the same. First, kill your conda install command if it is still solving the environment, start a new terminal, and get rid of the anvi'o environment that is now lacking an anvi'o installation:

conda env remove --name anvio-6.2

Then, run this command, using the file attached to my e-mail:

conda env create -f anvio-environment.yml

conda activate anvio-6.2

With this, resolving the environment should not take longer than 5 minutes. Then you can continue following the installation document as if you just run the line that starts with `conda install -y -c conda-forge ..`

Please let me know how this goes so I can suggest it to other people too :)

Best wishes,

--

A. Murat Eren (Meren)
http://merenlab.org :: twitter

On Fri, Jul 3, 2020 at 10:34 AM Podar, Mircea <pod...@ornl.gov> wrote:

We have been trying to install it and it has been running that initial step for 80 hours now, not sure whats doing. I know you wrote that it can take a long time, but I wonder how long and why, this hasnt happened with previous releases. Anything else we can do?

anvio-environment.yml

Julie Meyer

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Jul 3, 2020, 4:33:36 PM7/3/20

to an...@googlegroups.com, Podar, Mircea, Peter Podar

What great timing! I had been stuck on the conda resolving environment step for about 24 hours. I just tried your little work-around and it worked like a charm - finished the installation in about 10 minutes. Thanks!

--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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Mircea Podar

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Jul 3, 2020, 9:12:10 PM7/3/20

to Anvi'o

Dear Meren,

worked like a charm! Thank you!

Mircea

A. Murat Eren

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Jul 3, 2020, 9:23:12 PM7/3/20

to Anvi'o, Blake Sanders, Podar, Mircea, Peter Podar

I'm very happy to hear that, Julie! Thank you very much for reporting back. I also heard from Dr. Mircea Podar: it worked for him as well.

I am CC'ing this response to Blake Sanders so he can see how his solution has already saved two people hours and hours of unnecessary wait :)