How to install silva and busco through quast?

[yangyue]

My download of moshpit 2025.4 has encountered some problems, it lacks of silva and busco, just like this:

I've downloaded and installed gridss

conda install -c quast gridss

But the other two can't installed by command

conda install -c quast silva
conda install -c quast busco

How it works?
Did resources of "Data resources — QIIME 2 2024.10.1 documentation" equals to the second command? Where the downloaded *.qza database files be stored?

[timanix (Timur Yergaliyev)]

Hello!

@yangyue

My download of moshpit 2025.4 has encountered some problems

With the exception of the message you shared, is it complete? I received the same message and simply ignored it, as the moshpit environment was completely functional.

@yangyue

How it works?
Did resources of "Data resources — QIIME 2 2024.10.1 documentation" equals to the second command? Where the downloaded *.qza database files be stored?

Not sure I am following your question here. You installed moshpit version for metagenomic samples, while the page you are referring to is for 16S rRNA gene amplicon data.

[yangyue]

@timanix

while the page you are referring to is for 16S rRNA gene amplicon data.

Did you met this message?

[SoilRotifer (Mike Robeson)]

Hi @yangyue,

Did you follow the instructions at the end of that message? That is simply run all of the quast-download-* commands while in the moshpit environment. There is no need to run the conda install commands.

Note that BUSCO only works in Linux.

[yangyue]

Now, I want to install moshpit, it means at this time, it has not been installed. In other words, I am dealing with the installing problems, so how can I use moshpit to download anything before it has been download in my local conda environment？

[SoilRotifer (Mike Robeson)]

@yangyue,

I am confused.... based on your initial screenshot, you've already installed it. Just run:
conda activate qiime2-moshpit-2025.7 and you should be in the moshpit environment, and be able to work through the documentation.

[yangyue]

@SoilRotifer

conda activate qiime2-moshpit-2025.7

I'm so sorry because I've not take a screenshot for my command line. I describe it simply, I am trying to install a metagenome or moshpit platform from April of this year, just for preparing a set of analysis for my new metagenome data, however, I tried many times to install, although the sentences were simple, but the effects were not workable usually. So I tried many times, the wrong messages usually show as my post described and the environment could not be installed. By some unknown reasons, I just successeded twice use the same command with qiime2-moshpit-2025.4. But while I using it dealing data analysis, I found my Ubuntu system of WSL occupy too large storage when the time was passing. So I have to uninstalled the platform, and then I tried to re-install it on my Oracle VirtualBox, because it runs so fast, compared to WSL. As usual, it was difficult to be installed. So I tried to install an older version, for example qiime2-metagenome-2024.10, the problems were as usual, just like my post described. Could you really didn't met errors like me？By the way, I think my Ubuntu Linux environment is completely and originally. Another link about busco discussion is here Failure to download BUSCO DB.

[colinvwood (Colin Wood)]

Hello @yangyue,

We are a little confused about the specific error(s) you are encountering. My understanding is that you have successfully installed a qiime2 metagenome 2025.4 environment but are now having difficulty adding additional packages to the environment. Is that correct?

[yangyue]

Thank you for all of yours attention!

@yangyue

I want to install moshpit, it means at this time, it has not been installed. In other words, I am dealing with the installing problems.

I'm trying to install different versions of metagenome or moshpit platform, but the results were same, not installable, it means theirs achieving were not easy as the installing sentences:

conda env create \
  -n qiime2-[metagenome/moshpit]-[one of version numbers] \
  --file https://……/released/qiime2-……-ubuntu-latest-conda.yml

I'm not judge a noble person by the standards of a petty person, DID THE QIIME2 TEAM HIDDEN ANY TECHNICAL SECRETS ABOUT INSTALLATION ?

[ebolyen (Evan Bolyen)]

Hey @yangyue,

I think you are bumping into network issues, let's see if Docker solves the issue in the other thread you have. I'm going to unqueue this one for the moment, since the docker container would have the finished installation and avoid a lot of these post-install problems.

Thanks!