Q2-scnic packagenotfounderror

Hello @Mdavrandi,

Can you show me what you see when you using qiime info? Also if you run conda search -c lozuponelab q2-SCNIC what do you see?

Mike

Hi @michael.shaffer,

Please find the outputs below:

qiime info

System versions
Python version: 3.5.5
QIIME 2 release: 2018.11
QIIME 2 version: 2018.11.0
q2cli version: 2018.11.0
Installed plugins
alignment: 2018.11.0
composition: 2018.11.0
cutadapt: 2018.11.0
dada2: 2018.11.0
deblur: 2018.11.0
demux: 2018.11.0
diversity: 2018.11.0
emperor: 2018.11.0
feature-classifier: 2018.11.0
feature-table: 2018.11.0
fragment-insertion: 2018.11.0
gneiss: 2018.11.0
longitudinal: 2018.11.0
metadata: 2018.11.0
phylogeny: 2018.11.0
quality-control: 2018.11.0
quality-filter: 2018.11.0
sample-classifier: 2018.11.0
taxa: 2018.11.0
types: 2018.11.0
vsearch: 2018.11.0

Application config directory
/Users/mehmetdavrandi/Library/Application Support/q2cli

conda search -c lozuponelab q2-SCNIC

Loading channels: done
#Name Version Build Channel
q2-scnic 2018.6.1 py_0 lozuponelab
q2-scnic 2018.8.0 py_0 lozuponelab
q2-scnic 2018.11.0 py_0 lozuponelab

Hey @Mdavrandi,

Can you try running the install command again inside your qiime 2 environment? Since your search is working then the q2-scnic package should be found and be able to be installed.

Mike

Hi Mike,

Unfortunately the problem persists. Not sure whats going wrong here. Is there any other way of installing this plugin?

Thanks!
Mehmet

Hi @michael.shaffer,

I encountered the same problem with @Mdavrandi, and my QIIME 2 version is 2018.6.0. I can search for the package but when I tried to install it the “packagenotfounderror” message came up. Would be great if you can help with this!

Thanks,
Allie.

@AllieNguyen - did you remember to include the lozuponelab channel in your install command?

conda install -c lozuponelab q2-SCNIC

Please copy-and-paste the complete error message you observed.

Hi @thermokarst,

This is the message I got:

"(qiime2-2018.6) [lunguyen@titan15 ~]$ conda install -c lozuponelab q2-SCNIC
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  • q2-scnic
  • scnic[version=’>=0.5.3’]

Current channels:

To search for alternate channels that may provide the conda package you’re
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page."

It looks like @michael.shaffer’s install instructions might need to be updated — the scnic package is up on the bioconda channel:

conda install -c lozuponelab -c conda-forge -c bioconda -c defaults --override-channels q2-SCNIC
5 Likes

Hi Matthew,

Thanks for the new instructions, it worked!

Best
Mehmet

1 Like

Thanks @thermokarst, the new instruction work for me too!
Kind regards,
Allie.

1 Like

An off-topic reply has been split into a new topic: Module ‘SCNIC.module_analysis’ has no attribute ‘make_modules’

Please keep replies on-topic in the future.

I used the command above, but still get the “UnsatisfiableError”. Has SCNIC been moved?

(qiime2-2019.4) -bash-4.1$ conda install -c lozuponelab -c conda-forge -c bioconda -c defaults --override-channels q2-scnic
Collecting package metadata: done
Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:

  • q2-scnic
    Use “conda search --info” to see the dependencies for each package.

(qiime2-2019.4) -bash-4.1$ conda search *q2-scnic* --info
Loading channels: done

PackagesNotFoundError: The following packages are not available from current channels:

  • q2-scnic

Current channels:

To search for alternate channels that may provide the conda package you’re
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

This error means that conda found q2-scnic, but was unable to install it, because it conflicts with the packages in the environment you are trying to install into. If I recall correctly, q2-scnic is only compatible with QIIME 2 2018.11 (not sure why the plugin hasn't been updated to work with newer versions of QIIME 2).

Oops, you forgot to include the necessary channels (-c lozuponelab):

1 Like

So, is it not compatible with any qiime version after 2018.11.0?

That is correct.

q2-scnic, like many other plugins, is developed by a different team of developers than QIIME 2. Most of these plugins are maintained to remain compatible with the latest release of QIIME 2, but unfortunately q2-scnic has not been updated for a while, so 2018.11 was the last release with which it was compatible.

We are all hoping @michael.shaffer or another developer can update q2-scnic soon, since it is a fairly popular one judging from the forum traffic!

1 Like

Gotcha! Thanks @Nicholas_Bokulich for the clarification! I guess I’ll just use the older version of qiime for downstream SCNIC analyses.

1 Like