Q2-scnic packagenotfounderror

Community Plugin Support
1

Hi Michael,

I run into an error while trying to instal q2-SCNIC. I follow the instructions given above but I get this error:

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.

I really appreciate your help with this.

Thanks
Mehmet

2

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

3

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

4

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

5

Hi Mike,

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

Thanks!
Mehmet

6
7

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.

8

@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.

9
10

Hi @thermokarst,

This is the message I got:

"(qiime2-2018.6) [[email protected] ~]$ 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."

11

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
12

Hi Matthew,

Thanks for the new instructions, it worked!

Best
Mehmet

1 Like
13

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

1 Like
14

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.

15

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.

16
17

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):

Screen Shot 2020-03-10 at 7.38.21 AM
Screen Shot 2020-03-10 at 7.38.21 AM797×129 16.6 KB

1 Like
18
19

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

20

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