Q2-scnic packagenotfounderror

(Mehmet Davrandi) #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

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q2-SCNIC: A tool for making correlation networks, finding modules of observations and summarizing them
Identifying bacterial taxa (16S) that correlate with eukaryotic taxa (18S)
(Michael Shaffer) #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

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(Mehmet Davrandi) #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

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(Michael Shaffer) #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

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(Mehmet Davrandi) #5

Hi Mike,

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

Thanks!
Mehmet

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(Matthew Ryan Dillon) assigned michael.shaffer #6
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(Quynh anh Nguyen) #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.

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(Matthew Ryan Dillon) #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.

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(Matthew Ryan Dillon) unassigned michael.shaffer #9
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(Quynh anh Nguyen) #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."

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(Matthew Ryan Dillon) #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
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Correlation analysis
(Mehmet Davrandi) #12

Hi Matthew,

Thanks for the new instructions, it worked!

Best
Mehmet

1 Like

(Quynh anh Nguyen) #13

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

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(Matthew Ryan Dillon) split this topic #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.

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