Mdavrandi
(Mehmet Davrandi)
January 21, 2019, 9:17am
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
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
Mdavrandi
(Mehmet Davrandi)
January 23, 2019, 6:22pm
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
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
Mdavrandi
(Mehmet Davrandi)
January 24, 2019, 11:18pm
5
Hi Mike,
Unfortunately the problem persists. Not sure whats going wrong here. Is there any other way of installing this plugin?
Thanks!
Mehmet
AllieNguyen
(Quynh anh Nguyen)
February 14, 2019, 9:16pm
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.
@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.
AllieNguyen
(Quynh anh Nguyen)
February 14, 2019, 9:41pm
10
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
Mdavrandi
(Mehmet Davrandi)
February 15, 2019, 4:07pm
12
Hi Matthew,
Thanks for the new instructions, it worked!
Best
Mehmet
1 Like
AllieNguyen
(Quynh anh Nguyen)
February 17, 2019, 11:46pm
13
Thanks @thermokarst , the new instruction work for me too!
Kind regards,
Allie.
1 Like
thermokarst
Split this topic
February 18, 2019, 3:50pm
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.
drish_k
(Drishti K)
March 9, 2020, 11:59pm
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:
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
drish_k
(Drishti K)
March 11, 2020, 11:49pm
19
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