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tseemann
Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module)
Installed snippy in conda environment in ubuntu 20.04 LTS. Following message was obtained. Assistance will be greatly appreciated.
Thank you very much Bjerling Taul. I tried the scripts and got following message. Had you also encountered such issue? How did you solve it?
@Jeewan-Thapa have you configured the bioconda channels https://bioconda.github.io/user/install.html#set-up-channels ?
Thanks @apetkau, No I haven't. Do I need to set-up bioconda channel and then again reinstall snippy?
Yes, you will need to do that.
On Thu., Aug. 26, 2021, 7:36 p.m. Jeewan-Thapa, @.***> wrote:
Thanks @apetkau https://github.com/apetkau, No I haven't. Do I need to set-up bioconda channel and then install snippy?
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@apetkau It looks like something went wrong or am I missing something. Thank you.
@apetkau It looks like the snippy has been correctly installed in a snippy environment. When I run the snippy, do I have to always run in the snippy environment, and when I want to run other programs, for example, fastqc, I have to come back again to the conda environment by deactivating snippy and activating conda. Furthermore, it is suggested to upgrade snpEff to v4.3. So, this should be upgraded in the snippy environment. I am sorry for my simple queries as I am new to these works. I am very thankful to you.
That's great. I'm glad to hear it's working.
Yes, you will have to run conda activate snippy first before running snippy (and switch to a different environment for other software). Or, alternatively you could directly run conda run --name snippy snippy .... and avoid running conda activate. You can also try installing other software in the snippy environment (e.g., fastqc).
If you wish to upgrade snpEff for snippy, you will want to do it in the snippy environment (e.g., conda activate snippy then conda update snpeff).
One of the reasons for using different conda environments is that different software can have dependencies that conflict with each other (likely the source of your original issue here). You can read more about environments here https://conda.io/projects/conda/en/latest/user-guide/concepts/environments.html
Thank you very much for your kind explanation. I noticed that snpeff is still not upgraded even after using the above update script. Even after reinstalling by "conda install -c bioconda snpeff" (v5.0), snpEff is not upgraded and shows same information. I will try troubleshooting this issue.
@apetkau I am very sorry to trouble you again. I am not able to upgrade to snpEff version >=4.3. Do you have idea how to do it.
@BjoerlingTaul Did you encounter this issue?
@tseemann Do you have any suggestions?
