Sweet. 2nd one didn't work - just hung the window, but first one did for 4.0.5. Thanks!
Snippy install "Can't locate Bio/SeqIO.pm in @INC
Hello, I installed via miniconda bioconda instructions but installation check came up with this error message. Can you please tell me how to fix this? (PS. I'm very new to this.)
Can't locate Bio/SeqIO.pm in (you may need to install the Bio::SeqIO module) ( contains: /home/sharb/miniconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/sharb/miniconda3/lib/site_perl/5.26.2 /home/sharb/miniconda3/lib/5.26.2/x86_64-linux-thread-multi /home/sharb/miniconda3/lib/5.26.2 .) at /home/sharb/miniconda3/bin/snippy line 11. BEGIN failed--compilation aborted at /home/sharb/miniconda3/bin/snippy line 11.
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Hi, I just installed 4.2 using Conda and have run into the same issue.点赞 评论 复制链接分享
snippy 4.2.3 is now in conda and brew. i am told the channel order has changed in brew now. you might have to do
conda install -c conda-forge -c bioconda snippyinstead. Make sure you
conda update condaand
conda update --alltoo!点赞 评论 复制链接分享
Great - a Brew reinstall did the trick but the Conda is still not quite working. Thank you for your help and for making these tools available Torsten, much appreciated.点赞 评论 复制链接分享
Conda is in so much flux at the moment it is hard to debug, but we will get there. I think it's a python problem now, the freebayes helper scripts. I will replace them with my own perl ones.点赞 评论 复制链接分享
I'm still having problems installing Snippy on MacOS using latest (Bio)Conda. Any ideas? snippy --version Can't locate Bio/SeqIO.pm in (you may need to install the Bio::SeqIO module) ( contains: /Users/nick/miniconda3/envs/metaphylo/bin/../perl5 /Users/nick/miniconda3/envs/metaphylo/lib/perl5/site_perl/5.22.0/darwin-thread-multi-2level /Users/nick/miniconda3/envs/metaphylo/lib/perl5/site_perl/5.22.0 /Users/nick/miniconda3/envs/metaphylo/lib/perl5/5.22.0/darwin-thread-multi-2level /Users/nick/miniconda3/envs/metaphylo/lib/perl5/5.22.0 .) at /Users/nick/miniconda3/envs/metaphylo/bin/snippy line 15. BEGIN failed--compilation aborted at /Users/nick/miniconda3/envs/metaphylo/bin/snippy line 15.点赞 评论 复制链接分享
Howdy. This issue popped up for me with a conda install as well. I used
and still nothing.
conda update --all点赞 评论 复制链接分享
I have also just come across this same problem点赞 评论 复制链接分享
I did not write the conda package for snippy. Please make a whole new conda env for it and see what happens:
conda activate base conda update --all --yes conda create -n snippy_env snippy>=4.6 conda activate snippy_env snippy --check
does it work for you now?点赞 评论 复制链接分享
I tried the solution you posted 15 days ago after running into the same issue and it did not fix the error. Not sure why but the install from the readme seemed to download a 3.1v originally.
The command hung on conda create -n snippy_env snippy>=4.6
I got it working with conda activate base conda update --all --yes conda create -n snippy_env conda activate snippy_env conda install -c conda-forge -c bioconda -c defaults snippy conda list (To check version is above 4) snippy --check点赞 评论 复制链接分享
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- I had the same issue which resolved when I used this slight fix: conda create -n snippy_env snippy=4.6.0 Snippy has worked fine subsequently.
Same problem here, and new environment, followed by
conda install -c conda-forge -c bioconda -c defaults snippydid not solve the problem.点赞 评论 复制链接分享
conda install snippy >snippy 3.1 run error github clone snippy>snippy 4.6 run ok here: git clone https://github.com/tseemann/snippy.git
You'll need to add Snippy's bin directory to your $PATH
maybe conda snippy is old version not upgrade点赞 评论 复制链接分享
I am told bioperl is currently broken on bioconda, and that it will be fixed within a week.
Snippy 4 will not appear until that is fixed first.点赞 评论 复制链接分享
Wow! so fast - thank you. So do I need to undo the install for now and re-install when the fix is done? (if so, how?) And will you post a note to say when it's fixed?
thanks again.点赞 评论 复制链接分享
i think 4.0.0 now works on bioconda. i am not sure how to upgrade it. maybe
conda update --all?点赞 评论 复制链接分享
Thanks for that. I used conda update --all and it all went through without a hitch, but still v3.1.点赞 评论 复制链接分享
conda install snippy==4.05
conda install -c bioconda -c conda-forge snippy>=4.0点赞 评论 复制链接分享
I have the same question and use conda update --all. Final I still can't used snippy. Do you have any advice?点赞 评论 复制链接分享