I am a postdoctoral fellow at the NYC Public Health Laboratory and I am trying to get the Genome Sampler plugin installed on our secure server. We are having difficulties with the install and I wanted to see if anyone would be able to offer insight.
When we try to install the plugin we find that it either hangs during the installation or it can’t find packages that Genome Sampler claims to exist:
(/opt/conda-env/genome-sampler) $ conda env update --prefix /opt/conda-env/genome-sampler/ --file ~/genome_sampler.yml
Collecting package metadata: done
Solving environment: failed
We also checked on conda’s repository page and can’t find genome sampler.
Then finally, instead of using the QIIME2 conda install, a link that is referenced that is not approved by our IT security for install.
Would anyone be able to offer suggestions for the install? Any help is greatly appreciated. Thanks!
Someone will hopefully be with you soon (we are all teaching a QIIME 2 workshop this week and pretty tied up) Just kidding, I edited my post to include some more information. In the meantime, can you provide with us with the full list of commands you have run? It looks like you might be “updating” the conda env, but that might just be one small part of what you have attempted so far, so some additional information would be really helpful.
If you haven’t already seen this, please double check the official installation guide:
Please note, since the install guide uses conda envs, we don’t recommend “updating” an env, but instead simply creating a new env (you can change the name of the env with the
-n my-env-name portion of the installation commands).
Ah, that’s because Genome Sampler isn’t hosted on anaconda.org! QIIME 2 has its own conda server, at https://packages.qiime2.org.
One last thing to point out - you should delete the
genome-sampler.yml file, and redownload (according to the install guide linked to above) - I bet you have a stale old file or something (or perhaps you created that file by hand?). You can also share that file here and we can try to take a closer peek.
FWIW, I was able to run an
conda env update locally, so if you did want to go that route, you could - you just need to have the latest install media on hand (i.e. the newest