Updating phyluce through conda to 1.6

[hintzam33]

I'm hoping you can help me with updating my version of phlyuce to the latest or at least a newer version that has spades. I've tried to use your update to 1.6.6 script, but couldn't figure out how to get it to work - running it didn't do anything. The version created by conda is 1.5 and therefore doesn't have spades despite your website stating it should be version 1.6.2 (installation guide).

I tried manually updating my version by downloading the tar.gz for version 1.6.7, but I broke conda in the process, so I'm trying to avoid making the same mistake twice. Any advice would be much appreciated! Thank you.

[brantfaircloth]

Not sure which operating system you are using but bioconda has 1.6.7 for macos and linux. To check this, run:

conda search phyluce

Those results should look something like:

Loading channels: done
# Name                  Version           Build  Channel
phyluce                   1.6.2          py27_0  bioconda
phyluce                   1.6.3          py27_0  bioconda
phyluce                   1.6.3          py27_2  bioconda
phyluce                   1.6.4          py27_0  bioconda
phyluce                   1.6.5          py27_0  bioconda
phyluce                   1.6.6          py27_0  bioconda
phyluce                   1.6.7          py27_0  bioconda

To update, you should be able to run:

conda update phyluce

And conda should do what you need. If that's problematic, you should be able to create a specific environment for phyluce v1.6.7 by running something like:

conda create -n phyluce-updated phyluce=1.6.7

then using conda activate phyluce-updated to switch to the new environment. If you are not seeing any of the above, you'll need to setup whatever your installation is to use bioconda to install phyluce.

[hintzam33]

I'm using Ubuntu and was finally able to update phyluce with your suggestions. Thank you very much for the quick response!

[brantfaircloth]

Cool.