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thh32 / Protologger

Protologgger is a tool for the description of novel taxa by providing taxonomic, functional and ecological insights
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Installation bugs #3

Open jamesabbott opened 3 years ago

jamesabbott commented 3 years ago

I'm trying to install protologger using the setup-protologger-env.sh script. So far I have hit two problems

1) The script includes 'set -e' and the following commands:

 # Download GTDB database
source ~/anaconda3/etc/profile.d/conda.sh
source ~/miniconda3/etc/profile.d/conda.sh

In my case, I have a ~/miniconda3 directory, but no ~/anaconda3, so as a result of 'set -e' the script fails when trying to source a path which does not exist.

These two commands are also assuming that conda is installed in the default directories of ~/anaconda3 or ~/miniconda3, and would also fail if someone who had their conda installation in a non-standard location tried to run it.

You could test for the presence of these files before trying to source them which would stop the script failing, or try to detect the conda installation location before trying to source them.

2) line 45

sudo python3.6 setup.py install

That is going to fail for the vast majority of users trying to install the software on a system they do not control i.e. an HPC cluster. Only root users will have sudo access to run this command, and it would be dangerous for them to do so without being aware of what it would do in advance. I saw nothing in the installation docs about root access being required, but for users with sudo access, scripts running commands as root potentially without warning (for example, a sysadmin who has considered sudo to trust them impicitly) could result in very bad things happening. There should be no need to run commands via sudo when installing into a conda environment.

I'll carry on trying to get this running while hacking on the installation script, and will pas on any further findings!

thh32 commented 3 years ago

Hi James,

Thanks for your feedback!

I hope to release a conda package for Protologger in the next iteration to make self-installation easier, especially as we are aware that the current installation guide was designed for our setup.

I will hopefully have time to try and improve the installation soon so any feedback you can provide is great, thanks alot!

Thanks, Tom