We have just made the transition of most of the servers from CentOS6 or CentOS7 to CentOS8. Most everything should be unified on CentOS8 (unless you know what you are doing).
This brings several new changes (as always) and some added benefits. This is a summary and does not reflect all the changes.
To check your servers operating system version, use this command:
The biggest changes should allow you to install software by yourself! There are two different ways you can install easily install software if either are supported by whatever you are trying to install.
Please note, that if you do not want to do either of these, it is fine. Just let me know and I am happy to install software for you (and everyone else) to use.
A lot of bioinformatics software is now available via conda. It is installed globally, but you can not install packages globally. You can create your own environment and then use that.
The first time you use conda, you will need to create a local environment. Start with:
conda create --name <username>
But use your username instead of
After this has run, any time you need to use conda, you can use the command
conda activate <username>
And you will get into your environment.
A simple test is to install my
fastq-pair package and see if it works:
conda install -c bioconda fastq-pair
once it has installed, this command should give some output
Another popular way of sharing software is by using docker. We don’t support docker, but we support a drop-in replacement called podman.
Anywhere you see docker, you can use podman instead. For example, we created a focus docker image for the cami challenge described here: https://hub.docker.com/r/linsalrob/cami-focus and you can install that with
podman pull linsalrob/cami-focus
If you are trying to run some python code and don’t have the appropriate library, you should be able to use pip install as a user to add it. For example:
pip3 install --user xmlschema
this will install the appropriate libraries into your account. Of course, if you want them globally installed, just let me know.
Deprecated software and alternatives
|screen||tmux||Virtual terminals. You should use this!||tmux has similar keys to screen but uses |
|cd-hit||mmseqs||Clustering sequences||cd-hit is still an option if you want, but mmseqs2 appears to be much better|