URL to manually download the databases?

[ruizhao087]

Hi CompareM2 developers, Thanks for the efforts to make comparative genomic analysis easier! I am getting it installed to give it a try. I wonder whether it is possible to post the URL of the databases? I easily exceeded the quota limit of my account on our HPC when downloading the databases using "comparem2 --until downloads", given that they are 200 GB. I hope to store them somewhere else rather than the default Miniforge directory within my home directory. Thank you in advance!

Rui

[cmkobel]

Hi Rui

Assuming that you want to change the path, where the databases are stored.

You can set the COMPAREM2_DATABASES environment variable (in your conda env or in your ~/.bashrc file) to anything you'd like. (When this environment variable is not set, CompareM2 defaults to storing the databases inside the software environment.)

https://comparem2.readthedocs.io/en/latest/10%20installation/#shared-database

Just put this in your ~/.bashrc file:

export COMPAREM2_DATABASES="/absolute/path/to/where/dbs/should/be"

Log in again or source it once:

$ source ~/.bashrc

And CompareM2 will download all databases to that directory, from there on out.

Even though it is called "shared database" in the documentation, you don't need to share it with anyone, it can just be a private dir as well. I will update the documentation to reflect this point.

Good luck.

[ruizhao087]

Hi Carl, Thank you for the help! It worked. I downloaded the databases and can finish the testing runs. Awesome and comprehensive tool!

Rui