No colors in mLocARNA structure predictions from conda installation

[BGemler]

Installation: conda install -c bioconda locarna
Version: LocARNA 1.9.1
Platform: Ubuntu 22.04 LTS

The RNA structures (alirna.ps) produced by mLocARNA do not contain any colors (example below). Any ideas/guidance on how to implement colors in the predicted structures would be appreciated.

Thank you!

[s-will]

Thanks for pointing me to a problem with the locarna conda package. In your case, Conda installed a (very) old version of LocARNA.

I could reproduce the problem. It seems like strict channel priority causes inconsistencies for the newer locarna packages. For me, deactivating channel_priority: strict in my .condarc was sufficient to let conda automatically install the newest locarna version (2.0.0RC10), which solves your problem.

If installing the newest LocARNA (which would be the best solution) does not work for you, there would be a workaround. Simply generate the figure with color using RNAalifold from locarna's result alignment. In the result directory (which contains result.aln, alirna.ps, ...), call

RNAalifold --aln --col --mis --cfactor=0.6 --nfactor=0.5 result.aln

[BGemler]

Hello Sebastian,

Thank you for the quick response! After some troubleshooting with no luck I conducted a fresh install of conda (some tweaking with glibc appeared to break my conda isntall) and ran into the below same errors.

Steps:
conda config --set channel_priority false
conda install -c bioconda locarna=2.0.0RC10

I get the following error message:
UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:

• feature:/linux-64::__glibc==2.35=0
• python=3.9 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.35

Are there any additional channels or parameters necessary for the conda install?

[s-will]

Please add conda-forge to your list of channels. I observed that viennarna requires a recent version of libgomp which is not found on defaults and bioconda.

I hope, this is working for you as well:

conda install -c conda-forge -c bioconda locarna

in order to install the most recent version of locarna.