Installing Plant Tribes

[FranciscoMenendez]

Hey Plant Tribes community! I wanted to post a few of issues. First the Galaxy instance is not working currently. It always gives an error when attempting any analysis, be it the integrator, post processor or builder. It failed no matter what data I am using, even previously stored files from when it was working. Second: Installing it in my computer is full of challenges. The manual way seems the only one that is working. The Conda website does not find the repository, basically seems like it's no longer available. Third: The scaffolds are hard to find. Even when installing them manually they seem to not be available from the Github site.

Any help using this resource would be helpful it seems that the only way is local installation but then try finding the data is also not straightforward Sincerely, Francisco

[Huiting120]

Hi Francisco, Thank you for your feedback. We will contact Galaxy again about the issue. Have you tried to run with Docker or Singularity? I think that's the easier way to use PlantTribes at the moment. There is a link under PlantTribes scaffolds datasets to download the scaffolds. We are in the process to establish a globus connections point and hopefully that will make the downloading much faster. Best Huiting

[FranciscoMenendez]

Huiting! Thanks for getting back to the issue! I eventually was able to install it using the following steps on the ROAR server (RedHat Linux) after installing anaconda and running a virtual environment:

 $ module load anaconda3

 $ conda create -n vir_planttribes

 $ source activate vir_planttribes

 $ conda config --add channels bioconda

 $ conda config --add channels defaults

 $ conda config --add channels conda-forge

 $ conda config --set channel_priority true

 $ conda install plant_tribes_assembly_post_processor

 $ conda install plant_tribes_gene_family_classifier

 $ conda install plant_tribes_gene_family_integrator

 $ conda install plant_tribes_gene_family_phylogeny_builder #did not work

 $ conda install plant_tribes_gene_family_aligner
 $ cd /gpfs/scratch/fmm18/vir_planttribes
 $ AssemblyPostProcessor

I think the key steps to remember are to add the Conda forge and the priority. Also, although I believe I did this on a Mac it wasn't successful. Might attempt again later.

In regards to the scaffold yes it seems that there might be some difficulty since they are so large. They recommended a globus endpoint. I will update as this might be a good reference for future researchers.