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nf-core / airrflow

B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
https://nf-co.re/airrflow
MIT License
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Error in value[[3L]](cond) #323

Closed rasmirnov closed 3 months ago

rasmirnov commented 3 months ago

Description of the bug

Hello!

I'm trying to build a B cell tree based on your tutorial here. Currently, I'm working on getting switch count statistics using IgPhyML to be able to color branches based on the tissue type. I was able to successfully install the IgPhyML package on a server without using docker container and I used your installation guide here. However, when I used tried to run the command:

igphyml_location <- '/home/user/extra_libs/igphyml/src/igphyml'
trees = getTrees(clones, build="pml", trait='tissue', 
                 igphyml=igphyml_location, nproc = 8)

I've gotten an error: Error in value[[3L]](cond)

It also says above the error, but I don't understand where I have to specify IGPHYML_PATH. I tried in terminal, but it didn't help:

Hotspot tables not found in install directory and IGPHYML_PATH not set. 
 Try specifying their location with the IGPHYML_PATH environment variable. 
 e.g. export IGPHYML_PATH=<path to directory>/igphyml/src/motifs/

Command used and terminal output

No response

Relevant files

No response

System information

R version 4.0.2 (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.4 LTS dowser_2.1.0

### Tasks
rasmirnov commented 3 months ago

Ohh, I'm sorry, I mix up the place for posting this issue...