search

Gibbons-Lab / medi

Metagenomic Estimation of Dietary Intake and Content.
Apache License 2.0
8 stars 4 forks source link

May need to add R curl to .yaml #5

Closed LesleyHoyles closed 7 months ago

LesleyHoyles commented 7 months ago

Just installing medi. It requires curl package in R for fread function for nextflow run database.nf command. You may want to add r-curl to the .yaml file.

LesleyHoyles commented 7 months ago

Same applies to taxonkit re .yaml file: could not be found for following command. taxonkit lineage --data-dir taxdump -i 1 taxids.tsv > raw.txt && taxonkit reformat --data-dir taxdump -i 3 raw.txt > lineage.txt && taxonkit reformat --data-dir taxdump -t -i 3 raw.txt > lineage_ids.txt

LesleyHoyles commented 7 months ago

This may be a non-issue if curl and taxonkit included in r-reutils (I had to install packages individually after setting up basic conda environment to get to work on my system and forgot to conda install conda-forge::r-reutils - apologies if this the case).

cdiener commented 7 months ago

Reutils depends on RCurl but best yo add it explicitly as well maybe. Taxonkit was an oversight. I will add those, thanks!