Entering edit mode
2.8 years ago
AnnaS
•
0
I am trying to make a snakemake pipeline for "DPclust". I generated dpclust.yaml with all required packages (all downloaded from anaconda repository). However, I need to get dpclust3p from their GitHub repository.
I added a rule to my snakefile
rule install_dpclust3p:
output:
complete = "dpclust3p_dependencies_installed.success"
conda:
"/projects/multiple_myeloma/envs/dpclust.yaml"
log:
input = "input.log"
shell:
"""
R -q -e 'devtools::install_github("Wedge-Oxford/dpclust3p")' >> {log.input} &&
touch {output.complete}
"""
but when it runs the main rules coming after installation rule, I get this error message
Activating conda environment: /projects/multiple_myeloma/envs/.snakemake/conda/fef65038
Error in library(dpclust3p) : there is no package called ‘dpclust3p’
Execution halted
So I am confused, how can I install this non-condo dependency (dpclust3p) to my dpclust.yaml env file? I appreciate any help