how to install non-condo dependency and add it to .yaml env file?
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7 weeks 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

snakemake • 79 views
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