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JihedC / Snakemake_ATAC_2020

Repository for Jianhui's snakemake pipeline
MIT License
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HMMRATAC is not downloaded by the pipeline #8

Closed JihedC closed 3 years ago

JihedC commented 3 years ago

Now HMMRATAC works but the tool is not downloaded by the pipeline. We can either add a rule to download it from GitHub (also include a touch command) or try to use the conda version of HMMRATAC.

First try conda, it's the simplest.

WJH58 commented 3 years ago

@JihedC I used "touch" in the output, see below:

  rule download_hmmratac:
    output:
        touch(WORKING_DIR + "hmmratac.java")
    params:
        hmmratac = config["HMMRATAC"]
    log:
        RESULT_DIR + "logs/hmmratac/download_hmmratac_github.log"
    shell:
        "wget {params.hmmratac}"

We're going to download HMMRATAC_V1.2.10_exe.jar rather than via conda installation. This rule downloads hmmratac, but the problem becomes how to make it work before rule hmmratac works.