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wrapper need to support native code #770

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wenyuhaokikika opened this issue Oct 31, 2022 · 1 comment
Closed

wrapper need to support native code #770

wenyuhaokikika opened this issue Oct 31, 2022 · 1 comment
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bug Something isn't working

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@wenyuhaokikika
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Snakemake version
7.17.1

Describe the bug
Need to support native code
i want to modify some code.

smk file

rule get_vep_cache:
    output:
        directory("resources/vep/cache"),
    params:
        species=config["ref"]["species"],
        build=config["ref"]["build"],
        release=config["ref"]["release"],
    log:
        "logs/vep/cache.log",
    wrapper:
        "./snakemake-wrappers/bio/vep/cache"

Logs

Rules claiming more threads will be scaled down.
Conda environments: ignored
Job stats:
job              count    min threads    max threads
-------------  -------  -------------  -------------
get_vep_cache        1              1              1
total                1              1              1

Select jobs to execute...

[Mon Oct 31 23:02:03 2022]
rule get_vep_cache:
    output: resources/vep/cache
    log: logs/vep/cache.log
    jobid: 0
    reason: Missing output files: resources/vep/cache
    resources: tmpdir=/tmp

Failed to open source file https://github.com/snakemake/snakemake-wrappers/raw/snakemake-wrappers/bio/vep/cache/wrapper.py
ConnectionError: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /snakemake/snakemake-wrappers/raw/snakemake-wrappers/bio/vep/cache/wrapper.py (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7fa797de7eb0>: Failed to establish a new connection: [Errno 110] Connection timed out')), attempt 1/3 failed - retrying in 3 seconds...

Similar to this issue #154 (comment)

@wenyuhaokikika wenyuhaokikika added the bug Something isn't working label Oct 31, 2022
@wenyuhaokikika
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fix

rule get_vep_cache:
    output:
        directory("resources/vep/cache"),
    params:
        species=config["ref"]["species"],
        build=config["ref"]["build"],
        release=config["ref"]["release"],
    log:
        "logs/vep/cache.log",
    wrapper:
        "file:///data/wenyuhao/55/runWGS/snakemake-wrappers/bio/vep/cache"

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