bebatut / PylProtPredictor

Prediction of PYL proteins

http://bebatut.fr/PylProtPredictor/

Apache License 2.0

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Snakemake migration fixes #8

Closed keuv-grvl closed 7 years ago

keuv-grvl commented 7 years ago

New rules

help : print help message, default rule
version: arbitrarily set to 0.2
purge : brutually delete the output directory

Uniref90

One rule to download UniRef90 and format it for Diamond
data/uniref90.fasta is no longer needed, only data/uniref90.dmnd
If you already have uniref90.dmnd on your computer, you may symlink it: ln -s /path/to/uniref90.dmnd data/uniref90.dmnd. You may need to run snakemake --cleanup-metadata data.uniref90.dmnd

Multithreading

User may define a maximum number of threads to use in config.yaml (eg: max_threads: 12)
If none is used-defined, use the maximum number of available CPU
Number of CPU is limited by snakemake --cores X in all cases

Usage

$ snakemake           # print the help
$ snakemake --list    # list all available rules (+ description)
$ snakemake
    --cores           # use all CPU
    -p                # print executed commands
    PylProtPredictor  # run the complete pipeline
$ xdg-open results/YOURGENOME/report.html # open the report in your web browser

bebatut commented 7 years ago

Thanks for this !!