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CLI for gogetdata (ggd)

Project description

# ggd-cli

The command-line interface to GGD. Build and check recipes.

### Installation

This assumes that you have installed [anaconda]( or at
least [conda](

To get the required software, use:

$ conda config --add channels bioconda
$ conda config --add channels conda-forge
$ conda install -y conda-build-all --channel conda-forge
$ conda install -y anaconda-client
$ pip install -r requirements.txt
$ conda install -y "gsort>=0.0.2" samtools htslib zlib

$ pip install ggd

Then the `ggd` executable will be available.

## from-bash

Make a recipe from a bash script that is likely to pass the tests in ggd-recipes.

Most of the arguments are required. For example, we don't want a recipe to litter
the user-space with extra files so if the recipe downloads a `.zip`, and processes
the files inside of it, it should clean-up (`rm`) the .zip file upon completion.

usage: ggd from-bash [-h] --species
--genome-build GENOME_BUILD [--authors AUTHORS] --version
[--extra-file EXTRA_FILE] --summary SUMMARY --keyword
name script

positional arguments:
name name of recipe
script bash script that contains the commands that build the

optional arguments:
-h, --help show this help message and exit
--species {Homo_sapiens,Mus_musculus,Canis_familiaris}
species recipe is for
--genome-build GENOME_BUILD
genome-build the recipe is for
--authors AUTHORS authors of the recipe
--version VERSION version of data itself, e.g. dbsnp-127
--dependency DEPENDENCY
any software dependencies (in bioconda, conda-forge)
or data-dependency (in ggd). May be as many times as
--extra-file EXTRA_FILE
any files that the recipe creates that are not a *.gz
and *.gz.tbi pair. May be used more than once
--summary SUMMARY a comment describing the recipe
--keyword KEYWORD a keyword to associate with the recipe. may be
specified more that once.


## check-recipe

After you make a new recipe, likely with the `ggd from-bash`. Running `ggd check-recipe` will
run the same checks as our testing framework. It will build and install the recipe.

It may miss dependencies if you have them installed on your system, but they are not specified in
the recipe.

usage: ggd check-recipe /path/to/my/recipe/

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