The command-line interface to GGD. Build and check recipes.
This assumes that you have installed [anaconda](https://www.continuum.io/downloads) or at
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.
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
VERSION [--dependency DEPENDENCY]
[--extra-file EXTRA_FILE] --summary SUMMARY --keyword
name name of recipe
script bash script that contains the commands that build the
-h, --help show this help message and exit
species recipe is for
genome-build the recipe is for
--authors AUTHORS authors of the recipe
--version VERSION version of data itself, e.g. dbsnp-127
any software dependencies (in bioconda, conda-forge)
or data-dependency (in ggd). May be as many times as
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.
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
usage: ggd check-recipe /path/to/my/recipe/
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.