The command-line interface to GGD. Build and check recipes.
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
$ conda install -y "gsort>=0.0.2" samtools htslib zlib check-sort-order
Finally:
$ 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] -s
{Canis_familiaris,Homo_sapiens,Drosophila_melanogaster,Mus_musculus}
-g GENOME_BUILD [--authors AUTHORS] --version VERSION
[-d DEPENDENCY] [-e EXTRA_FILE] --summary SUMMARY -k
KEYWORD
name script
positional arguments:
name name of recipe
script bash script that contains the commands that build the
recipe
optional arguments:
-h, --help show this help message and exit
-s {Canis_familiaris,Homo_sapiens,Drosophila_melanogaster,Mus_musculus}, --species {Canis_familiaris,Homo_sapiens,Drosophila_melanogaster,Mus_musculus}
species recipe is for
-g GENOME_BUILD, --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
-d DEPENDENCY, --dependency DEPENDENCY
any software dependencies (in bioconda, conda-forge)
or data-dependency (in ggd). May be as many times as
needed.Using Anaconda API: https://api.anaconda.org
hg19-cosmic
install a recipe with:
conda install -c ggd-alpha --override-channels {recipe-name}
-e EXTRA_FILE, --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
-k KEYWORD, --keyword KEYWORD
a keyword to associate with the recipe. may be
specified more that once.
Used 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. This will cause the recipe to fail when tested in our testing framework.
usage: ggd check-recipe /path/to/my/recipe/
Shows the status of variables available in the conda environment. This is important as installation of a new ggd package will create a new environment variable to access data installed with the package, but will not activate that variable.
No arguments are required for show-env, but it will accept a regex pattern to filter results.
$ ggd show-env -p "ggd.*"
*****************************
Active environment variables:
> $ggd_hg19_cpg_islands
Inactive or out-of-date environment variables:
> $ggd_grch37_reference_genome
Using Anaconda API: https://api.anaconda.org
hg19-cosmic
install a recipe with:
conda install -c ggd-alpha --override-channels {recipe-name}
To activate inactive or out-of-date vars, run:
source activate root
*****************************
The environment variables store the location of the installation directory for the package. When activated, these variables can be used to simplify data access considerably, as shown below:
$ echo "$ggd_grch37_reference_genome"
/scratch/ucgd/lustre/u1072557/a2/share/ggd/Homo_sapiens/GRCh37/grch37-reference-genome
$ ls "$ggd_grch37_reference_genome"
hs37d5.fa hs37d5.fa.fai
Shows files that have been installed locally from a ggd recipe. Uses Python's glob.glob to list files, so pattern must use shell wildcards or literals, rather than regex.
$ ggd list-files -h
usage: ggd list-files [-h]
[-s {Canis_familiaris,Homo_sapiens,Drosophila_melanogaster,Mus_musculus}]
[-g GENOME_BUILD] [-v VERSION] [-p PATTERN]
name
positional arguments:
name pattern to match recipe name(s). Ex. `ggd list-files
"hg19-hello*" -s "Homo_sapiens" -g "hg19" -p "out*"`
optional arguments:
-h, --help show this help message and exit
-s {Canis_familiaris,Homo_sapiens,Drosophila_melanogaster,Mus_musculus}, --species {Canis_familiaris,Homo_sapiens,Drosophila_melanogaster,Mus_musculus}
species recipe is for
-g GENOME_BUILD, --genome-build GENOME_BUILD
genome build the recipe is for
-v VERSION, --version VERSION
pattern to match the version of the file desired
-p PATTERN, --pattern PATTERN
pattern to match the name of the file desired
usage: ggd list-files "hg19-hello*" -s "Homo_sapiens" -g "hg19" -p "out*" -v "1"
Allows user to search available ggd recipes. Performs a two-part search, first checking a locally-managed copy of the ggd-recipes repository and then going to the ggd-alpha channel to verify that only fully tested packages are reported. The keyword arguments, if provided, are matched against the keywords stored in the meta.yaml extra section.
$ ggd search -h
usage: ggd search [-h]
[-s {Canis_familiaris,Homo_sapiens,Drosophila_melanogaster,Mus_musculus}]
[-g GENOME_BUILD] [-k KEYWORD]
name
positional arguments:
name pattern to match the name of the recipe desired. Ex.
`ggd search "hg19*" -s "Homo_sapiens" -g "hg19"`
optional arguments:
-h, --help show this help message and exit
-s {Canis_familiaris,Homo_sapiens,Drosophila_melanogaster,Mus_musculus}, --species {Canis_familiaris,Homo_sapiens,Drosophila_melanogaster,Mus_musculus}
species recipe is for
-g GENOME_BUILD, --genome-build GENOME_BUILD
genome build the recipe is for
-k KEYWORD, --keyword KEYWORD
keywords to narrow search. Repeat argument to use
multiple keywords
usage: ggd search "hg19-c*" -s "Homo_sapiens" -g "hg19" -k "cosmic"
search also helps the user out by giving the command needed to install a package (results below from above example):
Using Anaconda API: https://api.anaconda.org
hg19-cosmic
install a recipe with:
conda install -c ggd-alpha --override-channels {recipe-name}