ggd show-env

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ggd show-env is a tool used to show the ggd data package environment variables created during package installation for the current conda environment.

During installation, ggd will place the processed files in a specific location on your system. To access these files ggd creates up to two environment variables for each data package within a specific conda environment. These variables contain either the directory path to the processed files or the file path to the main data file. You can use ggd get-files or ggd pkg-info to find additional file paths for a ggd data package, however, these environment variables provide quick access to the processed files without having to know the file paths.

For details on using these environment variables in your analysis scripts see: Using installed data.

Using ggd show-env

You can use ggd show-env to get a list of ggd data package environment variables. Running ggd show-env -h will give you the following message:

show-env arguments:

ggd show-env	Display the environment variables for data packages installed in the current conda environment
-h, --help	show this help message and exit
-p, --pattern	(Optional) Regular expression pattern to match the name of the variable desired

Additional argument explanation:

There are no required arguments for using ggd show-env, however, you can refine the results using the -p flag.

Note

Environment variables ending with _dir point to the directory path of the installed data package.

Environment variables ending with _file point to the main file from the installed data package.

Examples

1. Using ggd show-env

$ ggd show-env

  *****************************

  Active environment variables:
  > $ggd_hg19_repeatmasker_ucsc_v1_dir
  > $ggd_hg19_repeatmasker_ucsc_v1_file
  > $ggd_grch37_esp_variants_ensembl_v1_dir
  > $ggd_grch37_esp_variants_ensembl_v1_file
  > $ggd_hg38_repeatmasker_ucsc_v1_dir
  > $ggd_hg38_repeatmasker_ucsc_v1_file
  > $ggd_grch37_reference_genome_ensembl_v1_dir
  > $ggd_grch37_reference_genome_ensembl_v1_file
  > $ggd_hg19_phastcons_ucsc_v1_dir
  > $ggd_hg19_phastcons_ucsc_v1_file
  > $ggd_hg19_gaps_ucsc_v1_dir
  > $ggd_hg19_gaps_ucsc_v1_file
  > $ggd_hg38_simplerepeats_ucsc_v1_dir
  > $ggd_hg38_simplerepeats_ucsc_v1_file
  > $ggd_hg19_simplerepeats_ucsc_v1_dir
  > $ggd_hg19_simplerepeats_ucsc_v1_file
  .
  .
  .

  *****************************

2. Using the -p flag

$ ggd show-env -p ggd_hg19

  *****************************

  Active environment variables:
  > $ggd_hg19_phastcons_ucsc_v1_dir
  > $ggd_hg19_phastcons_ucsc_v1_file
  > $ggd_hg19_gaps_ucsc_v1_dir
  > $ggd_hg19_gaps_ucsc_v1_file
  > $ggd_hg19_repeatmasker_ucsc_v1_dir
  > $ggd_hg19_repeatmasker_ucsc_v1_file
  > $ggd_hg19_simplerepeats_ucsc_v1_dir
  > $ggd_hg19_simplerepeats_ucsc_v1_file
  .
  .
  .

  *****************************